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PM-8 - Water Infotech

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1. x ct 20 hA 74 jth YI Vertical leakance 10 Layer 2 9 fixed head h 1 foot column 4g 1 cell dimension 16 ft by 16 ft recharge cells Plan View i 5 infiltration pond 50 Fig 5 11 Hydrogeology and model grid configuration that horizontal flow and storage effects are negligible This unit is represented by the value for vertical leakance between model layers 1 and 2 The vertical leakance is assumed to be 0 0002 per day In areas not covered by the pond recharge is applied areally at a rate of 0 001 foot per day to simulate natural re charge The recharge option Recharge is applied to the highest active cell is used so that recharge will penetrate through inactive cells to the water table A recharge rate of 0 01 foot per day is applied to the area covered by the pond A steady state simulation is performed to simulate the formation of a perched water table Solution of the flow equation is obtained using the SIP solver Starting 310 5 Examples and Applications hydraulic head in layer 1 under the pond is set at 21 feet All other cells in layer 1 initially are specified as no flow cells The wetting iteration interval THRESH and wetting factor are set at 2 iterations 1 0 foot and 0 5 foot respectively see MODFLOW Wetting Capability A positive value of THRESH indicates that hor izontally
2. Constant head 1 100 meters 45 0123 l KILOMETERS Hydraulic Conductivity Zones wR EXPLANATION x AREAL RECHARGE HEAD OBSERVATION K1 N EVAPOTRANSPIRATION M MULTI LAYER HEAD OBSERVATION K2 G GENERAL HEAD BOUNDARY E K3 D DRAIN i K4 P PUMPAGE Fig 5 31 Test case 2 model grid boundary conditions observation locations and hydraulic conductivity zonation used in parameter estimation Adapted from Hill and others 63 5 3 Parameter Estimation and Pumping Test 339 Table 5 6 Parameters defined for MODFLOW 2000 test case 2 parameter values starting and estimated PARVAL PARNAM Description HK 1 HK 2 HK 3 HK 4 VANI_12 VANI_3 RCH_1 EVT_1 GHB 1 DRN_1 Hydraulic conductivity of zone 1 see Fig 5 31 Hydraulic conductivity of zone 2 see Fig 5 31 Hydraulic conductivity of zone 3 see Fig 5 31 Hydraulic conductivity of zone 4 see Fig 5 31 Vertical anisotropy of layers 1 and 2 Vertical anisotropy of layer 3 Areal recharge rate applied to the area shown in Fig 5 31 Maximum _ evapotranspiration rate applied to area shown in Fig 5 31 Conductance of head dependent boundaries represented using the General Head Boundary package G in Fig 5 31 Conductance of head dependent boundaries represented usin
3. Y L eet gt Fig 5 13 Configuration of the model grid and the location of the observation well 8000 n Inet 312 5 Examples and Applications 5 The transmissivity and storage coefficient are constant throughout the aquifer and remain constant in time 6 The aquifer is confined and Darcy s Law is valid 7 The flow of groundwater is horizontal 8 The water level in the river is constant along its length and with time 9 The infiltration of recharge to the aquifer is instantaneous no delay between the time precipitation infiltrates the surface until it reaches the water table 10 The discharge from the aquifer is only to the river Transmissivity of the aquifer used for both the analytical solution and in the model simulation was 3 200 ft d 3 45 x 1073 m s The storage coefficient is 0 20 Because the river is assumed to be fully penetrating and the aquifer is not separated from the river by any confining material the streambed conductance value was assumed equal to the transmissivity of the aquifer in this example the width of the river is assumed equal to the depth of the aquifer times the length of the river in each cell 1 000 ft divided by an assumed foot thickness of the riverbed Actually any large streambed conductance value can be used as long as the head value in the model cell containing the river
4. Fig 4 44 Model grid after the refinement 276 4 Tutorials convention the area outside the model domain is deemed to be a no flow zone and as such it is not necessary to set this area to inactive Click the button if the display mode is not Grid View Make sure the cell selected is 1 1 1 and press Enter or right click to open the Cell Value dialog box Since this is going to be a constant head boundary enter 1 and click OK to exit the dialog box The cell should now have a blue color signifying that it has been set as constant head To save doing this for the remaining constant head cells it is possible to copy the value in this case 1 to any other cell Click on the Duplication button Pal duplication is activated if the button is de pressed Simply left click in any cell that you want to specify as a constant head cell If you make a mistake turn off Duplication by clicking the duplication button and right click in the cell where you have made a mistake and replace it with the desired value Complete specification of the entire North boundary as constant head cells We will assign a head value to these cells a little later The outer grid boundaries are assigned as No Flow by default However the moun tain area in the south corner of the domain which is impervious and still falls inside the model grid needs to be explicitly assigned as No Flow i e IBOUND
5. 348 5 Examples and Applications 5 4 4 Cutoff Wall Folder pmdir examples geotechniques geo4 Overview of the Problem As shown in Fig 5 42 a highly contaminated area is located in the first stratigraphic unit of an unconfined aquifer To the west and east of the aquifer exist fixed head boundaries with the hydraulic head h 0 4 m and 0 5 m The aquifer consists of five stratigraphic units Each unit is horizontally isotropic with uniform thickness The elevations and horizontal hydraulic conductivities are illustrated in Fig 5 42 The vertical hydraulic conductivities are assumed to be a tenth of the horizontal hydraulic conductivities The effective porosity of the aquifer is 0 15 The recharge rate is 1 x 1078 m s Because of the high cost the contaminants cannot be removed The task is to develop a strategy to isolate the contamination There are four subtasks to be done 1 Construct a groundwater flow model and perform a steady state flow simulation by using the data given above and the model grid given in Fig 5 42 2 Geotechnical measures such as cutoff wall impervious cover drain etc can be considered as an alternative Calculate flowlines for the case that a cutoff wall has been built to a depth of 8m and the recharge rate within the cutoff wall is reduced to zero by an impervious cover The location of the cutoff wall is given in Fig 5 42 When calculating the flowlines particles should be started from t
6. Ow w N The following data repeat NPER times 6 Data ACTIVE PERLEN NSTP TSMULT DTO MXSTRN TTSMULT TRANS 7 Data Reserved Reserved Reserved Reserved Reserved Reserved Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space LABEL is the file label It must be PMWIN_TIME_FILE NPER is the number of stress periods in the simulation 380 6 Supplementary Information ITMUNI indicates the time unit of model data The time unit must be consistent for all data values that involve time For example if years is the chosen time unit stress period length time step length transmissivity etc must all be expressed using years for their time units Likewise the length unit must also be consistent 0 undefined 3 hours 1 seconds 4 days 2 minutes 5 years ACTIVE A stress period is active if ACTIVE 1 Set ACTIVE 0 if a stress period is inactive PERLEN is the length of a stress period It is specified for each stress period NSTP is the number of time steps in a stress period TSMULT is the multiplier for the length of successive time steps The length of the first time step DELT 1 is related to PERLEN NSTP and TSMULT by the relation DELT 1 PERLEN 1 TSMULT 1 TSMULT NSTP DTO is the length of transport steps If DTO 0 the length of transport steps will be determined by an automatic stepsize contro
7. 0 0 00 e eee eee eee The Reservoir Package dialog box 00 cee eee ee eee ee The Stage Time Table of Reservoirs dialog box The River Parameters dialog box 0 0 0 0 0c c eee eee eee The Stream Parameters dialog box 02 eee eee Specification of the stream structure 000000 45 XIV List of Figures 2 28 2 29 2 30 2 31 2 32 2 33 2 34 2 35 2 36 2 37 2 38 2 39 2 40 2 41 2 42 2 43 2 44 2 45 2 46 2 47 2 48 2 49 2 50 2 51 2 52 2 53 2 54 2 55 2 56 2 57 2 58 2 59 2 60 2 61 2 62 The stream system configured by the table of Fig 2 27 57 The Wetting Capability dialog box 005 61 The Direct Solution DE45 dialog box 0 0 2 eee ee ee 63 The Preconditioned Conjugate Gradient Package 2 dialog box 65 The Strongly Implicit Procedure Package dialog box 67 The Slice Successive Overrelaxation Package dialog box 68 The Geometric Multigrid Solver dialog box 69 The Head Observation dialog box 00 eee eee eee ee 71 The Modflow Output Control dialog box 0 74 The Run Modflow dialog box 0 e eee eee 76 The Data tab of the Scatter Diagram Hydraulic Head dialog box 78 Interpolation of simulated head values to an observation borehole 79 The Chart tab of the Scatter Diagram Hydraulic Head
8. 372 Supplementary Information 00 cece eee eee eee 375 6 1 Limitation Of PM srame eee bik oo hale Wek Gop E ae e ott 375 OLS Data Edora ee 44 aie nets eres wea eee las Ee Meee 375 6 1 2 Boreholes and Observations 000 cece ee eee 375 6 1 3 DIS Zr ee esra ey eee Mie Sewage dlntue gs eR ee ES 375 6 1 4 Field Interpolator seise oi us uee 0 0 2 eee eee eee 376 61 5 Field Generator oon eraa Ee Geetha eee eae pe K 376 6 1 6 Water Budget Calculator 0 22 ee eee 376 6 2 File Formats jie sisc cacti enea Meth RE ihe can Aiken s 376 6 2 1 ASCII Matrix File 2 2 eee 376 6 2 2 Contour Table File 2 0 eee ee eee 377 6 2 3 Grid Specification File 0 ee eee eee 378 6 2 4 Line Map File cinei stews cies vestige eters oe 379 6 2 5 ASCII Time Parameter File 00 379 6 2 6 Head Drawdown Concentration Observation Files 380 6 2 6 1 Observation Boreholes File 381 6 2 6 2 Layer Proportions File 0 381 6 2 6 3 Observations File 0 00 eee eee eee 381 6 2 6 4 Complete Information File 382 6 2 7 Flow Observation Files 0 00 cece eee eee eee 382 6 2 7 1 Cell Group File 0 000 eee 383 6 2 7 2 Flow Observations Data File 383 6 2 7 3 Complete Information File 384 6 2 9 Trace File wicischns tk
9. The user may add any number of comment lines following the header line and before the particle data records Comment lines must contain the symbol in column 1 Comment lines may not be interspersed with the particle data records The header and comment lines are followed by a sequence of lines Each line contains the following data items in the order specified 1 Particle index number The index number is positive if the forward particle tracking scheme is used A negative index number indicates that the backward particle tracking scheme is used Global coordinate in the x direction Global coordinate in the y direction Local coordinate in the z direction within the cell Global coordinate in the z direction Cumulative tracking time J index of cell containing the point I index of cell containing the point K index of cell containing the point RGB Color of the pathline SOMIADUNARWHYD f 388 6 Supplementary Information 6 2 11 2 MODPATH Format The standard text pathline file of MODPATH Pollock 93 95 is a text file that begins with the header of the form MODPATH Version 3 00 V3 Release 1 9 94 TREF 0 000000E 00 The user may add any number of comment lines following the header line and before the particle data records Comment lines must contain the symbol in col umn 1 Comment lines may not be interspersed with the particle data records The header and comment lines
10. Fig 5 37 Flowlines and calculated head contours for anisotropic medium 344 5 Examples and Applications 5 4 3 Seepage Surface through a Dam Folder pmdir examples geotechniques geo3 Overview of the Problem This example is adapted from Kinzelbach and Rausch 72 It demonstrates how to calculate the seepage surface using a vertical cross sectional model As shown in Fig 5 38 the length of the dam is 100 m the thickness and height are 10 m The water table is 10 m at the upstream side of the dam and 2 m at the downstream side The material of the dam is homogeneous and isotropic with a hydraulic conductivity of 1 x 1075 m s The unrealistic bank slope is used here to simplify the data input The task is to calculate the seepage surface and the seepage rate by using a ver tical cross sectional numerical model Compare the seepage rate with an analytical solution after Dupuit Modeling Approach and Simulation Results To compute the head distribution and the seepage surface it is sufficient to consider a vertical cross section of the aquifer with a uniform thickness of 1 m The aquifer is simulated using a grid of one layer 21 columns and 20 rows A regular grid spacing of 0 5 m is used for each column The layer type is 0 confined The boundary at the upstream side of the dam is modeled as fixed head boundary with the hydraulic head h 10 m On the right hand side of the dam there are four fixed head cells with h 2 m The other cel
11. INCTYP Rel_to_max The parameter increment is calculated as a fraction of the group member with highest absolute value that fraction again being DERINC A DERINC value of 0 01 is often appropriate If a group contains members which are fixed and or tied the user should note that the values of these parameters are taken into account when calculating parameter incre ments DERINCLB is the absolute lower limit of parameter increments for all group members If a parameter increment is calculated as Relative it may become too low if the parameter values become very small And if a parameter increment is calculated as Rel_to_max it may become too low if the modulus of the largest parameter in the group is very small A parameter increment be comes too low if it does not allow reliable derivatives to be calculated with respect to that pa rameter because of round off errors incurred in the subtraction of nearly equal model generated values DERINCLB is used to bypass this possibility Set DERINCLB to zero if the user does not wish to place a lower limit on param eter increments in this fashion Note that if INCTYP is Absolute DERINCLB is ignored FORCEN can be Always_2 Always_3 or Switch It determines how to calculate derivatives for group members FORCEN Always_2 Derivatives for all parameters belonging to that group will always be calculated using the forward difference method FORCEN Always_3 PEST will use the cen
12. 52 2 Modeling Environment is set to 1 if Brix is higher than the top of the first layer The layer number is set to the last layer if Rgor is lower than the bottom of the last layer Active Check this box to activate a vertex Clear the Active box to deactivate a vertex The properties of an active vertex will be used in the simulation The properties of an inactive vertex are ignored Hydraulic Conductivity of Riverbed Kpi LT Head in the river Hpi L Elevation of the Riverbed bottom B L Width of the river Wy L and Thickness of the riverbed Mpix L The value Kyi describes all of the head loss between the river and the aquifer It depends on the mate rial and characteristics of the riverbed itself and the immediate environment Since the river package requires the input of Hriv Briv and river hydraulic conductance C pry to each cell of a river the input values Kriv Hriv and Brix at active vertices are linearly interpolated or extrapolated to each cell along the trace of the polyline and the value C is obtained by Kriv L Wriv Criy Ma 2 19 where L is the length of the river within a cell Parameter Number Since Criy is usually unknown it must be estimated Parameter Number is used to group cells where the C values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimati
13. a Column gt Simulation Time Period1 Step 1 Time 3000 Layer Row j g Viewing Window Fig 2 6 The Data Editor Map View 2 2 The Data Editor 15 Table 2 4 Summary of the toolbar buttons of the Data Editor Button Name w Leave editor Assign value E Pan o Zoom in Zoom out aa Cell by cell in put method Polygon input method Polyline input method Grid view Map view Column View HEEB A Row View Duplication on off El Layer Row Column Copy on off Change stress period Action Leave the Data Editor and return to the main menu Allow the user to move the grid cursor and assign values to model cells Moves the Viewing Window up down or sideways to display areas of the model domain which at the current viewing scale lie outside the Viewing Window By dragging the mouse the model grid and sitemaps will be moved in the same direction as the mouse cursor When the left mouse button is released the grid and maps will be redrawn Allow the user to drag a zoom window over a part of the model domain Display the entire worksheet Switch to the Cell by cell input method Switch to the Zone input method Switch to the Polyline input method Switch to the Grid View display mode Switch to the Map View display mode Switch to the column cross sectional display mode Switch to the row cross sectional display mode If duplication is turn
14. constant head bourfdary h constant hea no flow boundary a E EE E Fig 4 15 The capture zone of the pumping well vertical exaggeration 10 Ss PMPATH sample1 pm5 Eile Run Options Help no flow boundary contamina area 3 5 f 3 a oO le D a O a Y Eaj pa au L g jad a o p a oO Z ta a 2i O no flow boundary A A RE OD Fig 4 16 The 100 day capture zone calculated by PMPATH 4 1 Your First Groundwater Model with PM 249 Particle Tracking Time Properties Lx Simulation Mode Time Pathline Colors RCH EVT Options Current Time _ Tracking Step Unit days z Stress Period 1 Step Length 100 Time Step fi Maximum steps 100 m Time Mark Plan View Cross Sections Interval 1 Visible I Visible Size E Size 3 m Simulation Mode Flowlines use the flow field from the current time step Pathiines lee transient iow telde m Stop Condition W Particles stop when they enter cells with internal sinks S Particles stop when the simulation tme limitis reached Fig 4 17 The Particle Tracking Time Properties dialog box 4 1 3 Simulation of Solute Transport Basically the transport of solutes in porous media can be described by three pro cesses advection hydrodynamic dispersion and physical chemical or biochemi cal reactions The MT3DMS and MOC3D models us
15. Add New Particles x Particles Properties Cell Faces r Particles on cell faces p Particles within cells Face1 NIxNKe 3 x fl N Fae2NixNKe B x n Face3 NWJxNK B ox fl Nk Face4 NJs NK 3 fi p Particles on _ FaceS NIxNJ 3 og fl a Fases anoo nki Fig 3 5 The Add New Particles dialog box 3 2 PMPATH Modeling Environment 213 uses the retardation factor to modify the average pore velocity of the groundwater flow The velocity vectors in Equation 3 3 become Vat Qai ne Ay Az R U22 Qr2 ne Ay Az R Vy Qyi Ne Av Az R Vy2 Qyo Me Av Az R 3 9 V21 Qii ne Ax Ay R Uz2 Qz2 Ne Ax Ay R 3 2 3 3 Erase Particle The user can only erase particles located in the current layer The current layer is shown in the tool bar Change it first if the user needs to erase particles in another layer gt To erase particles 1 Click the Erase particle button K 2 Move the mouse pointer to where the user wants a corner of the Erase window 3 Drag the mouse pointer until the window covers the particles to be deleted 4 Release the mouse button 3 2 3 4 Zoom in By default PMPATH displays the entire model grid Zoom in is useful for viewing a part of the model domain in greater detail or for saving plots of a certain part of the model area see Section 3 4 1 for how to save plots gt To zoom in on a part of the model 1 Click th
16. File Format 1 2 Data LABEL Data NZONES XXX XXX XXX XXX Data 3 6 repeat NZONES times 3 4 Die Data NP Data PARNO Data Value 1l Value 2 Value 3 Value I Value 16 The following data repeats NP times 386 6 Supplementary Information 6 Data X J Y J Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space LABEL is the file label It must be PMWIN4000_ASCH_ZONEFILE or PMWIN_ASCII_POLYGONFILE NZONES is the number of polygons Maximum is 20 XXX reserved NP is the number of vertices of each polygon The first and the last vertices must overlap The maximum number of NP is 41 PARNO is the parameter number see Sections 2 6 7 2 6 8 for how to define an estimated parameter Value I I 1 to 16 Value I are the polygon values For aquifer parameters such as porosity or transmissivity only the first value or two values if a param eter number can be defined is used For MODFLOW packages such as Drain Package as many values as required by the package are used For example two values Hydraulic conductance and the elevation of the drain required for defin ing a drain will be saved in Value 1 and Value 2 Other values that are not used must be specified as zero Table 6 1 gives the assignment of the parameters in the Value I vector X J Y J are the x y coordinates of the J th vertex of the
17. Options m Observation Borehole Name Active X feasting Vinoth H M 2390 310 2 mM 330 310 CE m 2590 310 mE m 330 310 ES _ m j0 310 _ DE mM 390 310 O m Observation Data Time Concentration Weight Fig 4 18 The Concentration Observation dialog box 4 1 Your First Groundwater Model with PM 251 Reaction Definition MT3DMS x Type of Reaction No kinectic reaction is simulated bs Species Stoichiometry Fig 4 19 The Reaction Definition dialog box 2 Select File Leave Editor or click the leave editor button ee Since MT3DMS is capable of handling multiple species we need to define the num ber of species involved in the simulation This is done by defining the reaction types and species in the following steps gt To set reaction definition 1 Select Models MT3DMS Reaction Definition The Reaction Definition dialog box Fig 4 19 appears 2 In the Reaction Definition dialog box set the Type of Reaction to No kinetic reaction is simulated and activate the first species by checking the Active box of the first row of the table Modify the description of the species as needed 3 Click OK to close the dialog box gt To set the initial concentration 1 Select Models MT3DMS Initial Concentration For the current example we accept the default value 0 for all c
18. Select this menu item to open a Scatter Diagram Hydraulic Head dialog box Refer to Section 2 6 1 20 for details PEST Parameter Estimation View Drawdown Scatter Diagram This menu item is available only if Drawdown Observations have been defined see Section 2 6 1 15 Select this menu item to open a Scatter Diagram Drawdown di alog box which is identical to the Scatter Diagram Hydraulic Head dialog box 176 2 Modeling Environment except the drawdown values replace the head values Refer to Section 2 6 1 20 for details PEST Parameter Estimation View Head Time Curves This menu item is available only if Head Observations have been defined see Sec tion 2 6 1 14 Select this menu item to open a Time Series Curves Hydraulic Head dialog box Refer to Section 2 6 1 20 for details PEST Parameter Estimation View Drawdown Time Curves This menu item is available only if Drawdown Observations have been defined see Section 2 6 1 15 Select this menu item to open a Time Series Curves Drawdown dialog box which is identical to the Time Series Curves Hydraulic Head dialog box except the drawdown values replace the head values Refer to Section 2 6 1 20 for details 2 6 9 PMPATH Advective Transport Select this menu to call the particle tracking model PMPATH which runs indepen dently from PM Refer to Chapter 3 for details Note PMPATH can be started by selecting this menu or from the Start menu of Wind
19. Sink Source Concentration Recharge 2 Assign 12500 g m to the cells within the contaminated area This value is the concentration associated with the recharge flux Since the recharge rate is 8 x 107 m3 m2 s and the dissolution rate is 1 x 1074 ug s m the concentration associated with the recharge flux is 1 x 1074 8 x 107 12500 ug m Subgrid for Transport MOC3D xj Subgrid C Outside of Subarid Number of first layer for transport fi Number of last layer for transport jf Number of first row for transport i Number of last row for transport fo Ss Number of first column for transport fi Number of last column for transport fs Cancel Help Fig 4 28 The Subgrid for Transport MOC3D dialog box 3 4 1 Your First Groundwater Model with PM 259 Select File Leave Editor or click the leave editor button ee gt To assign the parameters for the advective transport 1 2 3 Select Models MOC3D Advection to display a Parameters for Advection Transport MOC3D dialog box Enter the values as shown in Fig 4 29 into the dialog box Select Bilinear X Y directions for the interpolation scheme for particle ve locity As given by Konikow and others 74 if transmissivity within a layer is homogeneous or smoothly varying bilinear interpolation of velocity yields more realistic pathlines for a given discretization than does linear interpolation Click OK to close the dialog box gt T
20. Statistic statistic value for the observation Reserved reserved for future use Enter 0 in the file 6 2 8 Trace File A Trace file can be saved or loaded by the Search and Modify dialog box see Section 2 8 5 File Format 1 Data LABEL 6 2 File Formats 385 The following data repeats 50 times one record for each search range 25 Data ACTIVE COLOR MIN MAX VALUE OPTION Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space LABEL is the file label It must be PMWIN_TRACEFILE ACTIVE Set ACTIVE 1 to activate a search range see MIN MAX below COLOR is the fill color The color is defined by a long integer using the equation color red green 256 blue 65536 where red green and blue are the color components ranging from 0 to 255 COLOR is assigned to the finite difference cells that have a value located within the search range see MIN MAX below MIN MAX define the lower limit and upper limit of the search range VALUE According to OPTION see below you can easily modify the cell val ues OPTION defines the actions OPTION 0 Display only OPTION 1 Replace The cell values are replaced by VALUE OPTION 2 Add VALUE is added to the cell values OPTION 3 Multiply The cell values are multiplied by VALUE 6 2 9 Polygon File A polygon file can be saved or loaded by the Data Editor by selecting Value Polygon
21. WFMA Regularization weight factor adjustment factor WFFAC 13 Convergence criterion for regularization weight factor WFTOL 0 01 Continue optimizing regularization objective function even if measurement objective function less than PHIMLIM IT Activate conservation of memory at cost of execution speed and quantity of model output MEMSAYVE I All regularization constraints are linear LINREG IV Perform inter regularization group weight factor adjustment IREGADJ Load Save OK Cancel Help Fig 2 81 The Regularization tab of the Simulation Settings PEST dialog box ularization constraints will mostly result in a slight diminution of PEST s ability to fit the field data exactly e Acceptable measurement objective function PHIMACCEPT During each optimization iteration just after it has linearized the problem through calculating the Jacobian matrix and just before it begins calculation of the pa rameter upgrade vector PEST calculates the optimal value of the regularization weight factor for that iteration This is the value which under the linearity as sumption encapsulated in the Jacobian matrix results in a parameter upgrade vector for which the measurement component of the objective function is equal to PHIMLIM However due to the approximate nature of the linearity assump tion PEST may not be able to lower the measurement component of the objective function to PHIMLIM on that iteration
22. ation parameter should be tried Relaxation Parameter is used only if the op tion No Coarsening is selected 2 6 1 14 MODFLOW Head Observations Select Head Observations from the MODFLOW menu or from MODFLOW 2000 Parameter Estimation or PEST Parameter Estimation menus to specify the loca tions of the head observation boreholes and their associated observed measurement data in the Head Observations dialog box Fig 2 35 Using the Save button the user can save the tables in separate ASCII files see Section 6 2 6 for the formats which can be loaded at a later time by using the Load button The other options of this dialog box are described below Head Observation x Observations Options r Observation Borehole 2 6 The Models Menu 1 Time DE 100 225 _ Name Active X eastingh Y nothing lal 0851 v 500 15500 0852 3500 14500 0853 m 8500 8500 0854 Mo 3500 5500 0855 mM 5500 4500 _ 0856 M 30 14500 _ 0657 M 50 8500 x r Observation Data Head Observation s Hoss Weight 87163 100 225 __ 2 44396 07 100 1283 71 Fig 2 35 The Head Observation dialog box The Observations Tab Observation Borehole The Name OBSNAM and the coordinates expressed in the world coordinates according to the user defined coordinate system of each borehole are
23. lation If NPRS lt 0 simulation results will be saved whenever the number of transport steps is an even multiple of NPRS If NPRS gt 0 simulation results will be saved at times as specified in the table shown in Fig 2 54 There are two ways for specifying the output times The user may click the table header Output Time and then enter a minimum time a maximum time and a time interval between each output into an Output Time dialog box PM will use these entries to calcu late NPRS and the output times The other way is to specify a positive NPRS and press the Tab key then enter the output times into the table Note that the output times are measured from the beginning of the simulation e Misc CINACT is the predefined concentration value for an inactive concentration cell CBUND 0 This value is a marker for these cells only and has no physical meaning THKMIN is the minimum saturated thickness in a cell expressed as the deci mal fraction of the model layer thickness below which the cell is considered inactive NPRMAS indicates how frequently the mass budget information should be saved in the mass balance summary file MT3Dann MAS where nnn is the species number 2 6 2 13 MT3DMS SEAWAT Run If the Simulation Mode is set as Constant Density Transport with MT3DMS the Run MT3DMS dialog box Fig 2 55 will be displayed If the Simulation Mode is set as Variable Density and Transport with SEAWAT the Run SEAWAT dialo
24. 2 86 shows the effects of different weighting exponents Five data points are regularly distributed along the x axis Using higher values for the exponent e g F 4 the interpolated cell values will approach the value of the nearest data point The surface is therefore relatively flat near all data points Lower values of the exponent e g F 1 produce a surface with peaks to attain the proper values at the data points A value of F 2 is suggested by Shepard 108 e Akima s bivariate interpolation This method creates a triangulation of the mea surement data points and performs interpolation by using a bivariate fifth order Hermite polynomial for the interpolation within a triangle It uses a user specified number of data points closest to a model cell for estimating the value at the cell 180 2 Modeling Environment Interpolated data value gt F 1 F 2 F4 data point Fig 2 86 Effects of different weighting exponents e Renka s triangulation This method first creates a triangulation of the measure ment data points and then uses a global derivative estimation procedure to com pute estimated partial derivatives at each point The program determines a piece wise cubic function F x y F has continuous first derivatives over the created mesh and extends beyond the mesh boundary allowing extrapolation e Kriging The Kriging method has been popularized by Math ron 84 and is named in honor of D G Kri
25. 5 8 1 Using the Field Interpolator Folder pmdir examples misc misc1 Overview of the Problem This example illustrates the use of the Field Interpolator Fig 5 56 shows the plan view of the model area the model grid and the locations of measurement points The model grid consists of 1 layer 70 rows and 60 columns The mea sured hydraulic heads and the coordinates of the measurement points are saved in pmdir examples misc misc1 measure dat To obtain the starting head distribution of a flow simulation the measured hydraulic heads should be interpolated to each model cell Modeling Approach and Simulation Results The starting heads are interpolated to model cells using the four interpolation meth ods provided by the Field Interpolator The interpolation results are shown in the form of contours in Figures 5 57 5 60 The octant search method with Data Per Sector 1 is used by all gridding methods A weighting exponent of F 2 is used by Shepard s inverse distance method The Kriging method uses the linear variogram model with co 0 and a 1 There is no significant difference observed in these fig 370 5 Examples and Applications ures when sufficient data points are available The major difference is observed in the southern part of the model area where only one measurement point is found and the system is not well conditioned Fig 5 58 Contours produced by the Krig
26. 5825800 0 0049024 5825800 1 8828E 10 5825800 0 0037226 5825800 1 6391E 10 8738800 0 0097708 8738800 1 0897E 08 8738800 0 090093 8738800 7 6243E 08 ATANAN A AATArE Save Table Copy te Clipboard Fig 4 34 The Time Series Curves Concentration dialog box 264 4 Tutorials xi Data r X Axis Time Concentration Time Curve I FixBounds T Logarithmic Lower Bound 0 700 J Upper Bound 94670000 600 Reset Bounds a 500 i S c I FixBounds M Logarithmic 5 400 Lower Bound 0 5 S x00 Upper Bound 730 06 fs 200 Reset Bounds ool Data Type 1004 4 oA M Calculated V Observed 0 Use results of all observations g Sool g Use results of the following Time OBSNAM Copy to Clipboard Save Plot As Ok Cancel Help Fig 4 35 The Chart tab of the Time Series Curves Concentration dialog box value is unknown We want to find out this value through a model calibration by using the measured hydraulic heads at the observation boreholes listed in Table 4 5 Three steps are required for the parameter estimation 1 Define the region of each parameter Parameter estimation requires a subdivision of the model domain into a small number of reasonable regions A region is defined by using the Data Editor to assign a parameter number to the model cells 2 Specify the coordinates of the observation boreholes and the measured hydraulic head values 3 Specify the starting va
27. 59 this applies to outer iterations and not inner it erations The reason for adjusting IWETIT is that the wetting of cells sometimes produces erroneous head changes in neighboring cells during the succeeding itera tion which may cause erroneous conversions of those cells Waiting a few iterations until heads have had a chance to adjust before testing for additional conversions can prevent these erroneous conversions When setting IWETIT greater than one there is some risk that cells may be prevented from correctly converting from dry to wet If the solution for a time step is obtained in less than IWETIT iterations then there 2 6 The Models Menu 61 Wetting Capability Iteration Interval for Attempting to Wet Cells 1 Wetting Factor WETFCT 1 Initial Heads at Rewetted Cells h BOT WETFCT hn BOT C h BOT WETFCT THRESHI BOT Bottom of cells THRESH Wetting threshold hn heads at the neighboring cells Click OK to edit wetting threshold Cancel Help Fig 2 29 The Wetting Capability dialog box will be no check during that time step to see if cells should be converted from dry to wet The potential for this problem to occur is greater in transient simulations which frequently require only a few iterations for a time step The method of wetting and drying cells used in the BCF2 Package can cause problems with the convergence of the iterative solvers used in MODFLOW Conver gence problems can occur in MODFL
28. Configuration of the physical system 0004 341 Simulated head distribution and catchment area of the excavation pit 341 Configuration of the physical system 004 343 Model grid and the boundary conditions 343 Flowlines and calculated head contours for isotropic medium 343 Flowlines and calculated head contours for anisotropic medium 343 Seepage surface through a dam 0 0 eee eee eee 345 Model grid and the boundary conditions 346 Calculated hydraulic heads after one iteration step 346 Calculated hydraulic heads distribution and the form of the seepage SUPLACE seg ee eee ee eas te awe et els ew ay 347 Model grid and boundary conditions 000 349 Plan and cross sectional views of flowlines Particles are started from the contaminated area The depth of the cutoff wall is 8 m 350 Plan and cross sectional views of flowlines Particles are started from the contaminated area The depth of the cutoff wall is 10 m 350 Model grid and boundary conditions 000 352 Distribution of the land surface subsidence maximum 0 11 _m 353 Comparison of the calculated breakthrough curves with different dispersivity Values cacc6 c 0i isis k een Ge lls Mewes oN balou bes 355 Configuration of the model and the location of an observation borehole357 Comparison of the b
29. DCHMOC is used to select be tween MOC and MMOC in the HMOC solution scheme MOC is selected at cells where DCCELL gt DCHMOC MMOC is selected at cells where DCCELL lt DCHMOC 2 6 2 4 MT3DMS SEAWAT Dispersion The following values must be specified for each layer in the Dispersion Package dialog box Fig 2 50 2 6 The Models Menu 95 Dispersion Package You need to specify the following values for each layer When finished click OK to specify the longitudinal dispersivity L for each cell TRPT Horizontal transverse dispersivity Longitudinal dispersivity TRPV Vertical transverse dispersivity Longitudinal dispersivity DMCOEF The effective molecular diffusion coefficient L 2 T DMCOEF is ignored if Species dependent Diffusion is used ayer TRPT TRPV DMCOEF 103 0 3 0 3 03 03 0 3 03 0 3 0 3 OK Cancel Fig 2 50 The Dispersion Package dialog box TRPT is the ratio of the horizontal transverse dispersivity to the longitudinal dis persivity The longitudinal dispersivity for each finite difference cell is specified in the Data Editor Longitudinal dispersivity is used to approximate the spread ing of the solute concentration in groundwater caused by the irregular shape of the interconnected pore space and the velocity variations at the microscopic level as well as the unresolved macroscopic level The velocity of groundwater varies according to the siz
30. First labeled contour line fi Labeled line frequency fi OK Cancel Fig 2 109 The Contour Labels dialog box 202 2 Modeling Environment Exponential This option displays numbers in scientific format and E is in serted between the number and its exponent Decimal digits The value of Decimal digits determines the number of digits to the right of the decimal separator For example if Decimal digits 2 the value 1241 2 will be displayed as 1241 20 for the fixed option or 1 24E 03 for the exponential option Prefix is a text string that appears before each label Suffix is a text string that appears after each label e Restore Defaults Clicking on this button PM sets the number of contour lines to 11 and uses the maximum and minimum values found in the current layer as the minimum and maximum contour levels The label height and spacing will also be set to their default values e Load and Save The contents of the contour level table can be loaded from or saved in separate Contour files Refer to Section 6 2 2 for the format Labeirormat x O 5 Format C Exponential Decimal digits 2 Prefix Suffix Cancel Fig 2 110 The Label Format dialog box 3 The Advective Transport Model PMPATH PMPATH is an advective transport model running independently from PM PMPATH retrieves the groundwater models and simulation result from PM and MODFLOW A semi analytical particle tracking scheme Pol
31. H e Ee eb ao tT z South Granite Hills Fig 4 51 Model grid of the 1st layer and 3rd layer 4 3 Aquifer System with River 289 Granite Hills Big River Wall nou Weallt_ South Granite Hills E Fig 4 52 Model grid of the 2nd layer a Select Value Matrix Load to import examples tutorials tutorial3 aq2top dat as the elevation of the top of aquifer 1 Move to Layer 3 Select Value Matrix Load to import examples tutorials tutorial3 aq3top dat as the elevation of the top of aquifer 1 Select File Leave Editor or click the leave editor button eel gt To specify the bottom elevation of each aquifer 1 Select Grid Bottom of Layers BOT PM will ask if you want to use the Top of Layer 2 as the Bottom of Layer 1 and Top of Layer 3 as the Bottom of Layer 2 We will accept this Move to the layer 3 and select Value Reset Matrix to set the elevation of the bottom of the layer 3 to 0 0 m Select File Leave Editor or click the leave editor button w Specification of the geometry of the system is now complete all we need to do now is enter the physical parameters of the system gt To specify the time parame
32. In MODFLOW an aquifer system is replaced by a discretized domain consisting of an array of nodes and associated finite difference blocks cells Fig 4 2 shows the spatial discretization scheme of an aquifer system with a mesh of cells and nodes at which hydraulic heads are calculated The nodal grid forms the framework of the numerical model Hydrostratigraphic units can be represented by one or more model layers The thickness of each model cell and the width of each column and row may be variable PM uses an index notation Layer Row Column for locating the cells For example the cell located in the first layer 6th row and 2nd column is denoted by 1 6 2 In this example the model domain is discretized in cells of horizontal dimensions of 20 m by 20 m The first stratigraphic layer is represented by the first 230 Layers K Fig 4 Tutorials Columns J 1 23456789 10 i A 3 L SL eee a7 Rows a LA SATAN NN 4 2 The spatial discretization scheme and cell indices of MODFLOW model layer and the second stratigraphic layer is represented by two model layers It is to note that a higher resolution in the vertical direction is often required in order to correctly simulate the migration of contaminants gt To generate the model grid 1 2 4 Select Grid Mesh Size The Model Dimension dialog box appears Fig 4 3 Enter 3 for the number of layers 10 for model thickness O for the model top elevation
33. No flow conditions are assigned to the top and bottom boundaries A complete list of the in put values used for the problem is given in table 5 of the SEAWAT_V4 user s guide This problem is a simplified representation of what might occur in a coastal carbon ate platform Modeling Approach and Simulation Results Five cases of the example problem described in the user s guide of SEAWAT_V4 were re created by using the present version of PM and are given in Table 5 8 You can find the models in sub folders under path examples SEAWAT Table 5 8 SEAWAT Examples Example Description CASE1 Variable density simulation in which the fluid density is a function only of salinity CASE2 _ Variable density simulation in which the fluid density is a function of salinity and temperature CASE3 Variable density simulation in which the fluid density is a function of salinity and temperature while considering heat conduction in the simulation CASE4 _ Variable density simulation in which the fluid density is a function of salinity and temperature while considering heat conduction and thermal equlibration between the fluid and the solid matrix CASES _ Variable density simulation in which the fluid density is a function of salinity and temperature while considering heat conduction and thermal equlibration between the fluid and the solid matrix as well as heat conduction at the seawater boundary 5 8 Miscellaneous Topics 369 5 8 Miscellaneous Topics
34. P Ax aL Az is the grid spacing and aL is the longitudinal dispersivity is smaller than two the upstream finite difference method is reasonably accurate However it is advisable to use the upstream finite difference method for obtaining first approximations in the initial stages of a modeling study The third order TVD method is based on the ULTIMATE algorithm 80 81 82 which is in turn derived from the earlier QUICKEST algorithm 79 With the ULTIMATE scheme the solution is mass conservative without ex cessive numerical dispersion and artificial oscillation Weighting Scheme is needed only when the implicit finite difference method is used i e the solution scheme is finite difference and the iterative GCG solver is used In the finite difference method when computing the mass flux into a model cell by advection the concentration values at the cell interfaces between two neighboring cells are used For the upstream weighting scheme the interface concentration in a particular direction is equal to the concentration at the up stream node along the same direction For the central in space weighting scheme the interface concentration is obtained by linear interpolation of the concentra tions at the two neighboring cells As denoted in Zheng and Wang 121 the central in space scheme does not lead to intolerable numerical dispersion when the grid spacing is regular However if transport is dominated by advection the upstrea
35. S 120 Use results of all observations 20000000 C Use results of the following OBSNAM 10000000 Time OBS2 y Fig 2 42 The Chart tab of the Head Time Series Curves Diagram dialog box 84 2 Modeling Environment listed in the Data table should be used If the option Use results of the follow ing OBSNAM is chosen only the curves of the selected observation borehole OBSNAM are displayed Copy to Clipboard Press this button to place a copy of the chart on the clip board The user can recall this copy by pressing Ctrl v in almost all word or graphics processing software This button is enabled only when the Chart tab is chosen Save Plot As Press this button to save the chart in Windows bitmap or Metafile formats This button is enabled only when the Chart tab is chosen 2 6 2 MT3DMS SEAWAT The first step to use MT3DMS or SEAWAT is to define the simulation mode species and type of reactions to be simulated in the Simulation Settings dialog box Sec tion 2 6 2 1 Once the simulation settings are defined the appropriate menu items of the MT3DMS SEAWAT menu will be enabled allowing the user to specify re quired model parameters If the user selects menu items involving species dependent parameters PM will display a dialog box for selecting a species for which the pa rameter is to be specified For example if you select MT3DMS SEAWAT Initial Concentration the Initial Concentration d
36. Select Value Reset Matrix or press Ctrl R enter 0 0005 in the dialog box then click OK Select File Leave Editor or click the leave editor button wel gt To specify the vertical hydraulic conductivity 1 Select Parameters Vertical Hydraulic Conductivity PM displays the model grid 236 4 Tutorials 2 Move the grid cursor to the first layer 3 Select Value Reset Matrix or press Ctrl R enter 0 00001 in the dialog box then click OK 4 Move the grid cursor to the second layer 5 Select Value Reset Matrix or press Ctrl R enter 0 00005 in the dialog box then click OK 6 Move the grid cursor to the third layer 7 Select Value Reset Matrix or press Ctrl R enter 0 00005 in the dialog box then click OK 8 Select File Leave Editor or click the leave editor button ee gt To specify the effective porosity 1 Select Parameters Effective Porosity PM displays the model grid Since the default value of 0 25 is the same as the prescribed value nothing needs to be done here Note that although a flow simu lation does not require the effective porosity it is necessary for the computation of travel times and contaminant transport processes 2 Select File Leave Editor or click the leave editor button eel gt To specify the recharge rate 1 Select Models MODFLOW Recharge 2 Select Value Reset Matrix or press Ctrl R enter 8E 9 for Recharge Flux L T in the dialog box then cli
37. Sink Source Concentration 2 6 6 7 MT3D Concentration Observations 2 6 6 8 MT3D Output Control 2 6 6 9 MT3D Run 2 6 6 10 MT3D View MODFLOW 2000 Parameter Estimation 2 6 7 1 MODFLOW 2000 Parameter Estimation Simulation Settings VII Contents 2 6 7 2 MODFLOW 2000 Parameter Estimation Head Observations s aeree ne ccc ccc E a eee 141 2 6 7 3 MODFLOW 2000 Parameter Estimation Flow Observations zee s osne a cee eee eee 141 2 6 7 4 MODFLOW 2000 Parameter Estimation Run 144 2 6 7 5 MODFLOW 2000 Parameter Estimation View 147 2 6 8 PEST Parameter Estimation 0000 ee 149 2 6 8 1 PEST Parameter Estimation Simulation Settings 151 2 6 8 2 PEST Parameter Estimation Head Observations 171 2 6 8 3 PEST Parameter Estimation Flow Observations 172 2 6 8 4 PEST Parameter Estimation Run 172 2 6 8 5 PEST Parameter Estimation View 173 2 6 9 PMPATH Advective Transport 000s eee ee 176 27 The Tools Mene iiiaae eee Mae da eee eed 176 216M PASM ZEL narei ois Set ee eRe RE GOs REE EES 176 2 7 2 The Field Interpolator 00 0 0 0 eee eee 177 2 7 2 1 Interpolation Methods for Irregularly Spaced Data 177 2 7 2 2 Using the Field Interpolator 178 2 7 3 The Field Generator 0 00 2 eee eee eee eee 183 2
38. The abbreviation MS denotes the Multi Species structure for accommodating add on reaction packages MT3DMS includes three major classes of transport solution techniques i e the finite differ ence method the particle tracking based Eulerian Lagrangian methods and the higher order finite volume TVD method In addition to the explicit formulation of MT3D MT3DMS includes an implicit iterative solver based on generalized conjugate gradient GCG methods If this solver is used dispersion sink source and reaction terms are solved implicitly without any stability constraints MT3D99 122 MT3D99 is an enhanced version of MT3DMS 121 for simulating aerobic and anaerobic reactions between hydrocarbon contaminants and any user specified electron acceptors and parent daughter chain reactions for inorganic or organic compounds The multi species reactions are fully integrated with the MT3DMS transport solution schemes including the implicit solver RT3D 25 26 27 is a code for simulating three dimensional multispecies reactive transport in groundwater Similar to MT3D99 the code is based on 1 Introduction MT3DMS 121 MT3D99 and RT3D can accommodate multiple sorbed and aqueous phase species with any reaction framework that the user wishes to define With the flexibility to insert user specific kinetics these two reactive transport models can simulate a multitude of scenarios For example natural attenuation processes can be evaluated or
39. The location and orientation of the model grid are defined by the coordinates Xo Yo of its left upper corner and a rotation angle The rotation angle is expressed in degrees and is measured counterclockwise from the positive x direction 200 2 Modeling Environment Environment Options x Appearance Coordinate System Contours IV Ni le IV Display contour lines T Fill contours IV Orient labels uphill IV Ignore inactive cells Parameter Initial Hydraulic Heads 7 Label Height Label Spacing a C v 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 M 254 5584 2545 584 Vv 254 5584 2545 584 Ara Fraa TT Label Format Restore Defaults Load Save I Display polygons in the cell by cell mode OK Cancel Help Fig 2 107 The Contours tab of the Environment Options dialog box The Contours Tab The Data Editor displays contours based on the cell data The Contours tab Fig 2 107 controls the display of the contour levels labels and colors The options of this tab are listed below Visible Contours are visible if this box is checked Display contour lines Contour lines and labels are displayed if this box is checked e Fill contours Checking this box causes the space between contour lines to be filled with the color defined in
40. ance color of each simulated component A simulated component is visible if the corresponding Visibility box is checked To select a new color click on the colored cell a Zl button appears then click on the ZJ button and select a color from a Color dialog box The Vertical Exaggeration edit field controls the vertical exaggeration factor seen in the Row or Column view 198 2 Modeling Environment Environment Options x r Grid Postion p Viewing Windows Coordinate System x0 vee ieo0 Your model grid fhe fo Yo Yo m Viewing Window Size x1 0 nm x2 z0 A Rotation angle in degree Y2 20000 Pam K1LY1 J Display polygons in the cell by cell mode OK Cancel Help Fig 2 105 The Coordinate System tab of the Environment Options dialog box The Coordinate System Tab The Coordinate System Tab is used to define the extent and location of the the View ing Window and to define location and orientation of the model grid EON Viewing Window La DNA R x1 Y1 F Loog 2 9 The Options Menu 199 As illustrated in Fig 2 105 the Viewing Window is a window to the real world your model grid is placed within the Viewing Window The extent and location of the Viewing Window are defined by specifying the real world coordinates of its lower left and upper right corners i e by the coordinates X1 Y1 and X2 Y2 as shown in Fig 2 105 and Fig 2 106
41. dialog box 80 The Data tab of the Time Series Curves Hydraulic Head dialog box 82 The Chart tab of the Head Time Series Curves Diagram dialog box 83 The Initial Concentration dialog box 0005 84 The Simulation Settings MT3DMS SEAWAT dialog box 85 The Stoichiometry tab of the Simulation Settings MT3DMS SEAWAT dialog box 0 0 c eee eee ee ee 87 The Variable Density tab of the Simulation Settings MT3DMS SEAWAT dialog box 00 cece eee eee 89 The Advection Package MT3DMS dialog box 90 Initial placement of moving particles adapted from Zheng 117 a Fixed pattern 8 particles are placed on two planes within a cell b Random pattern 8 particles are placed randomly within acell 93 Distribution of initial particles using the fixed pattern adapted from Zheng 1990 If the fixed pattern is chosen the number of particles placed per cell NPL and NPH is divided by the number of planes NPLANE to yield the number of particles to be placed on each plane which is then rounded to one of the numbers of particles Shown here c o 6 24bs6e ein bones ee A Ped sa eye Ved eae 94 The Dispersion Package dialog box 0005 95 The Chemical Reaction MT3DMS dialog box 97 The Generalized Conjugate Gradient GCG dialog box 103 The Output Control MT3D MT3DMS dialog box 105 The Output Times ta
42. ing steps 8 to 11 with the Create New Frames box cleared in step 10 Note Since the number and the size of the image files can be very large make sure that there is enough free space on your hard disk To reduce the file size you can change the size of the PM window before creating the frames You may also wish to turn off the display of the model grid in the Environment Options dialog box so that you don t have the grid cluttering the animation x IV Create New Frame Files Frame File Click the open file button to select a file rm Delay s 3 OK Cancel Fig 4 41 The Animation dialog box 4 2 Unconfined Aquifer System with Recharge 271 4 2 Unconfined Aquifer System with Recharge Folder pmdir examples tutorials tutorial2 4 2 1 Overview of the Hypothetical Problem The model assumes a simple scenario which is designed to demonstrate the basic features of PMWIN and MODFLOW An unconfined aquifer Fig 4 42 is a coarse grained sand with a measured isotropic hydraulic conductivity of 160 m day the specific yield has been assessed as 0 06 Recharge to the aquifer only occurs through out the 4 month wet season at a rate of 7 5 x 1074m day outside the wet season there is no recharge to the aquifer The elevations of the aquifer top and bottom are 25 m and 0 m respectively The area of interest is 10000 m long and 6000 m wide and is bounded by no flow zones to the east and west There is also a volcanic mountain
43. of Parameters MODFLOW 2000 dialog box which lists all parameters defined in previous steps and provides an overview of all parameters The dialog box also allows selecting or un selecting parameters for estimation see Section 2 6 7 1 2 6 7 1 MODFLOW 2000 Parameter Estimation Simulation Settings The required parameters and execution options for MODFLOW 2000 are specified in the List of Parameters MODFLOW 2000 dialog box Fig 2 74 The available settings are grouped under four tabs described below Using the Save button the user can save the settings in separate ASCII files which can be loaded at a later time by using the Load button Click the Update button to retrieve the estimated parameter values saved in the MF2KOUT _B file The Update button is disabled and dimmed if this file is not available The Parameters Tab The Parameters Tab contains a table that gives an overview of the initial values and properties of estimated parameters The initial value PARVAL of parameter is the 2 6 The Models Menu 137 arithmetical mean of the cell values of that parameter The parameter s lower bound PARLBND and upper bound PARUBND default to two orders lower andhigher than PARVAL respectively If a parameter is removed by changing the parameter number to zero in the Data Editor the corresponding parameter in the table is ignored PM does not delete that adjustable parameter from the table To delete the parameter click on its reco
44. terval was used as input value The distribution used in the simulation is also shown in Fig 5 14 A total of six 360 day infiltration periods 144 stress periods each with a length of 15 days was used in the simulation The first five 360 day infiltration periods were computed to allow the model to reach a stable yearly cycle because the starting water level for each model cell was not known Results of the model simula tion from the sixth infiltration period are compared to the results from the analytical solution for an observation well 2 000 ft from the river Fig 5 15 The coordinates of the observation well are given in the Head Observation dialog box The Stream flow Routing package is not really needed to simulate this condition as the river could have been represented using fixed head or river cells The same results can be obtained using the River pack age The simulation was done to determine whether the STR1 package correctly accumulates flow from the aquifer into the stream simulation results analytical solution Se ee ey ee E Seb SSN Colusa peo ot oo Peta erases DETE ca S AA Ea eee ee aR oe eee e al 1 eee eee eee Cee 1 Groundwater level in feet above arbitrary datum 54E 1 1 56E 6 1 87E 5 Elapsed simulation time seconds Fig 5 15 Comparison of simulation results to analytical solution developed by Oakes and Wilkinson 90 314 5 Examples and Applications 5 1 7 Flood in a River Folder pmdir examples b
45. than the drain elevation ground water flows into the drain and is removed from the groundwater model Discharge to the drain is zero when the hydraulic head is lower than or equal to the median drain elevation Recharge from the drain is always zero regardless of the hydraulic head in the aquifer Using the Data Editor a drain system is defined by using the Cell by Cell or Polygon input methods to assign parameters to model cells or by using the Polyline input method and assigning parameters to vertices of the polylines along the trace of drain system The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress periods the input pa rameters can be different from period to period The input methods require different parameters as described below e When using the Polyline input method right click on a vertex to specify its properties in the Drain Parameters dialog box Fig 2 18 If the properties are assigned to one vertex only the properties of all vertices of the polyline are as sumed to be the same The settings of the dialog box are described below Layer Option and Layer Number Layer Option controls how the layer num ber of a drain is determined Tf Layer Option is Assign layer number manually the value of Layer Number defines the model layer number for all model cells downstream from a vertex until the next vertex redefines the layer number Dra
46. three tabs Files Grid Position and Search Gridding Method These tabs are de scribed below To start the interpolation simply click the GO button The Field Gen erator creates and writes the settings and the coordinates to a batch file PMDIS BAT and two ASCII files PMDIS_IN 1 and PMDIS_IN 2 After having created these files PMDIS BAT starts in a DOS window The created ASCII files are used by the interpolation program The Files Tab e PMWIN Model If the user has already opened a model within PM and started the Field Interpolator from the Tools menu this field contains the model file name If the text string Open a model first is shown click and select a PM model from an Open File dialog box A PM model file always has the extension PMS e Input File An input file contains the measurement data which are saved as an XYZ file see Section 6 2 10 for the format An input file can be prepared with the Digitizer or other software Click to select an existing input file The maximum number of data points is 5000 Field Interpolator iol xj Files Grid Position Search Griddina Method PMWIN Model c program files wt360 pmwin examples misc mis je Input File c program files wt360 pmwin examples misc mis o gt Output File c program files wt360 pmwin examples misc mis fo Fig 2 85 The Field Interpolator dialog box 2 7 The Tools Menu 179 e Output file An output file contains the interpolated data for each
47. which is displayed after selecting the menu item Tools 2D Visualization The dialog box contains several tabs each corresponds to a simulation model Use these tabs to select the desired result type and click the OK button to proceed to the 2D Visualization tool The 2D Visualization tool will load the selected model result and automatically display 11 contour levels ranging from the minimum to maximum values For a time dependent result type the user can select a time point from the Simulation Time drop down box on the tool bar 2 7 5 3D Visualization Select this menu item to start the 3D Visualization program defined in the Preferences dialog box see Section 2 3 4 for details Currently PM is supported by two 3D visualization software packages 3D Groundwater Explorer 21 and 3D Master 23 2 7 6 Results Extractor Normally simulation results from MODFLOW MT3DMS and other transport mod els are saved in unformatted binary files and cannot be examined by using usual text editors Using the Results Extractor the user may extract specific results from the re sult files and save them in ASCII Matrix see Section 6 2 1 for the format or Surfer Data files The Result Extractor dialog box Fig 2 93 is described below e Spreadsheet The spreadsheet displays a series of columns and rows which cor respond to the columns and rows of the finite difference grid By clicking the Read button the selected result type will be read and
48. 0 gt To specify the no flow zone 1 2 3 5 Ensure Duplication is off and then click in a cell within the No Flow zone Press Enter or Right click the cell to open the Cell Value dialog box Enter 0 as the value for IBOUND and click OK to exit the dialog box You will notice that the cell is now gray in color Either repeat the above 3 steps for the remaining no flow cells or turn on the Du plication and copy the value of IBOUND 0 to the other cells In some cases you will notice that the boundary cuts through part of a cell In these cases you need to make a judgment as to whether the cell should remain active IBOUND 1 or be specified as inactive IBOUND 0 Generally you should choose the option which applies to more than 50 of the cell area If all the steps were completed correctly the grid should now look similar to that in Fig 4 45 Select File Leave Editor or click the leave editor button eel The next step in the modeling process is to specify the top and bottom elevations of the model layer gt To specify the elevation of the top of the model layer 1 2 Select Grid Top of Layers TOP Since the aquifer top elevation is uniform throughout the model it is possible to set a single value to the entire grid by selecting Value Reset Matrix Enter 25 in the Reset Matrix dialog box and click OK to exit 4 2 Unconfined Aquifer System with Recharge 277 4 Select File Leave Editor or click the
49. 0 0 00 0 eee ee eee a Head distribution after 240 days of pumping period 1 time step 12 b Head distribution after 120 days of recharge period 2 time STEP O oenn E aed n leh anion ses the AE ee ed ee ae Configuration of the hypothetical model The Model Grid and Coordinate System dialog box Model grid after the refinement 0 cee ee eee ee eee ee Model grid of the Ist layer and 3rd layer 0 Model grid of the 2nd layer 0 ee eee eee Define the river using a polyline 0 000005 Parameters of the upstream vertex 10 00 0 eee eee eee eens Parameters of the downstream vertex 000000008 The Result Selection dialog box 0 000 Steady state hydraulic head distribution in the first model layer Steady state hydraulic head distribution in the 3rd model layer and capture zones of the pumping wells 00 e ee eee eee XVII XVIII List of Figures 4 59 5 1 5 2 5 3 5 4 5 5 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 17 5 18 5 19 5 20 5 21 5 22 5 23 5 24 3 25 5 26 5 27 5 28 5 29 5 30 125 year streamlines particles are started at the cell 6 5 1 and flow towards Well 2 errs e bo ee Reed Gi teks AE 296 Plan view of the model area 1 0 0 eee eee eee 298 Catchment area and 365 days isochrones of the pumping well 2D approach ground w
50. 0 00 eee eee eee Summary of menus in PM 0 0 Summary of the toolbar buttons of the Grid Editor Summary of the toolbar buttons of the Data Editor Versions and Filenames of MODFLOW 55 Model Data checked by PM 0 0 cee eee eee ee ne eee Names of the MOC3D output files 0 04 Adjustable parameters through MODFLOW 2000 within PM Adjustable parameters through PEST withinPM Output from the Water Budget Calculator Summary of the toolbar buttons of PMPATH Output files from MODFLOW 0 00 e eee eee Volumetric budget for the entire model written by MODFLOW Output from the Water Budget Calculator 0 Output from the Water Budget Calculator for the pumping well Measured hydraulic head values for parameter estimation Volumetric budget for the entire model written by MODFLOW River datas ovis ces gitinescy wad ee tise yeaah amide tin gutttluede eee gobo Analytical solution for the drawdown with time Parameters defined for MODFLOW 2000 test case 1 parameter values starting and estimated PARVAL 00 eee eee Parameters defined for MODFLOW 2000 test case 2 parameter values starting and estimated PARVAL 0002 eee eee PHT 3D Examples isons teen Sehr ies Pee nas Ree eae UK
51. 0 2 the first cell and the last cell of the model are specified as fixed head cells with initial hydraulic heads of 1 1 m and 1 0 m respectively The initial head of all other cells is 1 0 m A steady state flow simulation is carried out for a stress period length of 100 days The injected mass of 1 g is simulated by assigning an initial concentration of 5 g m to the cell 1 1 10 Using the Concentration Observation dialog box an ob servation borehole is set in the center of the cell 1 1 30 The breakthrough curves for the dispersivity values of 1 m and 4 m are shown in Fig 5 47 It is interesting to see that the concentration peak arrives earlier with a lower concentration value when the value of dispersivity is higher At the first glance this result is somewhat confusing because the center of mass should travel with the same velocity regardless of the value of dispersivity Because of a higher dispersivity the front of the concen tration plume travels faster and at the same time the intensity of the concentration drops faster This combination causes this phenomenon Analytical solutions for solute transport involving advection dispersion and first order irreversible decay in a steady state uniform flow field are available in many text books for example Javandel and others 68 Kinzelbach 69 or Sun 110 A computer program for the analytical solutions of 1 D and 2 D solute transport for point like pollutant injections is
52. 00 Q D or r B D T O T o QO o 3 2 BN 4 am ej contaminated p I area ll oe tT e gg 8 gs Sy Ere TE gt g 3 3 E PRIM Bin gt a well D 5 al 5 a DB fal 7 z a Fi i Q 3 nel 8 8 2 S 3 g 3 El D a de e ee El Ta Ta 2 F S R ela k 2 H ate I kei Kei oO ae kes re at S w E a 25 BS B n aw came DVT TT TT eT Toa Tet is 5 2i e t a 3 4 O ea Pa an w Ww Ww Ww wy Ww w tat S u W a Heja i 3 8 eS 3 3 a D 2 Ce no flow Boundary J 5894737 544 1296 8 1 3 30 2D Visualization JHvdraulic head 8001284 Fig 4 11 Contours of the hydraulic heads in the first layer 4 Click El to start the backward particle tracking 5 Click Elto start the forward particle tracking 245 Each time you press one of the buttons J or ca particle s may move back ward or forward for a defined time length Refer to Section 3 3 2 for the definition of the time length gt To delineate the capture zone of the pumping well 1 Select Models PMPATH Pathlines and Contours if PMPATH is not yet started 2 Click the Set Particle button Fl 3 Move the mouse pointer to the model area The mouse pointer turns into crosshairs 4 Place the crosshairs at the upper left corner of the pumping well as shown in Fig 4 12 5 Hold down the left mouse button and drag the crosshairs unti
53. 1 Select Tools Water Budget The Water Budget dialog box appears Fig 4 8 2 Click Subregions PM displays the model grid Click the I button if the display mode is not Grid View The water budget of each subregion will be calculated A subregion is indicated by a number ranging from 0 to 50 A number must be assigned to each model cell The number 0 indicates that a cell is not associated with any subregion Follow the steps below to assign subregion numbers to the first and 2 to the second layer Move the grid cursor to the first layer 4 Select Value Reset Matrix type 1 in the Reset Matrix dialog box then click OK Move the grid cursor to the second layer by pressing the PgDn key 6 Select Value Reset Matrix type 2 in the Reset Matrix dialog box then click OK 7 Select File Leave Editor or click the leave editor button w 8 Click OK in the Water Budget dialog box PM calculates and saves the flows in the file path WATERBDG DAT as shown in Table 4 3 The unit of the flows is LT 1 Flows are calculated for each subre gion in each layer and each time step Flows are considered as IN if they are en tering a subregion Flows between subregions are given in a Flow Matrix HORIZ EXCHANGE gives the flow rate horizontally across the boundary of a zone EX CHANGE UPPER gives the flow rate coming from IN or going to OUT to the upper adjacent layer EXCHANGE LOWER gives the flow rate coming from IN or going t
54. 10 percent of the thickness of a cell In the second simulation wetting of cells is based on comparison to heads both in horizontally adjacent and underlying cells THRESH is positive A wetting iteration interval of 2 and a THRESH of 1 5 feet are used in order to prevent continued oscillation between wet and dry for some cells Due to the steepness of the head gradient and the grid discretization the head difference between adjacent horizontal cells is generally much larger than the head difference between adjacent vertical cells along the mound For example the cell at layer 4 row 3 and column 4 is supposed to be dry even though the head 5 1 Basic Flow Problems 307 in the horizontally adjacent cell in column 3 is 1 4 feet above the bottom of the layer The vertical head difference between cells in this part of the model is much less the difference between the head at the cell in layer 4 row 3 column 3 and the cell below is only 0 05 foot Thus the neighboring cell to the right is repeatedly and incorrectly converted to wet during the solution process if horizontal wetting is used with a wetting threshold of 0 5 foot The larger wetting threshold and wetting iteration interval used in the second simulation allow convergence to occur but only after many iterations In this simulation head in adjacent vertical cells is the best indicator of when a dry cell should become wet The formation of the groundwater mound over time can be obtained wi
55. 1978a A method of bivariate interpolation and smooth surface fitting for irregularly distributed data points ACM Transactions on Mathematical Software 4 148 159 Akima H 1978b Algorithm 526 Bivariate interpolation and smooth surface fitting for irregularly distributed data points ACM Transactions on Mathematical Software 4 160 164 Akin H and Siemes H 1988 Praktische Geostatistik Springer Berlin Heidelberg New York Alexander M 1994 Biodegradation and Bioremediation Academic Press San Diego Calif 302 pp Andersen PF 1993 A manual of instructional problems for the USGS MODFLOW model Center for Subsurface Modeling Support EPA 600 R 93 010 Anderson MP 1979 Using models to simulate the movement of contaminants through ground water flow systems Critical Reviews in Environmental Control 9 2 97 156 Anderson MP 1984 Movement of contaminants in groundwater groundwater trans port advection and dispersion Groundwater Contamination 37 45 National Academy Press Washington DC Anderson MP and Woessner WW 1991 Applied groundwater modeling simulation of flow and advective transport 381 pp Academic Press San Diego CA Ashcraft CC and Grimes RG 1988 On vectorizing incomplete factorization and SSOR preconditioners SIAM Journal of Scientific and Statistical Computing 9 1 122 151 Axelsson O and Lindskog G 1986 On the eigenvalue distribution of a class of precon ditioning methods Numerical Mathematics
56. 48 479 498 Baetsle LH 1967 Computational methods for the prediction of underground movement of radio nuclides J Nuclear Safety 8 6 576 588 Bear J 1972 Dynamics of fluids in porous media American Elsevier Pub Co New York Bear J 1979 Hydraulics of Groundwater McGraw Hill N Y 569 pp Behie A and Forsyth Jr P 1983 Comparison of fast iterative methods for symmetric systems IMA J of Numerical Analysis 3 41 63 Borden RC and Bedient PB 1984 Transport of dissolved hydrocarbons influenced by oxygen limited biodegradation 1 theoretical development Water Resour Res 20 1973 1982 400 16 17 18 19 20 21 22 23 24 25 26 2T 28 29 30 31 32 33 34 35 36 37 References Cheng X and Anderson MP 1993 Numerical simulation of ground water interaction with lakes allowing for fluctuating lake levels Ground Water 31 6 929 933 Chiang WH and Kinzelbach W 1991 1993 Processing Modflow PM Pre and post processors for the simulation of flow and contaminant transport in groundwater system with MODFLOW MODPATH and MT3D Distributed by Scientific Software Group Washington DC Chiang WH 1993 Water Budget Calculator A computer code for calculating global and subregional water budget using results from MODFLOW Kassel University Ger many Chiang WH and Kinzelbach W 1994 PMPATH An advective transport model for Processing Modflow and Mod
57. 7 A gt 2D VisvialiZatiOne nees e socks tae i eel ogy Wied a wee aes 184 2 735 3D Vis alzation o cscs 38083 high ees Rha bee eda eee eS 184 2 7 6 Results Extractor 4s 68 ceed bes bw sede es 184 2 7 1 Water Budget sec sic itia Sea sh ol wns a ut 187 28 The Valye Menun s rea roa sete hes eA ee cag Rew eee 188 28d Maik a reat c eee lib aerial ates laa 188 2 8 2 Reset Matrix ynter e gee Pant Maree anet alice tebe es 191 2 8 3 V Poly Lons ean ea a oe ooo ne Seb E Lake USS 191 23 4 POMS sos oe oe oats BRERA SRS oe RL EO 192 2 8 5 Search and Modify 0 00 eee eee eee ee 192 2 8 6 Import Results si cscssrisi desiro p edges eee ech ese 193 2 8 7 Import Package 0 eee ee eee eee 193 2 9 The Options Menu ses sr neretas peeke a ae AE E a eee 194 BON Mapa eE gaere tates ails Stee ponies whee eS wh 194 2 9 2 Environment hosed oa bee rea tek ei ete eas 196 The Advective Transport Model PMPATH 203 3 1 The Semi analytical Particle Tracking Method 204 3 1 1 Consideration of the display of the calculated pathlines 207 3 1 2 Consideration of the spatial discretization and water table layers e iip t eed et bin eea Gidea Geddes 207 3 2 PMPATH Modeling Environment 0 000 208 3 2 1 Viewing Window and cross section windows 208 32 2 Stats Dat 2 cate etal oe eee ate eas 210 322 3 TOOLBAR p eee de Sak btet
58. ALL Width of the River Li 100 ALL Thickness of Riverbed ALL Parameter Number pooo aj Layer Number i _aut Cancel Help Fig 4 55 Parameters of the downstream vertex 4 3 1 5 Step 5 Perform steady state flow simulation gt To run the flow simulation 1 Select Models Modflow Run 2 Click OK in the Run Modflow dialog box to generate the required data files and to run MODFLOW you will see a DOS window open and MODFLOW perform the iterations required to complete the flow simulation 3 Press any key to exit the DOS Window 4 3 1 6 Step 6 Extract and view results gt To generate contour maps of the calculated heads 1 Select Tools 2D Visualization to display the Result Selection dialog box Fig 4 56 2 Click OK to select the default result type Hydraulic Head PM displays the model grid and sets 10 contour levels ranging from the lowest to the highest head value 3 Select Options Environment to customize the appearance of the contours The contour map for the first model layer should look similar to that in Fig 4 57 gt To delineate the capture zones of the pumping wells 1 Start PMPATH by selecting Models PMPATH Advective Transport PMPATH will load the current model automatically We will place particles around the pumping wells and examine their 10 year capture zones 2 Move to Layer 3 by pressing the PgDn key twice 294 4 Tutorials Result Selection S
59. All data in the same record are separated by at least one space NFOBS number of flow observations Time Observation time FOBS observed value at Time STWT STWT is the statistic value for the observation 384 6 Supplementary Information 6 2 7 3 Complete Information File Data PMWIN6000_FLOW_OBSERVATION Data NCELLGROUPS EVF Data Reserved Reserved Reserved Reserved Reserved Data STAT_FLAG Data Reserved Reserved Reserved Reserved Oo Pe WN BR The following data repeat for each cell group i e NCELLGROUPS times 6 Data OBSNAM GroupNumber Active NFOBS 7 Data Description The following data repeat NHOBS times for each cell group 8 Data Time FOBS statistic Reserved Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space The text string PMWIN_OBSERVATION_FILE must be entered literally NCELLGROUPS is the number of cell groups EVF default 1 STAT FLAG default 0 OBSNAM is the name of the cell group max 8 characters blank and special characters are not allowed GroupNumber is the unique group number associated with the cell group Active A cell group is active if Active 1 A cell group is inactive if Active 0 Description Description of the cell group NFOBS number of flow observations of a cell group Time observation time FOBS observed value at Time
60. Contours tab clear Display contour lines and check Visible and Fill Colors Click the table header Level A Contour Levels dialog box appears Set the value for Minimum to 100 Max imum to 1600 and Interval to 100 When finished click OK to close the dialog box 10 Click the table header Fill A Color Spectrum dialog box appears Set an appropriate color range by clicking the Minimum color and Maximum color buttons When finished click OK to close the dialog box 11 Click OK to close the Environment Options dialog box 12 Select File Animation The Animation dialog box appears Fig 4 41 OnNDN Ke 270 4 Tutorials 13 Click the button to display a Save File dialog box 14 Select an existing file or specify a new base file name without extension in the or specify a file name in Save File dialog box then click Open 15 In the Animation dialog box click OK to start the animation PM will create a frame image for each time point at which the simulation re sults here concentration are saved Each frame is saved in filename nnn where filename is the base file name specified in previous step and nnn is the serial num ber of the frame Note that if you have complex DXF base maps the process will be slowed down considerably When all frames are created PM will repeat the animation indefinitely until the Esc key is pressed Once a sequence is created you can playback the animation at a later time by repeat
61. In the dialog box type new values then click OK 2 2 The Data Editor 13 igi Grid Size xj Column lao o Row 2 z EET Column pooo a Layer 7 ooo pr Position Layer Row Column 1 13 15 Cancel Help Fig 2 4 The Grid Size dialog box m Size 2 2 The Data Editor The Data Editor is used to assign parameter values to the model To start the Data Editor select a corresponding item from the Grid Parameters or Models menus For example select Parameters Porosity to assign porosity values to the model The Data Editor provides four display modes Map View Grid View Column View and Row View It has three methods for specifying parameter values Cell by cell Polygon and Polyline methods The input methods are discussed in sections 2 2 1 2 2 2 and 2 2 3 The Polyline method is available only for specifying data to the River Drain General head boundary and Streamflow Routing packages In the Grid View display mode the Viewing Window is aligned with the model grid Fig 2 5 In the Map View display mode the Viewing Window is aligned with the orthogonal Northing and Easting coordinate axes A rotated model grid is dis played on the Map View similar to Fig 2 6 In the Row or Column cross sectional View the Viewing Window is aligned with the vertical axis Fig 2 7 Using the Environment Options dialog box see Section 2 9 2 the user can adjust the vertical exaggeration factor for th
62. MF2KOUT _B Select this menu item to use the Text Viewer see Section 2 3 4 to display this file The estimated parameter values are displayed using the parameter name PARNAM given in the Parameters tab of the List of Parameters MODFLOW 2000 dialog box Fig 2 74 The parameter names PARNAM of time varying parameters e g RCH WEL are combined with the stress period number to which the parameter pertains For example parameter num ber 2 of recharge in stress period 3 is indicated by RCH_2_3 For steady state simu lations the string 1 is used as the stress period number Using values from intermediate parameter estimation iterations that are likely to be closer to the optimal parameter values often reduces execution time MODFLOW 2000 Parameter Estimation View Dimensionless Scaled Sensi tivities 148 2 Modeling Environment Select this menu item to use the Text Viewer see Section 2 3 4 for linking a Text Viewer with PM to display the file MF2KOUT _SD which contains dimensionless scaled sensitivity values that can be used to compare the importance of different observations to the estimation of a single parameter or the importance of different parameters to the calculation of a simulated value Hill 62 MODFLOW 2000 Parameter Estimation View Composite Scaled Sensitivi ties Select this menu item to use the Text Viewer see Section 2 3 4 for linking a Text Viewer with PM to display the file MF2KOUT _SC
63. No of particles per cell in case of DCCELL gt DCEPS NPH 16 Minimum number of particles allowed per cell NPMIN 0 Maximum number of particles allowed per cell NPMA 30 Multiplier for the particle number at source cells SRMULT Pattern for placement of particles for sink cells NLSINK 0 No of particles used to approximate sink cells NPSINK 10 Critical relative concentration gradient BCHMOC 0 01 OK Cancel Help Fig 2 69 The Advection Package MTADV1 dialog box 128 2 Modeling Environment cell The particle is tracked backward to find its position at the old time level The concentration associated with that position is used to approximate the advection relevant average concentration at the cell where the particle is placed The MMOC technique is free of artificial oscillations if implemented with a lower order velocity interpolation scheme such as linear interpolation used in MT3D and MT3DMS However with a lower order velocity interpo lation scheme the MMOC technique introduces some numerical dispersion especially for sharp front problems The hybrid method of characteristics HMOC attempts to combine the strengths of the MOC and MMOC schemes by using an automatic adap tive scheme conceptually similar to the one proposed by Neumann 89 The fundamental idea behind the scheme is automatic adaptation of the solution process to the nature of the concentration field
64. Observation Process of MODFLOW 2000 STOB contains the observed flows to features represented by the Streamflow Routing package This file is used by the Observation Process of MODFLOW 2000 CHOB contains the observed flows to features represented by the Time Variant Specified Head package This file is used by the Observation Process of MODFLOW 2000 SEN for the Sensitivity Process of MODFLOW 2000 PES for the Parameter Estimation Process of MODFLOW 2000 6 3 Input Data Files of the supported Model 391 ZONE for the Zone Array file of MODFLOW 2000 MULT for the Multiplier Array file of MODFLOW 2000 DATA BINARY for binary unformatted files such as those used to save cell by cell budget data and binary unformatted head and drawdown data DATA for formatted text files such as those used for input of data from files that are separate from the primary package input files Nunit is the Fortran unit to be used when reading from or writing to the file Any legal unit number on the computer being used can be specified except units 96 99 Fname is the name of the file The path names may be specified as part of Fname Example of a Name File LIST 6 output dat BAS 1 bas dat BCF 11 bcf dat OC 22 oc dat WEL 12 wel dat RCH 18 rch dat PCG 23 pceg2 dat DATA BINARY 50 budget dat DATA BINARY 51 heads dat DATA BINARY 52 ddown dat DATA BINARY 32 mt3d flo 392 6 Supplemen
65. PEST Parameter Estimation Run Select this menu item to start a parameter estimation model calibration process with PEST The available settings of the Run PEST dialog box Fig 2 84 are described below e The File Table has three columns Generate PM uses the user specified data to generate input files for MOD FLOW and PEST An input file will be generated if it does not exist or if Run PEST Modflow Version MODFLOW 2000 MODFLOW 2005 4 c simcore pm8 examples calibration calibration5 bas Layer Property Flow LPF c simcore pm8 examples calibration calibrationS pf1 Output Control c simcore pm8 examples calibration calibration5 oc d General Head Boundary c simcore pm8 examples calibration calibrationS ghb River Te simcore pm8 examples calibration calibrationS yiv d Well c simcore pm8 examples calibration calibration5 wel Recharge c simcore pm8 examples calibration calibration5 ych Solver PCG2 c simcore pm8 examples calibration calibration5 pcgz Link MT3DMS Package LMT6 c simcore pm8 examples calibration calibration5 mt6 5515 5150 1 51 Options I Check model data I Regenerate all input files I Perform PESTCHEK prior to running PEST Generate input files only don t start PEST Can Fig 2 84 The Run PEST dialog box 2 6 The Models Menu 173 the corresponding Generate box is checked The user may click on a box to ch
66. Packages Wells are present at selected cells with pumpage at rates ranging from 100 to 200 m 3 d Modeling Approach and Simulation Results Ten parameters were identified for inclusion in the parameter estimation and are de scribed in Table 5 6 along with their true assigned values The observations used in the parameter estimation were generated by running the model with the true param eter values and the parameter multiplier PARVAL 1 for all parameters the actual parameter values used in the simulation are calculated as the product of the parameter values and the parameter multiplier PARVAL The locations of the 42 observed hydraulic heads are shown in Fig 5 31 The flows simulated at the head dependent boundaries also were used as observations for the parameter estimation In this ideal situation the estimated values of the parameter multiplier PARVAL are expected to be close to 1 If this is accomplished it suggests that the observation sensitivities are calculated correctly and that the regression is performing correctly The final parameter values are obtained by multiplying the estimated PARVAL with the parameter s initial values 338 5 Examples and Applications Model Grid Spacing and Boundary Conditions All boundary conditions apply to layer 1 except for Observation Locations constant head boundaries which apply to all layers 0 meters Constant head
67. Parameter Estimation and Pumping Test 325 5 3 2 Estimation of Pumping Rates Folder pmdir examples calibration calibration2 Overview of the Problem This example involves the encapsulation of a highly contaminated area The aquifer in which the contaminated area is buried is unconfined isotropic and of infinite areal extent The extent of the contamination area is about 65 m x 65 m The hydraulic head in the center of this area is about 9 45 m The elevation of the aquifer top is 10 m and the aquifer bottom is at 0 m The hydraulic conductivity is uniformly 3 x 1074 m s The unconfined storage coefficient specific yield is 0 2 Recharge is assumed to be zero The groundwater flow is directed from west to east with a hydraulic gradient of 0 05 To prevent contaminated water flow out of the area a remedial measure is re quired Different types and combinations of measures can be introduced for this pur pose including a cutoff wall around the area drains and pumping wells All mea sures are directed towards the same goal a reduction of the hydraulic head in the contaminated area itself such that groundwater flows towards the contaminated area To achieve this objective a cutoff wall around this area and four pumping wells have been chosen The cutoff wall is 0 5 m thick and the hydraulic conductivity of the material is 5 x 1078 m s The task is to estimate the required pumping rate of the wells such that the steady state piezometric hea
68. Parameter No 3 _ RCH Parameter No 1 RCH Parameter No 2 RIV Parameter No 1 Ss Parameter No 1 Ss Parameter No 3 WEL Parameter No 1 VK Parameter No 2 55 555 For Log Transformed Parameters Max Change Apply MAX CHANGE to native parameter value Cancel Fig 2 74 The Simulation Settings MODFLOW 2000 dialog box 138 2 Modeling Environment When switching from the BCF to LPF or from LPF to BCF package some aquifer parameters might become unadjustable e g T S are not adjustable when using the LPF package and they will be indicated by gray background color Normally the total number of active parameters should not exceed 10 although PM allows 500 parameters e Description A text describing the parameter can be entered here optional for example recharge zone one A maximum of 120 characters is allowed PARVAL is the initial parameter multiplier for PARNAM Minimum and Maximum are the reasonable minimum and maximum scaling fac tors for the parameter These values are used solely to determine how the final optimized value of this parameter compares to a reasonable range of values For log transformed parameters untransformed values should be used e Log transform Check this flag to log transform the parameter Typically log trans formed parameters are those for which negative values are not reasonable for example hydraulic conductivity The Prior
69. Parameters Horizontal Anisotropy When the BCF package is used horizontal anisotropy is constant for all cells in the layer and the anisotropy is the absolute value of the specified Horizontal Anisotropy value Vertical Anisotropy The setting of this column is either VK or VANI VK indicates that vertical hydraulic conductivity is used for the layer and is to be specified by selecting Parameters Vertical Hydraulic Conductivity VANT indicates that vertical anisotropy is used for the layer and is to be spec ified by selecting Parameters Vertical Anisotropy Transmissivity MODFLOW or exactly to say the BCF package requires trans missivity horizontal hydraulic conductivity LT7 x layer thickness L for layers of type 0 or 2 PM provides two options for each model layer to facilitate the data input Set the Transmissivity setting of a layer to User Specified The user specified transmissivity values of the layer are used in the simula tion Set the Transmissivity setting of a layer to Calculated PM calculates transmissivity of the layer by using user specified horizontal hydraulic conductivity and the elevations of the top and bottom of the layer The calculated transmissivity values are used in the simulation Leakance For flow simulations involving more than one model layer MOD FLOW BCF package requires the input of the vertical conductance term known as vertical leakance VCONT array betwee
70. Particles are tracked back to the groundwater surface by applying the groundwater recharge on the groundwater surface 3D approach To delineate the catchment area of a pumping well in a 3D flow field we must place enough particles around and along the well screen Fig 5 4 shows the catch ment area calculated by PMPATH First 425 particles are placed around the well by using the Add New Particles dialog box the settings are NI 5 NJ 5 on faces 5 and 6 and 25 particles on the circles with R 25 and NK 15 around the pumping well 300 5 Examples and Applications Then backward tracking is applied for a 100 years duration Finally the end points of the particles are saved by selecting File Save Particles As in PMPATH This file can be reloaded into PMPATH by selecting File Load Particles to display the catchment area Fig 5 4 Catchment area of the pumping well 3D approach 5 1 Basic Flow Problems 301 5 1 2 Use of the General Head Boundary Condition Folder pmdir examples basic basic2 Overview of the Problem This simple example Kinzelbach and Rausch 72 demonstrates the use of the general head boundary package of MODFLOW A confined homogeneous and isotropic aquifer is shown in Fig 5 5 The aquifer is bounded by no flow zones to the north and south The hydraulic heads at the west and east boundaries are 12 m and 10 m respectively The transmissivity of the aquifer is T 0 01 m s The aquif
71. Pattern 1 Fixed Pattern 2 Fixed Pattern 3 e 0o o eo ene 68 s e eo oe8 e e e e e Ld e o Fixed Pattern 4 Fixed Pattern 5 Fixed Pattern 6 Fig 2 49 Distribution of initial particles using the fixed pattern adapted from Zheng 1990 If the fixed pattern is chosen the number of particles placed per cell NPL and NPH is divided by the number of planes NPLANE to yield the number of particles to be placed on each plane which is then rounded to one of the numbers of particles shown here Maximum number of particles allowed per cell NPMAX If the number of particles in a cell exceeds NPMAX particles are removed from that cell until NPMAX is met Generally NPMAX 2 x NPH SRMULT is a multiplier for the particle number at source cells SSRMULT gt 1 In most cases SRMULT 1 is sufficient However better results may be obtained by increasing SRMULT Pattern for placement of particles for sink cells NLSINK is used to select a pattern for initial placement of particles to approximate sink cells in the MMOC scheme The convention is the same as that for NPLANE and it is generally adequate to set NLSINK equivalent to NPLANE Number of particles allowed to approximate sink cells NPSINK is used in the MMOC scheme The convention is the same as that for NPH and it is generally adequate to set NPSINK equivalent to NPLANE Critical relative concentration gradient
72. RT3D Spatially Constant dialog box Fig 2 61 Reaction Parameters for RT3D Spatially Constant Parameter Value Anaerobic decay rate for PCE K_p Anaerobic decay rate for TCE K_T1 Aerobic decay rate for TCE K_T2 Anaerobic decay rate for DCE K_D1 Aerobic decay rate for DCE K_D2 Anaerobic decay rate for VC K_V1 Aerobic decay rate for YC K_ 2 Anaerobic decay rate for ETH K_E1 Aerobic decay rate for ETH K_E2 No i 2 3 4 5 6 7 8 3 OK Cancel Help Fig 2 61 The Reaction Parameters for RT3D Spatially Constant dialog box 2 6 4 8 RT3D Reaction Parameters Spatially Variable Select this menu item to specify spatially variable cell by cell reaction parameters Note that this menu item cannot be used if the Reaction Module in the Simulation Settings RT3D dialog box Fig 2 59 is one of the following No Reaction tracer transport Instantaneous aerobic decay of BTEX or Instantaneous degradation of BTEX using multiple electron acceptors 2 6 4 9 RT3D Sink Source Concentration The use of this menu is the same as MT3D Sink Source Concentration except the use of the menu item Time Variant Specified Concentration A time varying specified concentration cell is defined by setting the following data in the Data Editor e Flag A non zero value indicates that a cell is specified as a constant concen tration cell In a multiple stress period simulat
73. SEAWAT Examples E EEE O E EI E EE Assignment of parameters in the Value I vector 1 Introduction Processing Modflow PM was originally developed to support the first official re lease of MODFLOW 88 85 to simulate the inundation process of an abandoned open cast coal mine Since the release of MODFLOW 88 many computer codes have been developed to add functionalities to MODFLOW or to use MODFLOW as a flow equation solver for solving specific problems Consequently several versions of PM 17 22 24 have been released to utilize latest computer codes to facilitate the modeling process and to free up modelers from tedious data input for more creative thinking The computer codes that are supported by present version of Processing Modflow are given in the following section 1 1 Supported Computer Codes MODFLOW 85 54 55 56 63 57 MODFLOW is a modular three dimensional finite difference groundwater model published by the U S Geological Survey The first public version of MOD FLOW was released in 1988 and is referred to as MODFLOW 88 MODFLOW 88 and the later version of MODFLOW 96 54 55 were originally designed to simulate saturated three dimensional groundwater flow through porous me dia MODFLOW 2000 56 attempts to incorporate the solution of multiple re lated equations into a single code To achieve the goal the code is divided into entities called processes Each process deals with a spec
74. Simulation Settings PEST dialog box Fig 2 79 The names of most input variables of this dialog box are inherited from the PEST manual 37 and the Addendum to the PEST Manual 39 which provide a great inside into to the theory and application of PEST The user is encourage to download and consult these references as needed The Op eration Mode dropdown box Fig 2 79is used to define how PEST should run and the rest of the available settings are grouped under six tabs described in the follow ing sections below The functions of Operation Mode dropdown box and the push buttons are defined as follows e Operation Mode Parameter Estimation PEST will use the available information to estimate parameters defined in the Parameters Tab by running the model as many times as needed Sensitivity Analysis When this option is selected the maximum number of optimization iterations see NOPTMAX in the Control Data tab will be set to 1 PEST will run in the Parameter Estimation mode but will terminate execution immediately after it has calculated the Jacobian matrix for the first time The parameter covariance correlation coefficient and eigenvector ma trices will be written to the run record file and parameter sensitivities will be written to the sensitivity file these are based on the initial parameter set defined in the Parameters tab Forward Model Run using PARVAL values given in the Parameters tab When this option is selected t
75. The first unit of the aquifer is uncon fined and the other units are confined The initial hydraulic head is 43 m everywhere The areal extent of the aquifer is assumed to be infinite large Except a confining bed clay in the second unit the sandy sediments of the aquifer are homogeneous horizontally isotropic with an average horizontal hydraulic conductivity of 0 0001 m s and vertical hydraulic conductivity of 0 00001 m s The specific yield of the first stratigraphic unit is 0 15 The specific storage of the aquifer is assumed to be 0 0001 1 m The properties of the confining bed are Horizontal hydraulic conductivity 1 x 10 m s Vertical hydraulic conductivity 1 x 1077 m s Elastic specific storage 0 002 1 m Inelastic specific storage 0 006 1 m To construct a new building an excavation pit with the size 200 m x 100 m is required The bottom elevation of the pit is 40 m The pit must be held dry for one year The task is to calculate the required withdrawal rate for keeping the pit dry and the delineate the distribution of subsidence after one year Modeling Approach and Simulation Results The aquifer is simulated using a grid of 3 layers 36 columns and 36 rows The extent of the model grid is fairly large Each model layer represents a stratigraphic unit The layer type 3 confined unconfined Transmissivity varies can be used for all layers as layers of this type switch between confined and unconfined automatical
76. The layer is strictly confined For transient simulations the confined storage coefficient specific storage x layer thickness is used to calculate the rate of change in storage Transmissivity of each cell is constant throughout the simulation Type 1 The layer is strictly unconfined The option is valid for the first layer only Specific yield is used to calculate the rate of change in storage for this layer type During a flow simulation transmissivity of each cell varies with the saturated thickness of the aquifer Type 2 A layer of this type is partially convertible between confined and unconfined Confined storage coefficient specific storage x layer thickness is used to calculate the rate of change in storage if the layer is fully saturated otherwise specific yield will be used Transmissivity of each cell is constant throughout the simulation Vertical leakage from above is limited if the layer desaturates Type 3 A layer of this type is fully convertible between confined and uncon fined Confined storage coefficient specific storage x layer thickness is used to calculate the rate of change in storage if the layer is fully saturated other wise specific yield will be used During a flow simulation transmissivity of each cell varies with the saturated thickness of the aquifer Vertical leakage from above is limited if the layer desaturates erty Block Centered Flow BCF Type 3 Confined Unconfined 1 w Calculated
77. When SVD is activated PEST writes a file named modelname svd in Simulation Settings PEST Operation Mode Parameter Estimation Parameters Parameter Groups Prior Information Regularization SVD Truncated Singular Value Decomposition IV Activate SVD for solution of inverse problem IV Set PEST variables RLAMBDA1 to zero and NUMLAM to one I Create complete SVD output file uncheck this box to save only eigenvalues to the output file Number of singular values at which truncation occurs MAXSING 1000 Eigenvalue ratio threshold for truncation EIGTHRESH in SVD Assist I Activate SVD Assist MV Automatic calculation of first iteration super parameter derivatives Computation of super parameters svo on Q 172 z Number of super parameters to estimate 2 Offset for super parameters 110 Parameter relative change limit RELPARMAX Parameter scaling control variable SVDA_SCALADJ 2 X I Save multiple BPA files I Save Multiple JCO files Save Multiple REI files Update Load Save OK Cancel Help Fig 2 82 The SVD SVD Assist tab of the Simulation Settings PEST dialog box 164 2 Modeling Environment addition to its normal output files This contains singular values arranged in decreasing order and corresponding eigenvectors computed on each occasion that singular value decomposition is carried out It also records the number of singular values that are actually used in computation
78. adjacent cells can cause dry cells to become wet This is the only way for cells in layer 1 to become wet because heads in layer 2 are always below the bottom of layer 1 a J Fa gt Yi J yy J lt sua 26 0 Zoi P ae 49 aaa o 920 ager 40 224 oo Fig 5 12 Simulated steady state head distribution in layer 1 5 1 Basic Flow Problems 311 5 1 6 An Aquifer System with Irregular Recharge and a Stream Folder pmdir examples basic basic6 Overview of the Problem This example is adapted from the first test problem of the Streamflow Routing STR1 package 98 Results from the STR1 Package were compared to results from an analytical solution developed by Oakes and Wilkinson 90 An idealized aquifer with a river flowing through the middle was chosen and is shown in Fig 5 13 The width of the aquifer perpendicular to the river was 4 000 ft on each side while the length parallel to the river was 13 000 ft Assumptions used in both the analytical solution and the model simulation include The lateral boundaries of the aquifer are impermeable no flow is allowed The rocks beneath the aquifer are impermeable The river penetrates the entire depth of the aquifer and has vertical banks The river is not separated from the aquifer by any confining material AUN columns 1 5 10 15 20 25 30 35 39 o co v lt i e 2 13000 feet t Rows 10 11 12 13
79. and vertical hydraulic conductivities and effective porosity gt To specify the temporal parameters 1 Select Parameters Time A Time Parameters dialog box appears The temporal parameters include the time unit and the numbers of stress periods time steps and transport steps In MODFLOW the simulation time is divided into stress periods i e time inter vals during which all external excitations or stresses are constant which are in turn divided into time steps Most transport models divide each flow time step further into smaller transport steps The length of stress periods is not relevant to a steady state flow simulation However as we want to perform contaminant transport simulation the actual time length must be specified in the table 2 Enter 9 46728E 07 seconds for the Length of the first period 3 Click OK to accept the other default values This implies that a steady state flow simulation will be carried out 4 1 Your First Groundwater Model with PM 235 Now we need to specify the initial hydraulic head for each model cell The initial hy draulic head at a constant head boundary will be kept the same throughout the flow simulation The other hydraulic head values are used as starting values in a transient simulation or first guesses for the iterative solver in a steady state simulation Here we firstly set all values to 8 and then correct the values on the west side by overwrit ing them with a value of 9 gt
80. and other values We will carry out the following tasks in this step 1 Use the Results Extractor to read and save the calculated hydraulic heads 2 Create a contour map based on the calculated hydraulic heads 3 Use PMPATH to compute pathlines as well as the capture zone of the pumping well gt To read and save the calculated hydraulic heads 1 Select Tools Results Extractor The Results Extractor dialog box appears Fig 4 9 The options in the Results Extractor dialog box are grouped under six tabs MODFLOW MOC3D MT3D MT3DMS and RT3D In the MODFLOW tab you may choose a result type from the Result Type drop down box You may specify the layer stress period and time step from which the result should be read The spreadsheet displays a series of columns and rows The intersection of a row and column is a cell Each cell of the spreadsheet corresponds to a model cell in a layer Refer to Section 2 7 6 for details about the Results Extractor For the current sample problem follow steps 2 to 6 to save the hydraulic heads of each layer in three ASCII Matrix files 2 Choose Hydraulic Head from the Result Type drop down box 3 Type in the Layer edit field For this example steady state flow simulation with only one stress period and one time step the stress period and time step number should be 1 4 Results Extractor x MODFLOW Macao mTaD MTaoMs RTaD Result Type gAllE tae Stress Period 1 Time Ste
81. and shifting the triangle after scaling and shifting a scale factor s and displacements X and Y are used Fig 2 102 Scaling a vector graphic 2 9 The Options Menu 197 Maps Options xj Vector Graphics Raster Graphics Filename c program files wt360 3dmaster examples ex1 refinery bmp Point 1 Point 2 Raster x 10 X _ IV Graphic Set Visible y 0 Y oo Extent of the map in real world coordinates 1819 923 1418 093 32806 51 22151 59 ae use Fig 2 103 Importing and Geo referencing a raster map Environment Options E x Appearance Coordinate System Contours visti Color Component a Grid Inactive cell Fixed head cell BOUND lt 0 Fixed concentration cell ICBUND lt 0 _ _ General boundary head cell Discharge well Recharge well Drain River or stream _ _ Horizontal flow barrier dike slurry wall Head Observation Boreholes for PEST UCODE MF2K Drawdown Observation Boreholes for PEST UCODE MF2K Concentration Observation Boreholes for all transport models Reservoir Digitized point xl aad hii qaqaqa Time variant snerified head Vertical Exaggeration 10 T Display polygons in the cell by cell mode Fig 2 104 The Appearance tab of the Environment Options dialog box The Appearance Tab The Appearance Tab Fig 2 104 allows the user to change the visibility and appear
82. and the local equilibrium assumption is assumed to be invalid The columns of the tables are defined as follows Active Check the box to include the respective reactant in the simulation Component Name of the reactant Stoichiometry Stoichiometry is expressed in the form of reactant mole_rl reactant2 mole_r2 product mole_p1 product2 mole _p2 and is pre defined in the database file of the selected reaction module Parm I to 8 Parameters used to define the reaction rate The parameters are pre defined in the database file of the selected reaction module Minerals equilibrium Each row of the table contains a mineral for which the local equilibrium assumption LEA is assumed to be valid Check the Active of a row to include the respective mineral in the simulation No transport step is carried out for minerals The columns of the table are defined as follows Active Check the box to include the respective mineral in the simulation Mineral Name of the mineral Options This is an optional argument that can be entered for each of the minerals that are included in a simulation This value represents the target Saturation Index SI for a pure phase in the aqueous phase Equation This column contains the exact definitions of the minerals Minerals kinetic Each row of the table contains a mineral for which a rate expression is defined in the database file of the selected reaction module a
83. are followed by a sequence lines Each line con tains the following data items in the order specified Particle index number Global coordinate in the x direction Global coordinate in the y direction Local coordinate in the z direction within the cell Global coordinate in the z direction Cumulative tracking time J index of cell containing the point I index of cell containing the point K index of cell containing the point Cumulative MODFLOW time step number SFPoOoMmArAINANFWN pei 6 2 12 Particles File A Particles File is a a text file that begins with the header of the form 1 Data PMPATH_V100_PARTICLES 2 Data NP The following data repeats NP times 3 Data Gi Wu bR L d Ke azar oC OR Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space The text string PMPATH_V100_PARTICLES must be entered literally NP is the number of particles LI Local coordinate in the row direction LJ Local coordinate in the column direction LK Local coordinate in the layer direction I Row index of cell containing the particle J Column index of cell containing the particle 6 3 Input Data Files of the supported Model 389 K Layer index of cell containing the particle Z global vertical coordinate of the particle C Color of the particle R Retardation factor associated with the particle The particl
84. bas6 d Vv Lapyer Property Flow LPF c program files eit pmwin examples mf2k ex1 SIpf6 da Vv Output Control c program files eit pmwin examples mf2k ex1 Soc dat Vv General Head Boundary c program files eit pmwin examples mf2k ex1 ghb6 d Vv River c program files eit pmwin examples mf2k ex1 riv6 da Vv Well c program files eit pmwin examples mf2k ex1 wel6 d Vv Recharge c program files eit pmwinexamples mf2k vex toh6 de Vv Hydraulic Head Observation c program files eit pmwin examples mf2k ex1 hob da M River Flow Observation c program files eit pmwin examples mf2k ex1 rvob de M Sensitivity Process c program files eit pmwin examples mf2k ex1 sen da Vv Parameter Estimation Process c program files eit pmwin examples mf2k ex1 pes da Vv Link MT3DMS Package LMT6 c program files eit pmwin examples mf2k ex1 Imt6 de Options I Check model data I Regenerate all input files J Generate input files only don t start PEST ASP I Let PEST ASP Calculate Derivatives Cancel Help Fig 2 78 The Run PEST ASP MODFLOW 2000 dialog box 2 6 The Models Menu 147 MODFLOW 2000 does not modify the original model data This provides a greater security to the model data because a parameter estimation process does not necessarily lead to a success 2 6 7 5 MODFLOW 2000 Parameter Estimation View MODFLOW 2000 Parameter Estimation View Global Listing File Select this menu item to use the Text Viewer
85. boundary h fixed head boundary h Width of each cell 50 m 25 20 25 Width of each cell 50 m Width of each cell Cross Section cut off wall K 2 0E 4 m s a K 7 0E 5 m s OLI K 4 0E 4 m s K 6 0E 4 m s TR AnA impervious Ssn Ss EAD Fig 5 42 Model grid a ae conditions 1 5m 8m 10m 42 m 18 m 35 m 349 350 5 Examples and Applications Cross section Fig 5 43 Plan and cross sectional views of flowlines Particles are started from the contaminated area The depth of the cutoff wall is 8 m Cross section Fig 5 44 Plan and cross sectional views of flowlines Particles are started from the contaminated area The depth of the cutoff wall is 10 m 5 4 Geotechnical Problems 351 5 4 5 Compaction and Subsidence Folder pmdir examples geotechniques geo5 Overview of the Problem Fig 5 45 shows a plan view and a cross section through an aquifer which consists of three stratigraphic units of uniform thickness
86. click the leave editor button w gt To draw a pathline l 2 3 Result Selection xj Select a model and the type of result that you want to display then click OK Select Models PMPATH Pathlines and Contours if PMPATH is not yet started PM calls the advective transport model PMPATH which will load the current model automatically PMPATH uses a grid cursor to define the column and row for which the cross sectional plots should be displayed You can move the grid cursor by holding down the Ctrl key and click the left mouse button on the de sired position Note If you subsequently modify and calculate a model within PM you must load the modified model into PMPATH again to ensure that the modifications can be recognized by PMPATH To load a model click and select a model file with the extension PM5 from the Open Model dialog box Click the Set Particle button E Right click on a point within the model area to set a particle MODFLOW Mocan MTD MTaoms ATaD Result Type Hydraulic Head i i Cancel Help Fig 4 10 The Result Selection dialog box 4 1 Your First Groundwater Model with PM I SAMPLE PMS EIT Processing Modflow Pro ejj e Layer gt Row Column gt Simulation Time dl EENES e fs s Period 1 Step t Time 9 467E 07 z File Value Options Help alall no flow imi 8 90E 00 8 B0E 00 8 70E 00 8 60E 00 8 10E
87. concentration scatter diagram MT3D 134 MT3DMS 108 RT3D 118 concentration time curves MOC3D 126 MT3D 134 MT3DMS SEAWAST 108 RT3D 118 contour table file 377 contours 184 200 217 color 201 217 label 201 218 level 200 217 Control Data 408 Index MODFLOW 2000 140 convert model 21 coordinate system 196 198 Courant number 121 criterion parameter estimation 140 171 cross sections 215 CSA 140 cutoff wall 348 Data Editor 13 DE45 solver package 63 decay rate 228 DERINC 156 DERINCLB 156 DERINCMUL 157 DERMTHD 157 Digitizer 176 dispersion 94 MOC3D 121 MT3D 130 RT3D 114 dispersive transport 354 dispersivity 122 horizontal transverse 122 longitudinal 122 vertical transverse 122 distribution coefficient 99 Double Monod model 114 Drain package 39 drawdown observations 73 drawdown scatter diagram MODFLOW 81 PEST 175 drawdown time curves PEST 176 dual domain mass transfer 99 DXF 26 224 effective porosity 37 EPA instructional problems 320 estimated parameter values MODFLOW 2000 147 PEST 175 estimation of pumping rates 325 Evapotranspiration package 41 excavation pit 340 FACORIG 170 FACPARMAX 169 FCONYV 140 Field Generator 183 Field Interpolator 177 field interpolator 369 file formats 376 first order decay rate 122 first order Euler algorithm 91 128 first order irreversible reaction 86 100 first order kinetic sorption 98 first order
88. convergence criterion discussed in Hill 62 p 12 If SOSC 0 0 parameter estimation will converge if the least squares objective function does not decrease more than SOSC x 100 percent over two parameter estimation iterations SOSC usually equals 0 0 Typical nonzero values of SOSC are 0 01 and 0 05 RMAR is used along with RMARM to calculate the Marquardt parameter which is used to improve regression performance for ill posed problems Theil 111 Seber and Wild 107 Initially the Marquardt parameter is set to zero for each parameter estimation iteration For iterations in which the parameter changes are unlikely to reduce the value of the objective function the Marquardt parameter is increased according to m RM ARM x m2 44 RM AR until the condition is no longer met or until m7 is greater than 1 Typically RMAR 0 001 RMARM is the Marquardt parameter multiplier which is used along with RMAR to determine the Marquardt parameter see above CSA is the search direction adjustment parameter used in the Marquardt proce dure Usually equals 0 08 FCONYV is a flag and a value used to allow coarser solver convergence criteria for early parameter estimation iterations If FCONV equals zero coarser conver gence criteria are not used Commonly FCONV 0 0 Typical non zero values would be 5 0 or 1 0 and these can produce much smaller execution times in some circumstances 2 6 The Models Menu 141 The Options Tab Two opt
89. coordinates of the observation boreholes into the Observation Borehole table as shown in Fig 4 36 3 For all boreholes set the proportion value of the third layer to 1 and other layers to 0 This means that all boreholes are screened in the third layer 4 In the Head Observatiion s group enter the observation time and hydraulic head of each borehole to Time and HOBS Set the value for Weight to 1 5 Click OK to close the dialog box 4 1 4 1 Parameter Estimation with PEST gt To specify the starting values for each parameter 1 Select Models PEST Parameter List The List of Parameters PEST dialog box Fig 4 37 appears The options of the dialog box are grouped under five tabs Parameters Group Definitions Prior Information Control Data and Options 266 4 Tutorials 2 In the Parameters tab enter values as shown in Fig 4 37 PARVAL is the initial guess of the parameter Minimum is the lower bound and Maximum is the upper bound of the parameter 3 Click OK to close the dialog box gt To perform Parameter Estimation with PEST 1 Select Models PEST Run The Run PEST dialog box appears Fig 4 38 2 Click OK to start PEST Prior to running PEST PM uses user specified data to generate input files for PEST and MODFLOW as listed in the table of the Run PEST dialog box An input file will be generated only if the corresponding Generate box is checked You can click on the box to check or uncheck Normally we
90. deactivate a selected item in the Models menu just select the item again If the user does not know which model data still needs to be specified one may try to run the model by selecting the menu item Run from the corresponding model in the Models menu PM will check the model data prior to running the model A summary of the menus in PM is given in Table 2 2 A toolbar with buttons representing PM operations or commands is displayed below the menus The toolbar is a shortcut for the pull down menus To execute one of these shortcuts move the mouse pointer over the toolbar button and click on it Most of the user specified data is saved in binary files Prior to running the sup ported models or the parameter estimation programs PM will generate the required ASCII input files The names of the ASCII input files are given in Section 6 3 The formats of the input files of can be found in the user s guides of the corresponding model The particle tracking model PMPATH retrieves the binary data files of PM directly thus no ASCII input file is required by PMPATH 2 1 The Grid Editor The first steps in the groundwater modeling process are to define the goals of the model select a computer code collect the necessary data develop a conceptual model of the groundwater system and define the spatial discretization of the model domain Anderson and Woessner 8 discuss the steps in going from aquifer sys tems to a numerical model grid Zheng and Benne
91. dialog box 137 2 75 The Flow Observation River dialog box 00 ee eee ee 142 2 76 The Flow Observation tab of the Flow Observation River dialog box 143 2 77 The Run MODFLOW 2000 Sensitivity Analysis Parameter Estimation dialog box 00 cece cee eee ee 144 2 78 The Run PEST ASP MODFLOW 2000 dialog box 146 2 79 The Simulation Settings PEST dialog box 152 2 80 The Parameter Groups tab of the Simulation Settings PEST dialog DOX aeien a sin hanes Esa gale Sheet teas views ike 155 2 81 The Regularization tab of the Simulation Settings PEST dialog box 160 2 82 The SVD SVD Assist tab of the Simulation Settings PEST dialog DOX os peace eats Meeks Ree ta a be es ee 163 2 83 The Control Data tab of the Simulation Settings PEST dialog box 168 2 84 The Run PEST dialog box 0 0 eee ee eee 172 2 85 The Field Interpolator dialog box 0 0000 e eee eee 178 2 86 Effects of different weighting exponents 0 180 2 87 The Variogram dialog box 0 eee eee ee eee 181 2 88 Linear Power and logarithmic models 00 182 2 89 Search patterns used by a the Quadrant Search method Data per sector 2 and b the Octant Search method Data per sector 1 182 2 90 The Field Generator dialog box 0 0 c eee eee eee ee 183 2 91 The 2D Visualization tool in action 0 00 0 0 185
92. do not need to worry about these boxes since PM will take care of the settings gt Check the Parameter Estimation Results Several result files are created through the parameter estimation process During a parameter estimation process PEST prints the estimated parameter values to the run record file PESTCTL REC in the model folder and writes the estimated param eter values to the corresponding input files of MODFLOW BCEDAT WEL DAT etc So after a parameter process the simulation results of MODFLOW are up dated by using the most recently estimated parameter values PEST does not modify the original model data This provides a greater security to the model data since a parameter estimation process does not necessarily lead to a success Follow the steps below if you want to operate on the estimated parameters List of Parameters PEST J x Modflow Version MODFLOWS96 INTERFACE TO MT3D96 AND LATER Flow Package Block Centered Flow BCF Parameters Group Definitions Prior Information Control Data Options _ PARNAM Active Description PARVAL und Minimum HK inlayer 3 0 00001 0 01 Load Save OK Cancel Help Fig 4 37 The List of Parameters PEST dialog box 4 1 Your First Groundwater Model with PM 267 LI x Modflow Version MODFLOW96 INTERFACE TO MT3D96 AND LATER Destination File w Vd Basic Package p c program files wt3BO0 pmwin exa
93. empty table 254 4 Tutorials Reset Matrix xj Type of Sorption Linear equilibrium isotherm hd F Use the initial concentration for the nonequilibrium sorbed or immobile liquid phase Distribution Coefficient Kd L 3 M 000125 Second Sorption Coefficient fo First order reaction rate for the dissolved phase 1 T pooo First order reaction rate for the sorbed phase 1 T pb Initial concentration for the sorbed phase M M po o Porosity of the immobile domain IV Concentration unformatted IV Cell by Cell mass unformatted only MT3D96 MT3D99 T Concentration ASCII J7 Number of particles ASCII J7 Ratardation factor ASCII I Dispersion coefficient ASCII Fig 4 23 The Output Control MT3D Family dialog box An Output Times dialog box appears Enter 3000000 to Interval Click OK to accept the other default values 3 Click OK to close the Output Control MT3D Family dialog box gt To perform the transport simulation 1 Select Models MT3DMS Run The Run MT3DMS dialog box appears Fig 4 24 2 Click OK to start the transport computation Prior to running MT3DMS PM will use user specified data to generate input files for MT3DMS as listed in the table of the Run MT3DMS dialog box An input file will be generated only if the corresponding Generate box is checked You can click on the box to check 4 1 Your First Groundwater Model with PM 255 x Gen
94. for the constant head cells Note that the associated concentrations must be 32 2 Modeling Environment specified by selecting Models MOC3D Sink Source Concentration Fixed Head Cells 2 4 3 2 ICBUND MT3D MT3DMS The transport models MT3D MT3DMS and RT3D require an ICBUND array which contains a code for each model cell A positive value in the ICBUND ar ray defines an active concentration cell the concentration varies with time and is calculated a negative value defines a constant concentration cell the concentration is constant and the value 0 defines an inactive concentration cell no transport sim ulation takes place at such cells It is suggested to use the value 1 for an active concentration cell 1 for a constant concentration cell and 0 for an inactive concen tration cell Note that the ICBUND array applies to all species if MT3DMS or RT3D is used Other types of boundary conditions are implemented by assigning concen trations to inflows see sections 2 6 6 6 and 2 6 2 8 or assigning a mass loading rate to a cell Section 2 6 2 9 MT3D MT3DMS and RT3D automatically convert no flow or dry cells to in active concentration cells Active variable head cells can be treated as inactive con centration cells to minimize the area needed for transport simulation as long as the solute transport is insignificant near those cells For constant concentration cells the initial concentration remains the same at the cell through
95. given below Activate the variable density water table correction IWTABLE Check this option to activate the variable density water table corrections eq 82 of 51 Method for calculating internodal density values This option determines how the internodal density values used to conserve fluid mass will be cal culated Flow and transport coupling procedure 88 2 Modeling Environment One Timestep lag Flow and transport will be explicitly coupled using a one timestep lag as described in Guo and Langevin 51 With the ex plicit approach the flow equation is formulated using fluid densities from the previous transport timestep The explicit coupling option is normally much faster than the iterative option and is recommended by the authors of SEAWAT 77 for most applications Non linear Iterative The solution of the flow and transport equations is obtained in an iterative sequence for each timestep until the consecutive differences in the calculated fluid densities are less than a user specified value See Guo and Langevin 51 for detailed explanations Conditional The flow solution will be recalculated only for 1 The first transport step of the simulation or 2 The last transport step of the MOD FLOW timestep or 3 The maximum density change at a cell is greater than the Density change threshold for recalculating flow solution see be low Maximum number of non linear coupling iterations This value i
96. ground water systems and surface water features such as rivers lakes or reservoirs Using the Data Editor a river is defined by using the Cell by Cell or Polygon input methods to assign parameters to model cells or by using the Polyline input method and assigning parameters to vertices of the polylines along the trace of the river The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress periods the input parameters can be different from period to period The input methods require different parame ters as described below e When using the Polyline input method right click on a vertex to specify its prop erties in the River Parameters dialog box Fig 2 25 If the properties are assigned to one vertex only the properties of all vertices of the polyline are assumed to be the same The settings of the dialog box are described below Layer Option and Layer Number Layer Option controls how the layer num ber of a river is determined Tf Layer Option is Assign layer number manually the value of Layer Number defines the model layer number for all model cells downstream from a vertex until the next vertex redefines the layer number Tf Layer Option is Assign layer number automatically the river is as signed to a layer where the elevation of the riverbed bottom B see be low is located between the top and bottom of the layer The layer number
97. gt To import an ASCII Matrix or a SURFER GRD file js Water Budget x Specify the stress period and time step for which the water budget should be calculated Click the Subregions button to define subregions When finished click OK to start the calculation Stress Period 1 Time Step 1 Subregions Cancel Help Time Fig 2 94 The Water Budget dialog box Table 2 10 Output from the Water Budget Calculator eer 2 8 The Value Menu FLOW TERM IN CONSTANT HEAD 1 8595711E 04 EXCHANGE LOWER 0 0000000E 00 RECHARGE 2 6880163E 03 SUM OF THE LAYER 2 8739735E 03 DISCREPANCY 0 69 REGION 2 IN LAYER 2 OUT 2 4354266E 04 2 6107365E 03 0 0000000E 00 2 8542792E 03 IN OUT 7585552E 05 6107365E 03 6880163E 03 9694213E 05 WATER BUDGET OF THE WHOLE MODEL DOMAIN CONSTANT HEAD 2 2167889E 03 WELLS 0 0000000E 00 RECHARGE 2 6880163E 03 3 7117251E 03 1 2000003E 03 0 0000000E 00 4949362E 03 2000003E 03 6880163E 03 SUM 4 9048052E 03 DISCREPANCY 0 14 The value of the element i j matrix gives the flow rate from the i th region to the j th region Where i is the column index and j is the row index FLOW MATRIX Ki 2 6107E 03 0 000 2 0 000 1 9323E 03 Click the Load button to display the Load Matrix dialog box Fig 2 96 of the following flow 189 Click and select a file type i e ASCII Matrix or SURFER GRD and a file from an Open File dialog bo
98. head cells the initial hydraulic head remains the same throughout the simulation The initial hydraulic head is specified by selecting Parameters Ini tial and Prescribed Hydraulic Heads A constant head boundary exists whenever an aquifer is in direct hydraulic contact with a river a lake or a reservoir in which the water groundwater level is known to be constant It is important to be aware that a constant head boundary can provide inexhaustible supply or sink of water A ground water system may get or lose as much water as necessary from or to such a boundary without causing any change of hydraulic heads in the constant head boundary In some situations this may be unrealistic Therefore care must be taken when using constant head boundaries and it is suggested to avoid using this boundary condition on the upstream side of the groundwater flow direction Consider using the General Head Boundary or the Time Variant Specified Head packages if the hydraulic head at the constant head boundary varies with time Head dependent boundary conditions are modeled by means of the general head boundary river or drain package If it is planned to use MOC3D the user should be aware that MOC3D allows one to specify zones along constant head boundaries which are associated with different source concentrations Zones are defined within the IBOUND array by specifying unique negative values For example if a model has three zones one will use 1 2 and 3
99. in saturated and unsaturated porous media EPRI Report EA 4190 Electric Power Research Institute Palo Alto CA Gelhar LW Welty C and Rehfeldt KR 1992 A critical review of data on field scale dispersion in aquifers Water Resour Res 28 7 1955 1974 Guo Weixing and Langevin CD 2002 User s guide to SEAWAT A computer program for simulation of three dimensional variable density ground water flow U S Geological Survey Techniques of Water Resources Investigations book 6 chap A7 77 p Hantush MS and Jacob CE 1955 Non steady radial flow in an infinite leaky aquifer Trans Am Geophys Un 36 11 95 100 Harbaugh AW 1995 Direct solution package based on alternating diagonal ordering for the U S Geological Survey modular finite difference ground water flow model U S Geological Survey Open File Report 95 288 46 pp Harbaugh AW and McDonald MG 1996a User s documentation for MODFLOW 96 an update to the U S Geological Survey modular finite difference ground water flow model USGS Open File Report 96 485 Harbaugh AW and McDonald MG 1996b Programmer s documentation for MODFLOW 96 an update to the U S Geological Survey modular finite difference ground water flow model USGS Open File Report 96 486 Harbaugh AW Banta ER Hill MC and McDonald MG 2000 MODFLOW 2000 The U S Geological Survey modular ground water model User guide to modularization concepts and the ground water flow process U S Geological Survey Open file re
100. in the aquifer Indeed the calculated concentration profile with the Monod kinetics is nearly identical to the solution for the same transport problem but assuming a first order reaction with the rate coefficient A Mi Umar Ks 2 x 1073 day Case 2 with K in the same order as the aquifer concentrations shows the mixed order characteristics of the Monod kinetics In Case 3 the Monod 360 5 Examples and Applications kinetics approaches a zero order reaction i e OC Ot M imax since K is negligible compared to the concentrations in the aquifer Monod Case 1 Monod Case 2 4 Monod Case 3 First order reaction CciCo 100 200 300 400 500 Distance m Fig 5 52 Calculated concentration values for one dimensional transport from a con stant source in a uniform flow field 5 5 Solute Transport 361 5 5 4 Instantaneous Aerobic Biodegradation Folder pmdir examples transport transport4 Overview of the Problem The example problem considered in this section is adapted from Zheng 122 and is similar to the model described in Section 5 5 2 The problem involves two dimensional transport from a continuous point source in a uniform flow field The point source has a volumetric injection rate of 1 m day and the injected water contains hydrocarbon species 1 with a constant concentration of 1000 ppm The background concentration of oxygen species 2 in the aquifer is 9 ppm Hydrocar bon and oxy
101. in the southeast corner of the model area To the north an area of constant hydraulic head existed with a value of 15 m The southern boundary is a specified flux boundary with an inflow rate of 0 0672 m day per meter A total of nine wells in the area are pumped at 45 l s 3888 m3 d each during the 8 month dry season to supply water for irrigation and domestic purposes Fixed head h 15 m well 1 well2 well3 n well 4 well5 well 6 No flow boundary No flow boundary well 7 well8 well 9 K Specified flux boundary gt Q 0 0672 m day m Fig 4 42 Configuration of the hypothetical model 272 4 Tutorials The task is to assess the water levels in the aquifer under the following conditions 1 Steady state with the mean recharge rate 2 5 x 1074m day no pumping 2 After 8 months pumping during the dry season and 3 The water levels by the end of the followed 4 month wet season 4 2 2 Steady state Flow Simulation Seven main steps need to be done in this tutorial Create a new model Generate the model grid Refine the model grid Assign the model data Perform steady state flow simulation Extract and view results Produce output from the steady state simulation NAYDNBWN KE 4 2 2 1 Step1 Create a New Model The first step in running a flow simulation is to create a new model gt To create a new model 1 Select File New Model A New Model dialog box appears Select a f
102. is highly recommended to check the record file or at least take a glance at it Follow the steps below to generate contour maps of the calculated concentration values at the end of the simulation gt To generate contour maps of the calculated concentration values 1 Select Tools 2D Visualization A Result Selection dialog box appears 2 Select the MT3DMS tab in the Result Selection dialog box 3 Click OK to accept the default result type Solute Concentration and species 1 PM displays the model grid sets the Simulation Time on the toolbar to the beginning of the simulation and automatically loads the results pertained to the 256 4 Tutorials Simulation Time Contours are not visible at this stage since the initial concen tration values are zero over the entire model domain 4 Click the Simulation Time drop down list and set the simulation time to 9 467E 07 the end of the simulation By default PM sets 10 contour levels ranging from the minimum to the maximum concentration values of the selected simulation time Fig 4 25 One can customize the contour levels and the appearance of the contours by using the Environment Options dialog box Refer to Section 2 9 2 for details about this dialog box 5 To save or print the graphics select File Save Plot As or File Print Plot 6 Select File Leave Editor or click the leave editor button w Follow the steps below to generate the concentration time series curves at the obs
103. is the number of the upstream segment from which water is diverted For a segment that is not a diversion Iupseg must be specified as zero Iupseg is used only when the option Simulate diversions from segments is checked The values in Fig 2 27 indicate that segment 2 is diverted from segment 1 segment is a trib utary segment of segment 3 and segments 2 and 4 are tributary segments of segment 5 The configuration of the stream system is shown in Fig 2 28 2 6 The Models Menu 57 W Stream Parameters Parameters Stream Structure IV Simulate diversions from segments o ojojojojojololojojolojlojojlslojojojojojojojo Perr Crt rer Fig 2 27 Specification of the stream structure segment 1 segment 4 segment 3 segment 5 Fig 2 28 The stream system configured by the table of Fig 2 27 e When using the Cell by cell or Polygon input methods the following values are to be assigned to model cells alone the trace of a stream See the explanations above for the definition of the input values Segment Number Inflow to this Segment L3 T71 Reach Number is a sequential number in a segment that begins with one for the farthest upstream reach and continues in downstream order to the last reach in the segment Using the Cell by cell or Polygon methods only one 58 2 Modeling Environment reach can be as
104. is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start RT3D Check this option if the user does not want to run RT3D The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file RT3D BAT e OK Click OK to start generating RT3D input files In addition to the input files PM generates a batch file MT3DMS BAT saved in the model folder When all necessary files are generated PM automatically runs RT3D BAT in a Command Prompt window DOS box During a simulation RT3D writes a detailed run record to the file OUTPUT RT3 saved in the model folder See Section 2 6 2 12 on page 104 for details about the output terms 2 6 4 13 RT3D View RT3D View Run Listing File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run list file OUTPUT MTM which contains a detailed run record saved by MT3DMS RT3D View Concentration Scatter Diagram This menu item is available only if Concentration Observations have been defined see Section 2 6 4 10 on page 117 Select this menu item to open a Scatter Diagram Concentration dialog box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 on page 78 except the concentration values replace the head values RT3D View Concentration Time Curves This menu item is available only if Concentration Observations hav
105. it has found two successive weight factors which lie on either side of the optimal weight factor for that optimization iteration Once it has done this it uses New tons method to calculate the optimal weight factor through a series of successive approximations When two subsequent weight factors calculated in this way dif fer from each other by no more than a relative amount of WFTOL the optimal weight factor is deemed to have been calculated Continue optimizing regularization objective function even if measurement ob jective function less than PHIMLIM Under normal circumstances when working in regularization mode PEST ceases execution immediately if the measurement objective function falls below PHIM LIM There are some circumstances however where minimization of the reg ularization objective function is just as important as allowing the measurement objective function to reach PHIMLIM If this box is checked the variable REG CONTINUE of the PEST control data file will be as continue to ensure that PEST will continue optimizing regularization objective function after reached PHIMLIM 162 2 Modeling Environment e Activate conservation of memory at cost of execution speed and quantity of model output MEMSAVE If this box is checked the variable MEMSAVE of the PEST control data file will be set as memsave and Nonessential PEST tasks which are curtailed include the following The parameter covariance matrix and matric
106. it is useful to calculate flow terms for various subre gions of the model To facilitate such calculations MODFLOW saves the computed flow terms for individual cells in the file BUDGET DAT These individual cell flows are referred to as cell by cell flow terms and are of four types 1 cell by cell stress flows or flows into or from an individual cell due to one of the external stresses ex citations represented in the model e g pumping well or recharge 2 cell by cell storage terms which give the rate of accumulation or depletion of storage in an in dividual cell 3 cell by cell constant head flow terms which give the net flow to or from individual constant head cells and 4 internal cell by cell flows which are the flows across individual cell faces In the file BUDGET DAT the flow between the cells K I J and K I J 1 is denoted by FLOW RIGHT FACE the flow between the cells K I J and K I 1 J is denoted by FLOW FRONT FACE and the flow between the cells K I J and K 1 I J is FLOW LOWER FACE Follow the steps below to compute water budgets for the entire model user specified subregions and in and outflows between adjacent subregions gt To calculate water budget Select Tools Water Budget to display the Water Budget dialog box Fig 2 94 Change the settings in the Time group as needed PM calculates the water budget for the given stress period and time step 3 Click the Subregions button to u
107. iteration Therefore when one or more layers are under water table conditions iteration should always be tried The maximum change in head during each iteration printed by the solver provides an indication of the impact of all non linearities MODFLOW Solvers PCG2 The required parameters for the PCG2 package are specified in the Preconditioned Conjugate Gradient Package 2 dialog box Fig 2 31 They are described below e Preconditioning Method The PCG2 package provides two preconditioning op tions the modified incomplete Cholesky preconditioner MICCG 10 and the _Preconditioned Conjugate Gradient Package 2 Neuman Series Polynomial T Relaxation Parameter 1 Allowed Iteration Numbers Convergence Criteria Outer Iteration MITER Head Change L 50 001 Inner Iteration ITER 1 Residual L 3 T 30 001 Printout From the Solver Damping All available information Damping Parameter The number of iterations only i C None Printout Interval 1 Cancel Help Fig 2 31 The Preconditioned Conjugate Gradient Package 2 dialog box 66 2 Modeling Environment Neuman Series Polynomial preconditioner POLCG 105 Relaxation Parameter is used with MICCG Usually this parameter is equal to 1 Ashcraft and Grimes 9 found out that for some problems a value of 0 99 0 98 or 0 97 would reduce the number of iterations required for convergence The option Calculate the upper bound on the maxim
108. m and distribution coefficient Ka 0 0001m kg as the retardation factor R is calculated by fs Ki 5 3 Fig 5 55 shows the concentration distributions calculated by RT3D for all four species at the end of the 200 hour simulation period The calculated values agree 364 5 Examples and Applications closely with the solutions of MT3D99 122 which are not shown in the figure since the curves are nearly identical It can be seen that as PCE species 1 is transported from the source its mass lost to decay becomes the source for TCE species 2 some of which is in turn transformed into DCE species 3 and then VC species 4 C Co 0 5 10 15 20 25 30 35 40 Distance cm Fig 5 55 Comparison of calculated concentration values of four species in a uniform flow field undergoing first order sequential transformation 5 5 Solute Transport 365 5 5 6 Benchmark Problems and Application Examples from Literature Folder pmdir examples transport Overview of the Problem To test the accuracy and performance of the MT3D MT3DMS and MOC3D codes several benchmark problems and application examples are introduced in the user s guides of MT3D 117 MT3DMS 121 and MOC3D 74 You can find these documents on the folders document mt3d document mt3dms and docu ment moc3d of the companion CD ROM Modeling Approach and Simulation Results We have rebuilt most of the benchmark problems of MT3D MT3DMS and MOC3D by usi
109. matrix each line of the matrix contains up to 20 values Example If NCOL 6 and NROW S5 an ASCII Matrix file would be 6 5 121 152 133 144 315 516 221 252 233 244 215 216 321 421 521 Or 6 5 121 321 521 352 452 552 152 352 552 333 433 533 133 333 533 344 444 544 144 344 544 315 415 515 315 S15 515 6 2 File Formats 377 316 416 516 516 221 252 233 244 215 216 316 421 452 433 444 415 416 516 6 2 2 Contour Table File A contour table file can be saved or loaded by the Environment Options dialog box see Section 2 9 2 File Format t4 2 Data LABEL Data NL XXX XXX XXX XXX The following data repeats NB times 33 Data LEVEL COLOR FILL LVISIBLE LSIZE LDIS XXX XXX XXX Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space LABEL is the file label It must be PMWIN5000 CONTOUR FILE The file format has been changed since PMWIN 5 0 NL is the number of contour levels XXX reserved LEVEL is the Contour level COLOR is the color used to draw the contour line The color is defined by a long integer using the equation color red green x 256 blue x 65536 where red green and blue are the color components ranging from 0 to 255 FILL is the color used to fill the space between the current contour and the next contour level LVISIBLE controls the visibility of the corresponding
110. met or perhaps another termination criterion such as zero objective function or zero objective function gradient for which no user supplied settings are required PEST writes some information concerning the optimized parameter set to its run record file PESTCTL REC This file is saved in the data directory of your model It tabulates the optimal values and the 95 confidence intervals pertaining to all adjustable parameters It also tabulates the model calculated values based on these parameters together with the residuals i e the differences between measured and model calculated values Write covariance matrix If checked PEST will write the parameter covari ance matrix to the run record file PESTCTL REC Write correlation coefficient matrix If checked PEST will write the param eter correlation coefficient matrix to the run record file PESTCTL REC Write normalized eigenvectors of covariance matrix If checked PEST will write the normalized eigenvectors of the covariance matrix to the run record file PESTCTL REC Save data for a possible restart If checked PEST will dump the contents of many of its data arrays to a binary file at the beginning of each optimization iteration this allows PEST to be restarted later if execution is prematurely terminated If subsequent PEST execution is initiated using the r com mand line switch see the PEST manual 34 for details it will recommence execution at the beginning of
111. mode is fully described in Chapters 7 and 8 of the PEST manual The user is required to supply control variables listed in the Regularization tab and to supply at least one prior information equation with the name of observation group Obgnme set to regul e Save and Load Using the Save button the user can save the settings in separate files which can be loaded at a later time by using the Load button e Update Click the Update button to retrieve the estimated parameter values saved in the PESTCTL PAR file that contains the estimated parameter values PESTCTL PAR is created by PEST after running it in the parameter estimation mode The Update button is disabled and dimmed if this file is not available The Parameters Tab The Parameters Tab contains a table that gives an overview of the initial values and properties of estimated parameters The initial value PARVAL of parameter is the arithmetical mean of the cell values of that parameter The parameter s lower bound PARLBND and upper bound PARUBND default to two orders lower andhigher than PARVAL respectively If a parameter is removed by changing the parameter number to zero in the Data Editor the corresponding parameter in the table is ignored PM does not delete that adjustable parameter from the table To delete the parameter click on its record se lector J before the first column of the table then press the Del key Note that the user cannot manually add a parameter to
112. model cell and is saved in the ASCII matrix format See Section 6 2 1 for the format of the ASCII matrix file The Grid Position Tab Using the rotation angle and the coordinates Xo Yo of the upper left corner of the model grid the user may rotate and place the grid at any position The rotation angle is expressed in degrees and is measured counterclockwise from the positive x direction See Section 2 9 2 for details about the coordinate system of PM As we normally define the grid position and the coordinate system at the beginning of a modeling process the grid position will rarely need to be changed here The Gridding Method Tab PMWIN provides four gridding methods The user may select a method from the drop down box There is a corresponding interpolation program for each gridding method The interpolation programs are written in FORTRAN and were compiled with the Lahey FORTRAN 95 compiler The following sections give details of the gridding or interpolation methods e Shepard s Inverse Distance The Shepard s inverse distance method uses Equa tion 2 65 to interpolate data for finite difference cells Mz fi af 2 f 2 65 LaF 5 Il Where d is the distance between data point i and the center of a model cell f is the value at the i th data point F is the weighting exponent and f is the estimated value at the model cell The weighting exponent must be greater than zero and less than or equal to 10 Fig
113. number of particles on Face 5 to NI 4 and NJ 4 and set all the other values to 0 Click OK to close the Add New Particles dialog box Open the Particle Tracking Time Properties dialog box by selecting Options Particle Tracking Time Inthe Tracking Steps group change the time unit to years step length to 1 and maximum number of steps to 75 When finished click OK to close the dialog box Start the backward particle tracking by clicking on the button Repeat the above for Maximum number of steps of 100 and 125 The plot gen erated after 125 steps should look similar to Fig 4 59 Fig towards Well 2 4 59 125 year streamlines particles are started at the cell 6 5 1 and flow 5 Examples and Applications The examples contained in this chapter are intended to illustrate the use of PM and the supported programs The description of each problem is divided into three parts It starts out with Folder where you can find the ready to run model for example pmdir examples basic basic 1 pmdir is the installation folder of PM Next you ll find a discussion of the problem and finally you will find the simulation results 5 1 Basic Flow Problems 5 1 1 Determination of Catchment Areas Folder pmdir examples basic basic1 Overview of the Problem Fig 5 1 shows a part of an unconfined aquifer The extent of the aquifer to the North and South is assumed to be unlimite
114. one model layer the injection or pumping rate for each layer has to be specified The total injection or pumping rate for a multi layer well is equal to the sum of those from the individual layers For confined layers the injection or pumping rate for each layer Qk can be approximately calculated by dividing the total rate Q oza1 in proportion to the layer transmissivities McDonald and Harbaugh 85 Tk Qk Qiotal ST 2 28 where T is the transmissivity of layer k and XT is the sum of the transmissivity values of all layers penetrated by the multi layer well Another possibility to simulate a multi layer well is to set a very large vertical hydraulic conductivity or vertical leakance e g 1 m s to all cells of the well The total pumping rate is then assigned to the lowest cell of the well For display purposes a very small pumping rate say 1 x 10 m s can be assigned to other cells of the well In this way the exact extraction rate from each penetrated layer can be obtained by using the Water Budget Calculator See Section 4 1 2 5 for how to calculate subregional water budget e Parameter Number Parameter Number is used to group cells where the Qu values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps e Density of Injection Fluid M L This value is used by SEAWAT only if it is
115. parameter estimation 141 perform sensitivity analysis 141 run 144 scatter diagram 148 time series curves 149 MODFLOW 2005 393 MODFLOW 88 1 MODFLOW 96 1 392 MODFLOW ASP 2 MODFLOW Version 23 Modified method of characteristics 126 MODPATH 2 393 396 MODPATH format 388 MODPATH PLOT 393 molecular diffusion coefficient 122 228 Monod kinetics 86 100 359 MT3D 3 25 126 394 chemical reaction 130 concentration observation 131 concentration scatter diagram 134 concentration time curves 134 dispersion 130 sink source concentration 131 transport step size 97 MT3D99 3 MT3DMS 3 25 84 394 MT3DMS SEAWAT advection 89 chemical reaction 97 concentration observation 104 concentration scatter diagram 108 concentration time curves 108 Diffusion species dependent 97 Mass Loading 103 sink source concentration 102 Species dependent diffusion 97 MT3DMS SEAWAT Simulation Settings 85 MT3DMS SEAWAT 2000 dispersion 94 Multigrid 68 name file 389 New Model 21 nonequilibrium sorption 130 NOPTMAX 170 NPHINORED 171 NPHISTP 170 NRELPAR 171 numerical dispersion 91 127 NUMLAM 169 observation borehole 71 observation data 71 observation file Drawdown 380 flow 382 head 380 Observation Process 1 observations compaction 73 drawdown 73 head 70 subsidence 73 OFFSET 154 Open Model 21 output control MOC3D 123 MODFLOW 74 MT3D 131 MT3DMS SEAWAT 104 RT3D 117 output f
116. parameter file 379 time series curves MOODFLOW 2000 149 Time variant specified head package 58 TOL 140 toolbar buttons Data Editor 15 Grid Editor 12 PMPATH 211 top of layers 32 Index 413 trace file format 384 Transient Simulation Specifying Data 20 transmissivity 29 36 triangulation 180 tutorials 227 Type of Reaction 86 unconfined aquifer system 271 units 7 Upstream finite difference method 127 variable density 87 Variable Density Flow 85 variogram 180 VCONT 37 vector graphic 194 scaling 195 velocity 124 velocity vectors 216 vertical anisotropy 29 37 hydraulic conductivity 37 leakance 29 37 transverse dispersivity 95 96 Water Budget 187 Water Budget Calculator 4 Well package 59 XYZ file format 387
117. parameter space as the confidence limits themselves see PEST manual Parameter correlation coefficient matrix gt Tok rch_2 tl 1 000 0 9870 rch_2 0 9870 1 000 The diagonal elements of the correlation coefficient matrix are always unity The off diagonal elements are always between 1 and 1 The closer an off diagonal ele ment is to 1 or 1 the more highly correlated are the parameters corresponding to the row and column numbers of that element For this example transmissivity param eter t_1 and recharge parameter rch_2 are highly correlated as is indicated by the value 0 987 of the correlation coefficient matrix This means that these parameters are determined with a high degree of uncertainty in the parameter estimation pro cess A sensitivity analysis could be used to quantify the uncertainty in the calibrated model caused by uncertainty in the estimates of the aquifer parameters For our example the only discharge is to the river and the only source is recharge To be in steady state these two must balance Recharge must therefore be equal to 1 125 cfs the river gain equals 11 125 cfs 10 cfs Spreading over the modeled area 1 125 ft3 s RECHARGE 15 x 15 x 500 ft x 500 ft 2 x 1078 ft s 5 1 324 5 Examples and Applications The estimated parameter values are acceptable A better procedure would have been to compute the recharge right away from Equation 5 1 and estimate only transmis sivity 5 3
118. parent daughter chain reactions 86 101 first order rate reaction 121 flow net 342 Flow Package 24 flow velocity 225 flowlines 220 FORCEN 156 format 376 ASCII Matrix file 376 cell group file 383 complete information file of flow observation 384 complete information file of head observation 382 contour table file 377 flow observations file 383 grid specification file 378 line map file 379 MODPATH 388 observation boreholes file 381 observation file 380 382 observations file 381 particles file 388 pathline file 387 PMPATH 387 polygon file 385 time parameter file 379 trace file 384 transparent 5 unformatted sequential 5 XYZ file 387 Fortran compiler 5 fourth order Runge Kutta method 91 128 Freundlich isotherm 98 GCG solver 103 general head boundary 301 General head boundary package 42 geo reference 196 GEOKRIG 177 GMG solver package 68 Grid Editor 8 Grid Menu 27 grid specification file 378 GRIDZO 177 Groundwater Flow Process 1 GSLIB 177 half life 122 Hantush and Jacob Solution 331 head observations 70 head scatter diagram MODFLOW 78 PEST 175 head time curves MODFLOW 81 PEST 176 heat transport 4 horizontal anisotropy 29 36 hydraulic conductivity 36 transverse dispersivity 96 horizontal transverse dispersivity 95 Horizontal flow barrier package 44 Hybrid method of characteristics 126 hydrodynamic dispersion 95 IBOUND 31 ICBUND 32 imp
119. particles to the model Already existing particles will not be removed 4 Tutorials The tutorials provide an overview of the modeling process with PM describe the basic skills you need to use PM and take you step by step through hypothetical problems Each tutorial is divided into three parts It starts out with Folder where you can find the ready to run model for example pmdir examples tutorials tutori all where pmdir is the installation folder of PM Next you ll find a discussion of the hypothetical problem and the step by step tutorial will walk you through the tasks 4 1 Your First Groundwater Model with PM Folder pmdir examples tutorials tutorial 4 1 1 Overview of the Hypothetical Problem It takes just a few minutes to build your first groundwater flow model with PM First create a groundwater model by choosing New Model from the File menu Next de termine the size of the model grid by choosing Mesh Size from the Grid menu Then specify the geometry of the model and set the model parameters such as hydraulic conductivity effective porosity etc Finally perform the flow simulation by selecting Models MODFLOW Run After completing the flow simulation you can use the modeling tools provided by PM to view the results to calculate water budgets of particular zones or graphically display the results such as head contours You can also use PMPATH to calculate and save path lines or use the finite dif
120. particles when this button is highlighted i e the rectangle on the button is colored in red PMPATH redraws the particles whenever the PMPATH window has been covered by other windows and becomes visible again For example if the user switches to to another application and then returns to PMPATH it will redraw all particles If too many particles are placed it might be necessary to keep PMPATH from redrawing all of the particles all over again Under some circumstances PMPATH will take a long time to calculate the co ordinates of flow paths and travel times This is especially true if the flow velocities and the user specified time step length of particle track ing are very small Click the Stop Particle Tracking button if the particle tracking simulation appears too slow 3 2 3 10 Run Particles Forward Step by Step Click LE to move particles forward a single particle tracking step The particle track ing step length is defined in the Particle Tracking Time Properties dialog box See Section 3 3 2 for details 3 3 PMPATH Options Menu 215 3 2 3 11 Run Particles Forward Click EJ to execute forward particle tracking for a specified time length The time length is the product of the number of particle tracking steps and the particle tracking step length given in the Particle Tracking Time Properties dialog box See Section 3 3 2 for details 3 3 PMPATH Options Menu 3 3 1 Environment The Environment Options dialog box Fig
121. polygon The first and the last vertices must overlap Table 6 1 Assignment of parameters in the Value I vector Package Value 1 Value 2 Value 3 Value 4 WEL Recharge rate XXX XXX XXX DRN Hydraulic conductance Elevation XXX XXX RIV Hydraulic conductance Head in river Elevation XXX EVT Max ET rate ET Surface Extinction Depth Layer Indicator GHB Hydraulic conductance Head at boundary XXX XXX RCH Recharge Flux Layer Indicator XXX XXX HFB Barrier Direction K Thickness XXX XXX IBS Preconsolidation head Elastic storage Inelastic storage Starting compaction CHD Flag Start head End head XXX The values used by the STR1 package are Value 1 Segment Value 2 Reach Value 3 Streamflow Value 4 Stream stage Value 5 Hydraulic conductance Value 6 Elevation of the streambed top Value 7 Elevation of the streambed bottom Value 8 Stream width Value 9 Stream slope Value 10 n C Manning s roughness coefficient divided by C 6 2 File Formats 387 6 2 10 XYZ File An XYZ file must be saved as ASCII text using the following format N X Yi 21 X2 Y2 22 Xy Yn Zyn Where N is the number of points X and Y are the x y coordinate values and Z is the data value associated with the point i All values are are separated by at least one space 6 2 11 Pathline File 6 2 11 1 PMPATH Format A pathline file in the PMPATH format is a text file that begins with the header of the form PMPATH Version 6 00
122. procedure its initial value when implementing this procedure for the first optimization iteration is WFINIT Minimum regularization weight factor WFMIN and Maximum regularization weight factor WF MAX These are the minimum and maximum permissible val ues that the regularization weight factor is allowed to take If a regularization scheme is poor and does not lend too much stability to an already unstable parameter estimation process selection of appropriate values for WFMIN and WEMAX may be quite important for these can prevent PEST from calculating outrageous values for the regularization weight factor in an attempt to compen sate for inadequacies of the regularization scheme Regularization weight factor adjustment factor WF FAC and Convergence cri terion for regularization weight factor WFTOL When PEST calculates the appropriate regularization weight factor to use during any optimization iteration it uses an iterative procedure which begins at the value of the regularization weight factor calculated for the previous optimization iter ation for the first optimization iteration it uses WFINIT to start the procedure In the process of finding the weight factor which will result in a measurement objective function of PHIMLIM PEST first travels along a path of progressively increasing or decreasing weight factor In undertaking this exploration it either multiplies or divides the weight factor by WFFAC it continues to do this until
123. put into the spread sheet 2 7 The Tools Menu 185 sz CROSSSECTION PMS Processing Modflow Pro File Value Options Help e o alja lemja eee Se Ss S 1008718 21 56 D Visualization Salute Concentration IMTSDMSL Species 1 176877215 Fig 2 91 The 2D Visualization tool in action i Result Selection Select a model and the type of result that you want to display then click OK MODFLOW MOC3D MT3D MT3DMS SEAwaT PHTaD ATaD Result Type H ydraulic Head Cancel Help Fig 2 92 The Result Selection dialog box e Orientation and Layer Simulation results can be loaded layer column or row wise Orientation decides how the results should be loaded If Orientation is Plan View the user is asked to enter a layer number into the edit field If X section column or X section row is selected the user should enter a column or row number into the edit field next to drop down box e Column Width This drop down box is used to change the appearance width of the columns of the spreadsheet e Tabs Each tab corresponds to a simulation model MODFLOW The available Result Types include hydraulic head drawdown preconsolidation head compaction subsidence and cell by cell flow terms see Section 2 6 1 18 for the definition of each term The stress period and time step from which the result is read are given in the corresponding edit fields 186 2 Modeling Environment MOC3D
124. represents the prescribed den sity of fluid entering the groundwater system from the general head bound ary This value is used by SEAWAT only if it is running in a uncoupled 44 2 Modeling Environment mode i e the density effect of all species are turned off see 2 6 2 1 and the Density of general head boundary fluid options in the Simulation Set tings MT3TMS SEAWAT dialog box see Fig 2 46 on p 89 is set as User Specified in the GHB Package The ALL button Click the ALL button of a property to copy the property value to all other active vertices When using the Cell by cell or Polygon input methods the following values are to be assigned to model cells of a general head boundary See the explanations above for the definition of the input values GHB hydraulic conductance C L T Head on the External Source hy L Parameter Number GHB Elevation L and Density of GHB Fluid M L 2 6 1 4 MODFLOW Flow Packages Horizontal Flow Barrier The Horizontal Flow Barrier package simulates thin low permeability geologic fea tures such as vertical faults or slurry walls which impede the horizontal flow of groundwater These geologic features are approximated as a series of horizontal flow barriers conceptually situated on the boundaries between pairs of adjacent cells in the finite difference grid Refer to Hsieh and Freckleton 66 for the numerical implementation of the Horizontal Flow Barrier package A h
125. requires the use of consistent units throughout the modeling process For example if you are using length L units of meters and time T units of seconds hydraulic conductivity will be expressed in units of m s pumping rates will be in units of m s and dispersivity will be in units of m The values of the simulation results are also expressed in the same units Table 2 1 lists symbols and their units which are used in various parts of this text PHT3D requires the use of meters for the length the use of mol l for con centrations of aqueous mobile chemicals and user defined immobile entities such as bacteria and the use of mol l for mineral exchanger and surface concentrations where mol refers to moles l refers to liter of pore water and l refers to liter of bulk volume see Prommer and others 97 for details about the use of units in PHT3D PM contains the following menus File Grid Parameters Models Tools Value Options and Help The Value and Options menus are available only in the Grid Editor and Data Editor see Sections 2 1 and 2 2 for details PM uses an intelligent Table 2 1 Symbols used in the present text Symbol Meaning Unit m thickness of a model layer LL HK horizontal hydraulic conductivity along model rows LT VK vertical hydraulic conductivity LT T transmissivity T HK x m LT Ss specific storage E S storage coefficient or storativity S Ss x m Sy specific yield or drainable por
126. running in a uncoupled mode i e the density effect of all species are turned off see 2 6 2 1 and the Density of Injection Well Fluid options in the Simulation Settings MT3TMS SEAWAT dialog box see Fig 2 46 on p 89 is set as User Specified in the Well Package 2 6 1 12 MODFLOW Flow Packages Wetting Capability The wetting capability of the Block Centered Flow 2 BCF2 package 86 allows the simulation of a rising water table into unsaturated dry model layers The BCF2 package is identical to the BCF1 package of MODFLOW 88 85 except for the wetting and drying of cells A cell falls dry when the head is below 60 2 Modeling Environment the bottom elevation of the cell When a cell falls dry IBOUND is set to 0 which indicates a no flow or an inactive cell all conductance values to the dry cell are set to zero No water can flow into the cell as the simulation proceeds and the cell remains inactive even if neighboring water tables rise again To overcome this problem a value THRESH called wetting threshold is intro duced to the BCF2 package or later versions of this package The computer code uses this value to decide whether a dry or an inactive cell can be turned into a wet active cell e If THRESH 0 the dry cell or the inactive cell cannot be wetted e If THRESH lt 0 only the cell below the dry cell or inactive cell can cause the cell to become wet e If THRESH gt 0 the cell below the dry cell or in
127. that a simultaneous fit of highly correlated param eters for example HK and recharge values on the basis of observed heads only is of little value in steady state problems due to the non uniqueness of such a fit In those cases the ability of using prior information and flow observation data in MODFLOW 2000 could help in solving problems The parameters to be estimated are defined in the following steps Table 2 8 Adjustable parameters through MODFLOW 2000 within PM Packages Abbreviation Adjustable Parameters Block Centered Flow BCF No aquifer parameters can be estimated Layer Property Flow LPF All layer types HK HANI VANI VK Ss and Sy Drain DRN Conductance of drain cells Evapotranspiration EVT Maximum evapotranspiration rate General Head Boundary GHB Conductance of GHB cells Horizontal Flow Barrier HFB6 Hydraulic characteristic of barrier Recharge RCH Recharge flux River RIV Conductance of RIV cells Stream Flow Routine STR Conductance of STR cells Well WEL Pumping or injection rates of WEL cells 136 2 Modeling Environment gt To define an adjustable parameter for estimation 1 Select a parameter or a package from the Parameters or Models MOD FLOW Flow Packages menus for example Horizontal Hydraulic Conductivity Recharge or Well 2 Assign a parameter number and initial guessed parameter values to the cells where the parameter values should be estimated The parameter number needs to be unique within a para
128. the Particle Tracking Time dialog box Fig 3 12 are grouped under three tabs Simulation Mode Time Pathline Colors and RCH EVT options These tabs are described below The Simulation Mode Time Tab The options of the Simulation Mode Time tab Fig 3 12 are described below Current Time In MODFLOW simulation time is divided into stress periods which are in turn divided into time steps The time length of each stress period and time step is defined in PM In PMPATH the user can move to any stress period and time step as long as the resulting heads and budget data are saved for that stress period time step The starting time of each particle is always the beginning of the time step defined in Current Time Tracking Step To select a time unit for Step length click the down arrow on the Unit drop down box The step length is the time length that particles may move when one of the buttons J or Z is pressed Maximum steps is the allowed num ber of particle tracking steps Each time one of the buttons or Z is pressed 220 3 The Advective Transport Model PMPATH Particle Tracking Time Properties x Simulation Mode Time Pathline Colors RCH EVT Ontions Current Time p Tracking Step it seconds E Stress Period 1 i Step Length 31557600 it a 1 Tane Sii Maximum steps 100 r Time Mark ar Reece an View r Cross Sections Interval 1 IM Visible T Visible Size 10 Size J 3 r Simulation Mo
129. the Simulation Time on the toolbar to the beginning of the simulation and automatically loads the results pertained to the Simulation Time Contours are not visible at this stage since the initial concen tration values are zero over the entire model domain Click the Simulation Time drop down list and set the simulation time to 9 467E 07 the end of the simulation By default PM sets 10 contour levels ranging from the minimum to the maximum concentration values of the selected simulation time Fig 4 33 One can customize the contour levels and the appearance of the contours by using the Environment Options dialog box Refer to Section 2 9 2 for details about this dialog box To save or print the graphics select File Save Plot As or File Print Plot Select File Leave Editor or click the leave editor button w no flow boundary 8 m contaminated pumping well E constant head boundary h no flow boundary Fig 4 33 Contours of the concentration values at the end of the simulation 4 1 Your First Groundwater Model with PM 263 Follow the steps below to generate the concentration time series curves at the obser vation boreholes gt To generate the concentration time series curves at the observation boreholes 1 Select Models MOC3D View Concentration Time Curves pmp displays the Time Series Curves Concentration dialog box Fig 4 34 This dialog box has two tabs The Data tab displays th
130. the calculated pathlines and particle locations PMPATH 19 PMPATH is a Windows based advective transport model for calculating and animating path lines of groundwater PMPATH uses a semi analytical particle tracking scheme used in MODPATH 93 to calculate the groundwater paths and travel times PMPATH supports both forward and backward particle tracking schemes for steady state and transient flow fields The graphical user interface of PMPATH allows the user to run a particle tracking simulation with just a few clicks of the mouse Pathlines or flowlines and travel time marks are calculated and displayed along with various on screen graphical options including head or drawdown contours and velocity vectors MOC3D 74 1 1 Supported Computer Codes 3 MOC3D is a single species transport model computes changes in concentration of a single dissolved chemical constituent over time that are caused by advec tive transport hydrodynamic dispersion including both mechanical dispersion and diffusion mixing or dilution from fluid sources and mathematically simple chemical reactions including decay and linear sorption represented by a retar dation factor MOC3D uses the method of characteristics to solve the transport equation on the basis of the hydraulic gradients computed with MODFLOW for a given time step This implementation of the method of characteristics uses par ticle tracking to represent advective transport and explicit finite differenc
131. the groundwater system and the reservoir takes place across the bottom of the reservoir and the top of the model cells Leakage between the reservoir and the underlying groundwater system is sim ulated for each model cell corresponding to the inundated area by multiplying the head difference between the reservoir and the groundwater system by the hydraulic conductance of the reservoir bed Equation 2 16 defines the hydraulic conductance of the reservoir bed Cres HCres DELC I DELR J Ry 2 16 where DELC I is the width of the model row I DELR J is the width of the model column J Reservoir bed thickness is subtracted from the land surface elevation of the reser voir to obtain the elevation of the base of the reservoir bed sediments The elevation of the base of the reservoir bed sediments is used in computing leakage When the hydraulic head in the groundwater system is above the base of the reservoir bed sed iments leakage Q rgs LTT 1 from or to the groundwater system is computed by equation 2 17 Qres Cres Hres h 2 17 where Hpregs is the reservoir stage L and A is the hydraulic head in the aquifer underlying the reservoir L When the hydraulic head is lower than the elevation of the base of the reservoir bed sediments HRgsBor leakage from the reservoir to the groundwater system is computed by Qres Cres Hres Hreszor 2 18 gt To specify the water table elevations stages of reservoirs 50 2 Mo
132. the iteration during which it was interrupted Include decimal point even if redundant If cleared PEST will omit the dec imal point from parameter values on model input files if the decimal point is redundant thus making room for the use of one extra significant figure If this option is checked PEST will ensure that the decimal point is always present 2 6 8 2 PEST Parameter Estimation Head Observations Select the Head Observations from the PEST Parameter Estimation menu or from MODFLOW MODFLOW 2000 Parameter Estimation to specify the locations of 172 2 Modeling Environment the head observation boreholes and their associated observed measurement data in a Head Observation dialog box See Section 2 6 1 14 for details When this menu item is selected and checked PEST uses the head observation data for the parameter estimation 2 6 8 3 PEST Parameter Estimation Flow Observations Select Drawdown Observations from the PEST Parameter Estimation or MOD FLOW menu to specify the locations of the drawdown observation boreholes and their associated observed measurement data in a Drawdown Observations dialog box Its use is identical to the Head Observation dialog box The only difference is that the head observations are replaced by drawdown observations See Section 2 6 1 14 for details When this menu item is selected and checked PEST uses the drawdown obser vation data for the parameter estimation 2 6 8 4
133. the model layer number for all model cells downstream from a vertex until the next vertex redefines the layer number If Layer Option is Assign layer number automatically the river is assigned to a layer where the elevation of the Streambed bottom Botstr see below is located between the top and bottom of the layer The layer number is set to 1 if Botstr is higher than the top of the first layer The layer number is set to the last layer if Botstr is lower than the bottom of the last layer Segment Number is a number assigned to a polyline Segments must be numbered in downstream order The maximum number allowed is 1000 Inflow to this Segment L 7 is the streamflow entering a segment polyline When inflow into a segment is the sum of outflow from a specified number of tributary segments the segment inflow values are specified as 1 Parameters apply to the selected vertex x Active Check this box to activate a vertex Clear the Active box to de activate a vertex The input parameters at active vertices are linearly in terpolated or extrapolated to each cell along the trace of the polyline and used in the simulation The parameters of an inactive vertex are ignored Hydraulic Conductivity of Streambed Kstr LT71 Width of the Stream Channel Wstr L Elevation of the Streambed Top Topstr L and Elevation of the Streambed Bottom Botstr L The value Kstr de scribes all of the head loss between the stream and
134. to generate MODFLOW input files In addition to the input files PM creates a batch file MODFLOW BAT in the model folder When all input files Run Modflow Modflow Version MODFLOWS96 INTERFACE TO MT3D96 AND LATER Generate Description Destination File _j Basic Package c simcore pmwin8 examples transport transport4 bas Block Centered Flow BCF1 2 c simcorepmwin8 examples transport transport4 bcf Output Control _ c simcore pmwinS examples transport transport4 oc Well c simcore pmwinS examples transport transport4 wel Solver PCG2 c simcore pmwin8 examples transport transport4 pec Modpath Vers 1 x c simcore pmwin8 examples transport transport4 mai Modpath Vers 3 x c simcore pmwin8 examples transport transport4 mai gt Options I Check model data I Regenerate all input files M Don t generate MODPATH files anyway J7 Generate input files only don t start MODFLOW Cancel Help Fig 2 37 The Run Modflow dialog box 2 6 The Models Menu 71 Table 2 6 Model Data checked by PM Term Checking Criteria Layer thickness May not be zero or negative Top and bottom elevation of Model layers may not overlap each other layers Initial head at constant head A constant head cell may not be dry at the beginning of a cells simulation Horizontal hydraulic conduc May not be zero or negative tivity transmissivity vertical hydraulic conductivity ver tical leakance or effectiv
135. transient flow simulation is reached the most recent flow field can be treated as steady state and the movement of particles can go on 3 1 1 Consideration of the display of the calculated pathlines Because of the capability of calculating a particle s exit point from a cell directly pathlines displayed by PMPATH may sometimes intersect each other Consider the case shown in Fig 3 3 two particles within a two dimensional cell start at the same time The dashed curves represent the actual paths of these two particles The solid lines are the pathlines displayed by PMPATH The pathlines intersect each other although the particles exit points are exactly equal to that of the actual paths This spurious effect can be prevented by using a smaller particle tracking step length such that intermediate particle positions between starting point and exit point can be calculated See Particle Tracking Time Properties dialog box Section 3 3 2 for how to change the particle tracking step length o exit points of particles 1 and 2 Vy V x Ww Wyo 9 0 0 Starting point of particle 1 Fig 3 3 Schematic illustration of the spurious intersection of two pathlines in a two dimensional cell 3 1 2 Consideration of the spatial discretization and water table layers The method described above is based on the assumption that the model domain was discretized into an orthogonal finite difference mesh i e all model cells in the same l
136. transmissivity within a layer is homogeneous or smoothly varying bilinear interpolation of velocity yields more Interpolation scheme for particle velocity Bilinear X Y directions x Maximum number of particles NPMAx 10000 Courant number CELDIS 75 Fraction limit for regenerating initial particles FZERO 02 Initial number of particles per cell NPTPND s PNEWL PNEWR PNEWC Cancel Help Fig 2 64 The Parameter for Advective Transport MOC3D dialog box 2 6 The Models Menu 121 realistic pathlines for a given discretization than linear interpolation And in the presence of strong heterogeneities between adjacent cells within a layer it would usually be preferable to select the linear interpolation scheme Maximum number of particles NPMAX Maximum number of particles avail able for particle tracking of advective transport in MOC3D If it is set to zero the model will calculate NPMAX according to equation 2 54 NPMAX 2 NPTPND NSROW NSCOL NSLAY 2 54 where NPTPND is the initial number of particles per cell see below The values NSROW NSCOL and NSLAY are the number of rows columns and layers of the transport subgrid respectively Courant number CELDIS is the number of cells or the fraction of a cell that a particle may move through in one step typically 0 5 lt CELDIS lt 1 0 Fraction limit for regenerating initial particles FZERO If the fraction of active ce
137. values MOCS3D View Concentration Time Curves This menu item is available only if Concentration Observations have been defined see Section 2 6 5 9 Select this menu item to open a Time Series Curves Concen tration dialog box which is identical to the Time Series Curves Hydraulic Head dialog box Fig 2 41 except the concentration values replace the head values 2 6 6 MT3D 2 6 6 1 MT3D Initial Concentration MT3D requires the initial concentration of each active concentration cell i e ICBUND gt 0 at the beginning of a transport simulation The values specified here are shared with MOC3D 2 6 The Models Menu 127 2 6 6 2 MT3D Advection The available settings of the Advection Package MTADV1 dialog box Fig 2 69 are described below Note that some of the simulation parameters are only required when a particular solution scheme is selected e Solution Scheme MT3D provides four solution schemes for the advection term including the method of characteristics MOC modified method of character istics MMOC hybrid method of characteristics HMOC and upstream finite difference method Due to the problems of numerical dispersion and artificial oscillation the upstream finite difference method is only suitable for solving transport problems not dominated by advection When the grid Peclet number P Pe Ax aL Acz is the grid spacing and aL is the longitudinal disper sivity is smaller than two the upstream finit
138. values within an acceptable range of error Model calibration can be performed by the hand operated trial and error adjustment of aquifer param eters or by inverse models such as PEST MODINV 32 MODFLOW P 61 or MODFLOW 72000 56 63 This example provides an exercise in model calibration with PEST Specific details of this example are from Andersen 5 Fig 5 22 shows the idealized flow system and locations of observation boreholes The flow system is a small confined aquifer which is strongly controlled by the river flowing across it The aquifer is approximately 100 ft thick and is composed primar ily of silty sand The river is not in direct hydraulic connection with the aquifer but acts as a leaky boundary condition which can gain or lose water to the aquifer Stage data for the river and riverbed elevation are listed in Table 5 2 Other boundary conditions are no flow which surround the square and define the areal extent of the aquifer Given constraints of uniform transmissivity and recharge and additional data be low the task is to obtain a steady state calibration based on the measurements listed in Table 5 3 Initial hydraulic head 100 0 ft Grid size 15 x 15 Ax Ay 500 ft River base flow at western model boundary 10 cfs River base flow at eastern model boundary 11 125 cfs Riverbed conductance 0 01 ft s 322 5 Examples and Applications Fig 5 22 Configuration of the aquifer system Tabl
139. water mound The pond covers approximately 6 acres 23225m and pond leakage is 12 500 cubic feet per day 354 m d The specific yield is 20 percent The water table is flat prior to the creation of the recharge pond The flat water table is the result of a uniform fixed head boundary that surrounds the aquifer The task is to calculate the water table under the steady state condition and the formation of the groundwater mound over time Modeling Approach and Simulation Results Because of the symmetry heads are identical in each quadrant of the aquifer and there is no flow between quadrants therefore only one quarter of the system needs to be simulated The problem is simulated using a grid of 40 rows 40 columns and 14 layers Fig 5 9 A uniform horizontal grid spacing of 125 feet 38 1 m is used and each layer is 5 feet 1 52 m thick The pond is in the upper left corner of the grid The boundaries along row and column are no flow as a result of the symmetry A fixed head boundary of 25 feet 7 62 m is specified along row 40 and column 40 for layers 10 14 a no flow boundary is assigned along row 40 and column 40 for layers 1 9 Without the recharge from the pond layers 1 9 are dry and the head in all the cells of layers 10 14 is 25 feet Recharge from the pond is applied to the horizontal area encompassed by rows through 2 and columns 1 through 2 The recharge option Recharge is applied to the hi
140. when it runs The printed value can be used in future runs in order to minimize memory usage Max equations in lower part of A This is the maximum number of equations in the lower part of the equations to be solved This value impacts the amount of memory used by the solver If specified as 0 the program will calculate the value as half the number of cells in the model which is an upper limit The actual number of equations in the lower part will be less than half the number of cells whenever there are no flow and constant head cells be cause flow equations are not formulated for these cells The solver prints the actual number of equations in the lower part when it runs The printed value can be used in future runs in order to minimize memory usage Max band width of AL This value impacts the amount of memory used by the solver If specified as 0 the program will calculate the value as the product of the two smallest grid dimensions which is an upper limit Head change closure criterion L If iterating iteration stops when the absolute value of head change at every node is less than or equal to this value The criterion is not used when not iterating but a value must always be specified Relaxation Accelleration Parameter ACCL ACCL is a multiplier for the com puted head change for each iteration Normally this value is 1 A value greater than may be useful for improving the rate of convergence when using external iteration to solve no
141. 0 cc eee cece eee eee 315 Model calculated river stage 0 eee eee eee 315 Numbering system of streams and diversions after Prudic 98 316 Plan and cross sectional views of the model area 317 Steady state hydraulic head contours in layer4 319 Time series curve of the water stage in the lake 319 Configuration of the aquifer system 0004 322 Plan view of the model 0 0 cee ee eee 326 Location of the cutoff wall and pumping wells 326 Time series curve of the calculated hydraulic head at the center of the contaminated area 2 ee ce eee 327 Plan view of the model 00 0 c eee eee ee eee 329 Time series curves of the calculated and observed drawdown values 330 Configuration of the leaky aquifer system and the aquifer parameters 331 Configuration of the leaky aquifer system and the aquifer parameters 333 Physical system for test case 1 Adapted from Hill and others 63 334 5 32 5 33 5 34 3 35 5 36 5 37 5 38 5 39 5 40 5 41 5 42 5 43 5 44 5 45 5 46 5 47 5 48 5 50 5 49 5 51 5 52 5 53 5 54 5 53 5 56 5 57 5 58 5 59 5 60 5 61 6 1 List of Figures XIX Test case 2 model grid boundary conditions observation locations and hydraulic conductivity zonation used in parameter estimation Adapted from Hill and others 63 0 0 e eee eee ee eee ee 338
142. 0 001 m s Fig 5 6 shows the calculated contours For comparison the entire aquifer is mod eled with the east and west fixed head boundaries and the result is shown in Fig 5 7 The model is saved in the folder pmdir examples basic basic2a ical x o o 00 a 10 N a rel ra wo N Qa ire k lt Fig 5 6 Calculated head contours for the west part of the aquifer 00 t gt a o o N ce 3 a 3 4 at Q 2 2 a x a a a Fig 5 7 Calculated head contours for the entire aquifer 5 1 Basic Flow Problems 303 5 1 3 Two layer Aquifer System in which the Top layer Converts between Wet and Dry Folder pmdir examples basic basic3 Overview of the Problem This example is adapted from the the first test problem of the BCF2 package Mc Donald and others 86 In an aquifer system where two aquifers are separated by a confining bed large pumping rates from the bottom aquifer can desaturate parts of the upper aquifer If the pumping is discontinued resaturation of the upper aquifer can occur Fig 5 8 shows two aquifers separated by a confining unit No flow boundaries surround the system on all sides except that the lower aquifer discharges to a stream along the right side of the area Recharge from precipitation is applied evenly over the entire area The stream penetrates the lower aquifer in the region
143. 00 0 0000000E 00 CONSTANT HEAD 0 0000000E 00 0 0000000E 00 0 0000000E 00 HORIZ EXCHANGE 5 5900711E 04 0 0000000E 00 5 5900711E 04 EXCHANGE UPPER 6 3981197E 04 0 0000000E 00 6 3981197E 04 EXCHANGE LOWER 0 0000000E 00 0 0000000E 00 0 0000000E 00 WELLS 0 0000000E 00 1 2000001E 03 1 2000001E 03 SUM OF THE LAYER 1 1988191E 03 1 2000001E 03 1 1809170E 06 is abstracting 7 8003708E 05 m s from the first layer 5 6002894E 04 m3 s from the second layer and 5 5900711E 04 m s from the third layer Almost all water withdrawn comes from the second stratigraphic unit as can be expected from the configuration of the aquifer 4 1 2 6 Step 6 Produce Output In addition to the water budget PM provides various possibilities for checking sim ulation results and creating graphical outputs The particle tracking model PMPATH can display pathlines head and drawdown contours and velocity vectors Using the Results Extractor simulation results of any layer and time step can be read from the unformatted binary result files and saved in ASCII Matrix files An ASCII Matrix file contains a value for each model cell in a layer PM can load ASCII matrix files into a model grid The format of the ASCII Matrix file is described in Section 6 2 1 PM includes a built in 2D visualization tool which can be used to display contours of almost all kind of model results including hydraulic heads drawdown concen 4 1 Your First Groundwater Model with PM 243 tration
144. 000 Select this menu item to start parameter estimation with the coupled approach PEST ASP MODFLOW 2000 In this case the derivatives of model outputs with respect to adjustable parameters are calculated by MODFLOW ASP 35 a modified version of MODFLOW 2000 and the parameter estimation is done by PEST ASP This ap proach combines the strengths of both programs The available settings of the Run PEST ASP MODFLOW 2000 dialog box Fig 2 78 are described below e The File Table has three columns Generate Prior to running the program PM uses the user specified data to generate input files for MODFLOW ASP and PEST ASP An input file will be generated only if the corresponding Generate box is checked The user may click on a box to check or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options 146 2 Modeling Environment Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start PEST ASP Check this option if the user does not want to run PEST ASP MODFLOW 2000 The simulation can be started at a later time or can be starte
145. 1 Data NBOREHOLES The following data repeat for each borehole i e NBOREHOLES times 2 Data OBSNAM Active x y Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NBOREHOLES is the number of observation boreholes Active A borehole is active if Active 1 A borehole is inactive if Active 0 x x coordinate of the borehole y y coordinate of the borehole 6 2 6 2 Layer Proportions File 1 Data NLAYERS 2 Data PR 1 PR 2 PR NLAYERS Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NLAYERS Number of layers in the model PR layer proportion values for layer i 6 2 6 3 Observations File 1 Data NHOBS The following data repeat for each observation i e NHOBS times 2 Data Time HOBS STWT Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NHOBS number of observations Time Observation time HOBS observed value at Time STWT For MODFLOW 2000 STWT is the statistic value for the observation For PEST STWT is the weighting factor for the observation 382 6 Supplementary Information 6 2 6 4 Complete Information File Data PMWIN_OBSERVATION_FILE Data NBOREHOLES EVH Data Reserved Reserved Reserved Reserved Data ITT STAT_FLAG Data Reserved Re
146. 1 Hydraulic conductivity of 4x 10 7 m s 0 75 1 00000 layerl HK 3 Hydraulic conductivity of layer 4 4 x 107 m s 0 9 1 00013 3 under the river RCH_1 Recharge rate in zone 1 1 x 1078 m s 2 0 0 99997 RCH 2 Recharge rate in zone 2 1 5 x 1078 m s 0 66 1 00005 RIV_1 Hydraulic conductance of the 1 2 m s 1 2 1 00036 riverbed SS_1 Specific storage of layer 1 4 x 107 1 m 0 65 1 00006 SS 3 Specific storage of layer 3 2 x 107 1 m 2 0 0 999274 WEL_1 Pumping rate in each of layers1 1 0 m3 s Ll 1 00003 and 3 VK 2 Vertical hydraulic conductivity 2 x 1077 m s 0 50 1 00017 of layer 2 5 3 Parameter Estimation and Pumping Test 337 5 3 6 Parameter Estimation with MODFLOW 2000 Test Case 2 Folder pmdir examples calibration calibration6 Overview of the Problem This example model is adapted from Hill and others 63 The model grid shown in Fig 5 31 has a uniform grid spacing of 1500 m in the horizontal and has 247 active cells in each of three layers Layers 1 2 and 3 have a constant thickness of 500 m 750 m and 1500 m respectively Hydraulic conductivity is divided into four zones each of which is present in the middle layer and three of which are present in the top and bottom layers Constant head boundaries comprise portions of the western and eastern boundaries with no flow across the remaining boundaries Head dependent boundaries representing springs are simulated using both the Drain and General Head Boundary
147. 2 6848E 03 TOTAL IN 464094 1560 TOTAL IN 4 9022E 03 OUT OUT CONSTANT HEAD 350429 7810 CONSTANT HEAD 3 7016E 03 WELLS 113604 0160 WELLS 1 2000E 03 RECHARGE 0 0000 RECHARGE 0 0000 TOTAL OUT 464033 8130 TOTAL OUT 4 9016E 03 IN OUT 60 3438 IN OUT 6 3796E 07 PERCENT DISCREPANCY 0 01 PERCENT DISCREPANCY 0 01 4 1 2 5 Step 5 Calculate subregional water budget There are situations in which it is useful to calculate water budgets for various sub regions of the model To facilitate such calculations flow terms for individual cells are saved in the file path BUDGET DAT These individual cell flows are referred to as cell by cell flow terms and are of four types 1 cell by cell stress flows or flows into or from an individual cell due to one of the external stresses excitations represented in the model e g pumping well or recharge 2 cell by cell storage terms which give the rate of accumulation or depletion of storage in an individual cell 3 cell by cell constant head flow terms which give the net flow to or from indi vidual fixed head cells and 4 internal cell by cell flows which are the flows across individual cell faces that is between adjacent model cells The Water Budget Calculator uses the cell by cell flow terms to compute water budgets for the entire model user specified sub regions and flows between adjacent sub regions 240 4 Tutorials gt To calculate subregional water budget
148. 2 92 The Result Selection dialog box 0 eee eee eee 185 2 93 The Results Extractor dialog box 00 ee eee eee 186 2 94 The Water Budget dialog box 00 eee ee eee eee 188 2 95 The Browse Matrix dialog box 0 0 c eee eee eee 190 2 96 The Load Matrix dialog box 00 cece eee ee eee 190 2 97 The starting position of a loaded ASCII matrix 191 2 98 The Reset Matrix dialog box 0 0 eee eee ee eee 191 2 99 The Search and Modify dialog box 00 0005 192 2 100The Import Results dialog box 00 ce cee ee eee 193 2 101The Map Options dialog box 0 eee ee eee 194 2 102Scaling a vector graphic 0 eee ee eee 196 XVI List of Figures 2 103Importing and Geo referencing a raster map 0 2 104The Appearance tab of the Environment Options dialog box 2 105The Coordinate System tab of the Environment Options dialog box 2 106Defining the coordinate system and orientation of the model grid 2 107The Contours tab of the Environment Options dialog box 2 108The Color Spectrum dialog box 0 00 cece eee eee 2 109The Contour Labels dialog box 0 0 0 0 c eee ee eee eee 2 110The Label Format dialog box 0 0 cece ee eee 3 1 PMPATH inaction isses speti ase bee lesbos sage eee eee ees 3 2 a Flow through an infinitesimal volume o
149. 218 3 The Advective Transport Model PMPATH tour levels simply click on one of the colored buttons and select a color from a Color dialog box After clicking OK the contour colors levels in the table are updated to reflect the changes Label Defines whether a contour should be labeled The user may click on an individual box of the Label column to turn label on M or off C Click on the header to display the Contour Labels dialog box Fig 3 10 which can be used to define the display frequency of contour labels First labeled contour line defines the first contour line to be labeled Labeled line frequency spec ifies how often the contour lines are labeled After clicking OK the flags in the table are updated to reflect the changes Label height Specifies the appearance height of the label text It uses the same length unit as the model Label spacing Specifies the distance between two contour labels It uses the same length unit as the model Label height specifies the appearance height of the label text It uses the same length unit as the model Label spacing specifies the distance between two contour labels It uses the same length unit as the model e Label Format The Label Format dialog box Fig 3 11 allows the user to specify the format for the labels The options of this dialog box are described below Fixed This option displays numbers at least one digit to the left and N digits to the right of the dec
150. 3 1 125 136 Watson DF 1992 Contouring A guide to the analysis and display of spatial data with programs on diskette Pergamon ISBN 0 08 040286 0 Wexler EJ 1992 Analytical solutions for one two and three dimensional solute trans port in groundwater systems with uniform flow U S Geological Survey Techniques of Water Resources Investigations Book 3 Chapter B7 190 pp Wilson JD and Naff RL 2004 The U S Geological Survey modular groundwater model GMG linear equation solver package documentation U S Geogolical Survey Open File Report 2004 1261 Wilson JL and Miller PJ 1978 Two dimensional plume in uniform ground water flow J Hyd Div ASCE 4 503 514 Zheng C 1990 MT3D a modular three dimensional transport model S S Papadopulos amp Associates Inc Rockville Maryland 118 119 120 121 122 123 124 References 405 Zheng C and Bennett GD 1995 Applied contaminant transport modeling Theory and practice 440 pp Van Nostrand Reinhold New York Zhang Y Zheng C Neville CJ and Andrews CB 1995 ModIME An integrated model ing environment for MODFLOW PATH3D and MT3D S S Papadopulos amp Associates Inc Bethesda Maryland Zheng C 1996 MT3D Version DoD_1 5 a modular three dimensional transport model The Hydrogeology Group University of Alabama Zheng C and Wang PP 1999 MT3DMS A modular three dimensional multispecies model for simulation of advection dispersion and chem
151. 3 6 allows modifying the appearance of the model The available settings are grouped under 4 tabs namely Appearance Cross Sections Velocity vectors and Contours These tabs are described below The Appearance Tab The Appearance Tab Fig 3 6 allows changing the visibility and appearance color of each simulated component A simulated component is visible if the corresponding Visibility box is checked To select a new color click on the colored cell a J button appears then click on the ZJ button and select a color from a Color dialog box The Cross Sections Tab The options of the Cross Sections tab Fig 3 7 is given below e Visible Check this box to display the cross section windows If the model thick ness or the exaggeration value see below is too small such that the appearance Environment Options x Appearance Cross Sections Velocity vectors Contours Visi Color_ Component Grid Inactive cell Fixed head cell IBOUND lt 0 Fixed concentration cell ICBUND lt 0 General boundary head cell Discharge well Recharge well Drain River or stream Horizontal flow barrier slurry wall Reservoir Time variant specified head i Cancel Fig 3 6 The Environment Options dialog box of PMPATH 216 3 The Advective Transport Model PMPATH Environment Options x Appearance Cross Sect ions Velocity vectors Contours r Cro
152. 30 for the numbers of rows and columns 600 for the model extent in both row and column directions and 10 for the vertical exaggeration PM generates a uniform grid based on the specified dimensions Later the grid may be refined and the layer elevations can be adjusted In this example the first and second stratigraphic units will be represented by one and two model layers respectively Note that the model extent for the J Dimension is 600 m instead of 580 m because MODFLOW counts the distance between the center of the cells of the fixed head boundaries Click OK PM changes the pull down menus and displays the generated model grid Fig 4 4 PM allows you to shift or rotate the model grid change the width of each model column or row or to add delete model columns or rows For this example you do not need to modify the model grid Refer to Section 2 1 for more information about the Grid Editor Select File Leave Editor or click the leave editor button w The next step is to specify the type of layers and the cell status array of the flow model The cell status array IBOUND array contains a code for each model cell which indicates whether 1 the hydraulic head is computed referred to as active 4 1 Your First Groundwater Model with PM 231 iii Model Grid and Coordinate System Fig 4 4 The generated model grid variable head cell or active cell 2 the hydraulic head is kept fixed at a given value ref
153. 3D e Flag A non zero value indicates that a cell is specified as a constant con centration cell In a multiple stress period simulation a constant concentration cell once defined will remain a constant concentration cell for the duration of the simulation but its concentration value can be specified to vary in different stress periods To change the concentration value in a particular stress period simply set Flag to a non zero value and assign the desired concentration value to Specified Concentration e Specified Concentration M L This value is the concentration in the cell at the beginning of a stress period 2 6 6 7 MT3D Concentration Observations Select this menu item from the MT3D menu to specify the locations of the concen tration observation boreholes and their associated observed measurement data in a Concentration Observations dialog box Its use is identical to the Head Observation dialog box see Section 2 6 1 14 The only difference is that the head observations are replaced by concentration observations 132 2 Modeling Environment 2 6 6 8 MT3D Output Control Use the Output Control MT3D MT3DMS dialog box Fig 2 71 to set the out put options of MT3D The options in this dialog box are grouped under three tabs described below e Output Terms The MT3D transport model always generates a listing file OUT PUT MT3 which documents the details of each simulation step Optionally you can save other o
154. 3D MT3DMS For cells which went dry 1E 30 Cancel Help Fig 2 36 The Modflow Output Control dialog box 2 6 The Models Menu 75 Drawdowns are the differences between the initial hydraulic heads and the calculated hydraulic heads Drawdowns in each cell are saved in the unfor matted binary file DDOWN DAT Cell by cell Flow Terms are flow terms for individual cells including four types 1 cell by cell stress flows or flows into or from an individual cell due to one of the external stresses excitations represented in the model e g pumping well or recharge 2 cell by cell storage terms which give the rate of accumulation or deple tion of storage in an individual cell 3 cell by cell constant head flow terms which give the net flow to or from individual constant head cells and 4 internal cell by cell flows which are the flows across individual cell faces that is between adjacent model cells The cell by cell flow terms are used for calculating water budgets and for particle tracking and trans port simulations by PMPATH and MOC3D The cell by cell flow terms are saved in the unformatted binary file BUDGET DAT Subsidence is the sum of the compaction of all model layers for which the interbed storage calculation is turned on see Section 2 4 2 Compaction of individual layers is the sum of the calculated compaction and the user specified starting compaction in each layer Preconsolidation head
155. 3D saves the simulation results in various files which can be controlled by selecting Models MOC3D Output Control To check the quality of the simulation results MOC3D calculates mass balance and saves the results in the run record file The mass in storage at any time is calcu lated from the concentrations at the nodes of the transport subgrid to provide summa rized information on the total mass into or out of the groundwater flow system The mass balance error will typically exhibit an oscillatory behavior over time because of the nature of the method of characteristics and the finite difference approxima 262 4 Tutorials tion The oscillations reflect the fact that the mass balance calculation is itself just an approximation Follow the steps below to generate contour maps of the calculated concentration val ues at the end of the simulation gt To generate contour maps of the calculated concentration values 1 2 Fie Value Options Help Layer gt Re tle Column _ Simulation Time Ee ej olaja je omaj rp ee 9 m es SS gt c g S g Q a i g u al I 4 g g pe a E g 527 9352 582996 8 1 1 27 D Visualization Solute Concentration IMOC3D R ATEN Select Tools 2D Visualization A Result Selection dialog box appears Select the MOC3D tab in the Result Selection dialog box Click OK to accept the default result type Solute Concentration PM displays the model grid sets
156. 7 126 9377 zl 157 1483 157 1459 z zl z x xi z z D a rm 126 9389 126 9377 140 8609 140 8625 127 1545 127 1486 101 2448 101 2354 ojo oo Pat ae lt I lt II 4 ojo oo a ofa SI lt I 157 1377 157 1331 176 9176 176 946 1 140 9689 140 9724 87163 100 2251 100 225 87163 126 9414 126 9328 87163 154 6254 154 5827 87163 126 9329 126 929 87163 140 8447 140 842 87163 127 1516 127 1423 87163 101 2362 101 235 87163 153 2795 153 2272 87163 176 8989 176 9223 87163 140 9666 140 9705 348649 100 2246 100 224 348649 126 8069 126 7789 Rane An Tan RAAT Tea anna ojo joss T 08510 D a oa Save Table Fig 2 41 The Data tab of the Time Series Curves Hydraulic Head dialog box 2 6 The Models Menu 83 Right click on the chart to open a 2D Chart Control Properties dialog box which allows the user to change the titles and axes settings Most options of this dialog box are self explanatory however the user can click the Help button for detailed descriptions of all options To zoom an area of the scatter diagram Press the Shift or the Ctrl key and hold down left mouse button Drag mouse to select a zoom area and release the mouse button Performing a zoom with the Ctrl key enlarges the selected area of a chart while not necessarily showing the axes To remove the zooming effect press the r key X Axis Time The b
157. 7 1423 87163 101 2349 101 235 87163 153 2272 153 2272 87163 176 9223 176 9223 87163 140 9705 140 9705 87163 100 2243 100 224 348649 Save Table Copy to Clipboard Fig 2 38 The Data tab of the Scatter Diagram Hydraulic Head dialog box 2 6 The Models Menu 79 Fig 2 39 Interpolation of simulated head values to an observation borehole defined in Models MODFLOW Output Control is displayed As obser vation boreholes are rarely located at cell centers simulated head values at observation boreholes need to be calculated by means of interpolation At an observation borehole screened in the i th layer single layer observa tion PM calculates the simulated hydraulic head value H by interpolating within the layer using the following equation 4 XO h Aj moai A 0 for inactive cells 2 34 Ai j l where A are the areas and h are the computed values at the center of the cells surrounding the observation borehole Fig 2 39 For a multi layer ob servation borehole the simulated head value is calculated by equation 2 33 page 72 using the H values of all screened layers Observed Value The user specified observed values in the Head Observa tions dialog box Section 2 6 1 14 are linearly interpolated to the simulation times and displayed in this column Simulation Time Displays the times at the end of each stress period or time step to which th
158. Active flag is checked To add a cell group scroll down to the end of the table and simply type the name and group number to the last blank row To delete a cell group the user selects the row to be deleted by clicking on its record selector 4 before the first column of the table then pressing the Del key After a simulation the user may select View Scatter Diagram from the MOD FLOW 2000 Parameter Estimation menu to compare the observed and calcu lated values The user may also select View Time Series Curves from the same menu to display time series curves of both the calculated and observed values 2 Flow Observation Data of the selected Cell Group contains the data pertained to the cell group marked by gt on the Cell Group table Inserting or deleting an observation row is identical to the Cell Group table a Time The observation time to which the measurement pertains is measured from the beginning of the model simulation The user may specify the ob servation times in any order By clicking on the column header or the OK button the observation times and the associated values will be sorted in ascending order b Observation values HOBS contain the flow rates observed at the obser vation times Negative values should be assigned when water leaves groundwater system the c Statistic MODFLOW 2000 reads statistics from which the weights are cal culated The physical meaning of Statistic is contr
159. Basic Flow Problems solution from equation 5 flow assigned to stream for each stress period Ne 8 FT OM AQ QS mmo NAN puores Jad 21qnd Jo spuesnou N u 70 80 90 30 40 50 60 10 20 MOYLUe8 3S Time in days since start of flood Fig 5 16 Distribution of streamflow for a 30 day flood event used for the simulation after Prudic 98 eeeelbewae done See TEET 1 1 1 1 4 1 1 1 J 1 1 1 1 3 1 1 1 2A BOS SAOGe z334 UI aHej s Wests Time in days since start of flood Fig 5 17 Model calculated river stage 316 5 Examples and Applications cludes 7 stream segments with totally 16 reaches There is one diversion segment 2 and two places where streams join segments 2 and 4 join to make segment 5 and segments 3 5 and 6 join to make segment 7 Stream stages are also computed for each reach The streams range in width from 5 to 10 ft Streambed conductance val ues also vary depending on the length and width of each stream reach The hydraulic conductivity of the streambed is 4 x 1074 ft s Columns 1 2 3 4 5 6 stream segment dots indicate section of stream used to define a segment Arrow indicates the direction of flow segment number reach number within a segment section of stream not included in model simulation
160. D PATH are given in Sections 6 3 2 6 3 4 and 6 3 5 When using MODPATH or MODPATH PLOT version 3 x follow the steps below TO READ INPUT FROM AN EXISTING RESPONSE FILE ENTER FILE NAME lt CR gt ENTER DATA INTERACTIVELY Help WHAT TO DO Just press ENTER here When running MODPATH or MODPATH PLOT at the first time a response file does not exist and the user has to enter data interactively The user specified data will be saved by MODPATH or MODPATH PLOT in the response files MPATH RSP or MPLOT RSP respectively Using a re sponse file it is not necessary to go through the input procedures unless the data for MODPATH or MODPATH PLOT need to be changed Only for MODPATH PLOT TO REDEFINE SETTINGS ENTER NAME OF FILE WITH SETTINGS DATA lt CR gt USE DEFAULT SETTINGS FOR DEVICE Help WHAT TO DO Just press ENTER here unless the settings need to be changed ENTER THE NAME FILE Help 6 5 Define PHT3D Reaction Module 397 WHAT TO DO Type path MPATH30 at this prompt Where path is the path to the directory of your model data For example if model data are saved in C PMWIN DATA type C PMWIN DATA MPATH30 at this prompt After this prompt the user enters the interactive input procedure of MODPATH or MODPATH PLOT Just follow the prompts of the programs 6 5 Define PHT3D Reaction Module Before creating a new user defined reaction module a basic knowledge of PHREEQC 2 must be obta
161. D MT3D96 dialog box Generate input files only don t start MT3D Check this option if the user does not want to run MT3D The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file MT3D BAT e OK Click OK to generate MT3D input files In addition to the input files PM creates a batch file MT3D BAT saved in the model folder When all files are generated PM automatically runs MT3D BAT in a Command Prompt window DOS box During a simulation MT3D writes a detailed run record to the file OUTPUT MT3 saved in the model folder See the previous section for details about the output terms 2 6 6 10 MT3D View MTS3D View Run Listing File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run list file OUTPUT MT3 which contains a detailed run record saved by MT3D MTS3D View Concentration Scatter Diagram This menu item is available only if Concentration Observations have been defined see Section 2 6 6 7 on page 131 Select this menu item to open a Scatter Diagram Concentration dialog box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 on page 78 except the concentration values replace the head values 2 6 The Models Menu 135 MTS3D View Concentration Time Curves This menu item is available only if Concentration Observations have been defined see Section 2 6 6 7 on page 131 Select this me
162. DFLOW Flow Packages Evapotranspiration The Evapotranspiration package simulates the effects of plant transpiration and direct evaporation in removing water from the saturated groundwater regime Evapotranspiration is defined by assigning the following parameters to each ver tical column of cells The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress periods the in put parameters can be different from period to period Note that the user may move to other layers within the Data Editor and examine the grid configuration in each layer although the values are specified for each vertical column of cells Maximum ET Rate Repay LT7 Elevation of the ET Surface hs L ET Extinction Depth d L Layer Indicator Tgr and Parameter Number Parameter Number is used to group cells where the Rgrm values are to be esti mated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps The Evapotranspiration package removes water from the saturated groundwater regime based on the following assumptions 1 When groundwater table is at or above the elevation of the ET surface hs evapo transpiration loss from the groundwater table is at the maximum ET Rate RgT M 2 No evapotranspiration occurs when the depth of the groundwater table below the eleva
163. DPATH or PMPATH format is chosen coordinates along the path of each particle are recorded in the file specified below The file contains the start ing coordinates of a particle and the coordinates at every point where a particle leaves a cell exit point In addition coordinates of intermediate points are saved whenever a particle tracking step length is reached The saved files can be used by 3D Master 23 or 3D Groundwater Explorer 22 for advanced 3D visual ization Refer to Sections 6 2 11 2 and 6 2 11 1 for the format of the MODPATH and PMPATH files 3 Type in the file name in the File edit field directly or right click the edit field and select a file from a Plot File dialog box 4 Click OK to save the file Note that cross sectional plots can only be included in the DXF or BMP format PMPATH uses the same color resolution as the video screen to capture and save Windows Bitmap files A DXF file is saved more compact and can be processed PB Save Plot As x Format z File c program files eit pmwin examples mf2k ex1 mi2kex1 def Include the lower cross section IV Include the right cross section IT Use polyline to save contours E the right mouse button on the file fields to select a file Ceat Fig 3 16 The Save Plot As dialog box 3 4 PMPATH Output Files 225 by graphics software more efficiently if the option Use Polyline to save con tours is used However some graphics software packages do not supp
164. E 00 CONSTANT HEAD 1 0105607E 03 1 7374435E 03 7 2688283E 04 HORIZ EXCHANGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 EXCHANGE UPPER 2 6107365E 03 0 0000000E 00 2 6107365E 03 EXCHANGE LOWER 0 0000000E 00 1 9322647E 03 1 9322647E 03 WELLS 0 0000000E 00 1 0000000E 10 1 0000000E 10 DRAINS 0 0000000E 00 0 0000000E 00 0 0000000E 00 RECHARGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 SUM OF THE LAYER 3 6212972E 03 3 6697080E 03 4 8410846E 05 DISCREPANCY 1 33 WATER BUDGET OF THE WHOLE MODEL DOMAIN 0000000E 00 0 0000000E 00 STORAGE 0 0000000E 00 0 CONSTANT HEAD 2 2167889E 03 3 7117251E 03 1 4949362E 03 WELLS 0 0000000E 00 1 2000003E 03 1 2000003E 03 DRAINS 0 0000000E 00 0 0000000E 00 0 0000000E 00 RECHARGE 2 6880163E 03 0 0000000E 00 2 6880163E 03 SUM 4 9048052E 03 4 9117254E 03 6 9201924E 06 DISCREPANCY 0 14 FLOW RATES BETWEEN SUBREGIONS The value of the element i j of the following flow matrix gives the flow rate from the i th region to the j th region Where i is the column index and j is the row index FLOW MATRIX 1 2 3 1 0 000 0 000 0 000 2 2 6107E 03 0 000 0 000 3 0 000 1 9323E 03 0 000 In this example the percent discrepancy of in and outflows for the model and each zone in each layer is acceptably small This means the model equations have been correctly solved To calculate the exact flow rates to the well we repeat the previous procedure for calculating subregional water b
165. E 05 3000000 2 988483E 14 6000000 1 317812E 03 6000000 1 164769E 10 6000000 1 362983E 02 6000000 1 326899E 09 6000000 1 123862E 02 eooooo0 11949609 9000000 1 229994E 02 3000000 3 111404E 08 9000000 6 638029E 02 9000000 4 282277E 07 aAAgAAA IAM AT Save Table Copy to Clipboard Save Plot As OK Cancel Help Fig 4 26 The Time Series Curves Concentration dialog box LIT x Data Chat m XAxis Time Concentration Time Curve I FixBounds J Logarithmic Lower Bound jos Upper Bound 94670000 Reset Bounds m Y Aris I FixBounds M Logarithmic Lower Bound fo Upper Bound 703 3402 Reset Bounds r Data Type M Calculated I Observed Use results of all observations 0 50000000 gt Use results of the following Time OBSNAM 1 x m Saye Table Copy to Clipboard Save Plot As OK Cancel Help Fig 4 27 The Chart tab of the Time Series Curves Concentration dialog box Concentration 4 Use the button Save Plot As to save the chart to a file or use Copy to Clipboard to copy the chart to the Windows Clipboard An image in the clipboard can be pasted into most word or graphics processing software by using Ctrl V 5 Click OK to close the Time Series Curves Concentration dialog box 4 1 3 2 Perform Transport Simulation with MOC3D In MOC3D transport may be simulated within a subgrid which is a window within the primary m
166. FLOW 2000 Parameter Estimation Run MODFLOW 2000 PEST Parameter Estimation PEST 33 34 is a program for parameter es timation The associated program is used when selecting the menu item PEST Parameter Estimation Run or MODFLOW 2000 Parameter Estimation Run PEST ASP MODFLOW 2000 Note that the latter requires PEST ASP and a special version of MODFLOW 2000 called MF2K ASP which are au tomatically installed MT3D MT3Disasingle species solute transport model which has been pre pared by Zheng 117 120 and has been improved subsequently over years The associated program is used when selecting the menu item MT3D Run MOC3D MOC3D 74 is a single species solute transport model using the method of characteristics The associated program is used when selecting the menu item MOCS3D Run MT3DMS MT3DMS 121 123 is a multi species solute transport model The associated program is used when selecting the menu item MT3 DMS SEAWAT Run If the user intends to use MT3D99 122 the MT3D99 program should be assigned to this module and the MT3D99 and MODFLOW programs must be compiled with the same compiler 3D Visualization The software Seer3D is available separately When in stalled Seer3D can be started by selecting the menu item Tools 3D Visual ization RT3D The RT3D model 25 26 27 simulates reactive flow and transport of multiple mobile and or immobile species The PM installation inc
167. Fig 5 18 Numbering system of streams and diversions after Prudic 98 5 1 Basic Flow Problems 317 5 1 8 Simulation of Lakes Folder pmdir examples basic basic8 Overview of the Problem Fig 5 19 shows an unconfined aquifer with the boundary conditions and the lo cation of a planned opencast mining site The aquifer is bounded by a no flow zone to the north and to the south To the west and east exist fixed head boundaries with the hydraulic heads h 100 m and 95 m the elevations of the aquifer top and bottom are 100 and 0 m respectively The aquifer is homogeneous and isotropic with a measured horizontal hydraulic conductivity of 0 0001 m s and vertical hydraulic conductivity of 0 00001 m s The specific yield and effective porosity are assumed to be 0 25 The specific storage coefficient is 0 0001 In the final mining phase the hydraulic head beneath the mining pit must be drawn down to the level of h 21 m Afterwards the mining pit will be filled with water to form an artificial lake Plan Vie 100 m 95m open cast mining site 2000 m Fixed head boundary h Fixed head boundary h Pe ae Cross section open cast mining site Fig 5 19 Plan and cross sectional views of the model area 318 5 Examples and Applications The task is to 1 Construct a steady state flow model and calculate the necessary abstraction
168. HA gt HAE EE BEFEETEEA A eross sec Q wT x KE Ia aa Soe 3 o et E pos cross section Fig 5 33 Simulated head distribution and catchment area of the excavation pit 342 5 Examples and Applications 5 4 2 Flow Net and Seepage under a Weir Folder pmdir examples geotechniques geo2 Overview of the Problem This example is adapted from Kinzelbach and Rausch 72 An impervious weir is partially embedded in a confined aquifer The aquifer is assumed to be homogeneous with a hydraulic conductivity of the aquifer of 0 0005 m s and a thickness of 9 m The effective porosity of the aquifer is 0 15 The boundary conditions are shown in Fig 5 34 Calculate the flow net and the flux through the aquifer for the cases that 1 the aquifer is isotropic and 2 the aquifer is anisotropic with an anisotropy factor of 0 2 Modeling Approach and Simulation Results To compute the head distribution and the corresponding flowlines it is sufficient to consider a vertical cross section of the aquifer with a uniform thickness of 1 m In this example the vertical cross section is represented by a model with a grid of one layer 65 columns and 9 rows A regular grid spacing of 1 m is used for each column and row The layer type is 0 confined Fig 5 35 shows the cross section the selected model grid and the
169. INK equivalent to NPLANE e Number of particles allowed to approximate sink cells NPSINK is used in the MMOC scheme The convention is the same as that for NPH and it is generally adequate to set NPSINK equivalent to NPLANE o Critical relative concentration gradient DCHMOC is used to select between MOC and MMOC in the HMOC solution scheme MOC is selected at cells where DCCELL gt DCHMOC MMOC is selected at cells where DCCELL lt DCHMOC 2 6 6 3 MT3D Dispersion The use of this menu item is the same as MT3DMS Dispersion See Section 2 6 2 4 on page 94 for details 2 6 6 4 MT3D Chemical Reaction Layer by Layer Chemical reactions supported by MT3D include equilibrium controlled sorption and first order irreversible rate reactions such as radioactive decay or biodegradation It is generally assumed that equilibrium conditions exist between the aqueous phase and solid phase concentrations and that the sorption reaction is fast enough relative to groundwater velocity so that it can be treated as instantaneous Consider using MT3DMS if nonequilibrium rate limited sorption needs to be simulated Use this menu item to open the Chemical Reaction Package MTRCT1 dialog box Fig 2 70 to specify the required parameters on a layer by layer basis The parameters are described below e Type of sorption Sorption is implemented in MT3D through use of the retarda tion factor R MT3D supports sorption types of Linear isotherm equili
170. Information Tab It often happens that we have some information concerning the parameters that we wish to optimize and that we obtained this information independently of the current experiment This information may be in the form of other unrelated estimates of some or all of the parameters or of relationships between parameters It is often useful to include this information in the parameter estimation process because it may lend stability to the process To define prior information first check the Active box in the Prior Information tab and then enter the prior information equation in the Prior Information column The syntax of a prior information line is Eqnam Prm Sign Coef Pnam Sign Coef Pnam Sign STAT Statp Stat flag Plot Symbol 2 57 All components of equation 2 57 must be separated by one space Following Hill and others 63 the components are defined below e Eqnam is a user supplied name up to 10 nonblank characters for a prior information equation e Prm is the prior estimate for prior information equation Eqnam Prm always needs to be specified as a native untransformed value That is even if the pa rameter is specified as being log transformed see the Parameters tab above Prm needs to be the untransformed value indicates the equal sign Sign is either or The Sign after is optional and is assumed to be unless otherwise specified e Coef is the multiplication coefficient for the paramete
171. L T Head in the river H i L Elevation of the Riverbed bottom Bri L Parameter Number Thickness of the riverbed M L and Density of River Fluid M L In a model cell containing river parameters the flow rate Q between the river and groundwater is calculated by equations 2 20 and 2 21 By default MODFLOW saves the calculated flow rates in the BUDGET DAT which can be used for water balance calculations If the groundwater hydraulic head h is greater than Rgor the leakage rate Q rry from the river to the aquifer is calculated by Qriv Criv hriv ima h if h gt Brin 2 20 The value of Qrzrv is negative if the hydraulic head h is greater than Hrry It means that water flows from the aquifer into the river and is removed from the groundwater system When h falls below the bottom of the riverbed the leakage rate through the riverbed is given by Qriv Criv j Rriv Briv if h lt Briv 2 21 2 6 1 9 MODFLOW Flow Packages Streamflow Routing The Streamflow Routing STR package Prudic 98 is designed to account for the amount of flow in streams and to simulate the interaction between surface streams and groundwater Streams are divided into segments and reaches Each reach corre sponds to individual cells in the finite difference grid A segment consists of a group of reaches connected in downstream order Streamflow is accounted for by specifying flow for the first
172. Layer Options dialog box and the layer type drop down list 4 6 The Data Editor displaying the plan view of the model grid 4 7 The Run Modflow dialog box 0 0 cece cee eee ee eee 4 8 The Water Budget dialog box 00 eee eee 4 9 The Results Extractor dialog box 0 0 e eee eee ee 4 10 The Result Selection dialog box 0 0 eee eee eee 4 11 Contours of the hydraulic heads in the first layer 4 12 The model loaded in PMPATH 0 0 022 4 13 The Add New Particles dialog box 00 e ee eee 4 14 The capture zone of the pumping well vertical exaggeration 1 4 15 The capture zone of the pumping well vertical exaggeration 10 4 16 The 100 day capture zone calculated by PMPATH 223 4 17 4 18 4 19 4 20 4 21 4 22 4 23 4 24 4 25 4 26 4 27 4 28 4 29 4 30 4 31 4 32 4 33 4 34 4 35 4 36 4 37 4 38 4 39 4 40 4 41 4 42 4 43 4 44 4 45 4 46 4 47 4 48 4 49 4 50 4 51 4 52 4 53 4 54 4 55 4 56 4 57 4 58 List of Figures The Particle Tracking Time Properties dialog box The Concentration Observation dialog box The Reaction Definition dialog box 00054 The Advection Package MT3DMS dialog box The Dispersion Package MT3D MT3DMS RT3D dialog box The Reset Matrix dialog box for chemical reaction data of M
173. Layer by Layer This menu item is available only if Sorption Parameter of the Simulation Settings RT3D dialog box see Section 2 6 4 1 is set to Use Layer by Layer mode The available settings of the Sorption Parameters RT3D dialog box Fig 2 60 are given below e Type of Sorption RT3D supports three sorption types i e linear equilibrium isotherm Freundlich nonlinear equilibrium isotherm and Langmuir nonlinear equilibrium isotherm See Section 2 6 2 6 for details e Species Select a species for which the sorption coefficients are to be specified e Sorption Coefficients Use this table to specify the required parameters on a layer by layer basis Refer to Section 2 6 6 4 for details about the sorption coefficients 2 6 4 6 RT3D Sorption Cell by Cell This menu item is available only if Sorption Parameter of the Simulation Settings RT3D dialog box see Section 2 6 4 1 is set to Use Cell by Cell mode RT3D 2 0 and later only Using the Data Editor sorption coefficients may be entered on a three dimensional cell by cell basis This option provides the ability to have different coefficients for different areas 116 2 Modeling Environment 2 6 4 7 RT3D Reaction Parameters Spatially Constant In RT3D reaction parameter values of each species can be spatially constant for the entire model or can be variable from cell to cell Select this menu item to assign spatially constant parameter values to the Reaction Parameters for
174. M Since different length units are often used by various drawing or CAD software pack ages DXF files created by those packages may not be correctly imported into PM without modifying the scale factor and the X Y values If these values are incorrect a DXF map will be displayed too small too large or outside the Viewing Window If this happens use the Environment options dialog box to define a very large Viewing Window ensuring that the map can be displayed within the window Then check the units on the imported map by moving the mouse around the map and looking at the X and Y coordinates displayed in the status bar Choose two points that are a known distance apart and check their distance with the status bar If the distance is incor rect compute a scale factor and import the map again Once the correct scale factor is found the user may shift the scaled DXF map to the desired position by using X and Y Fig 2 102 uses a triangle as an example to demonstrate the use of X Y and the scale factor The Raster Graphics Tab Using the Raster Graphics tab raster graphics saved in Windows Bitmap bmp or JPEG jpg format can be imported and geo referenced gt To import a raster graphics map 1 Click the Raster Graphics tab 196 2 Modeling Environment 2 Click the open file button and select a file from a Raster Graphics dialog box The map is displayed in the Maps Options dialog box Fig 2 103 Using the following methods to in
175. MSDSP1 DAT MSMSGSG1 DAT MTMSSSM1 DAT PHT3DADV DAT PHT3DBTN DAT PHT3DRCT DAT PHT3DDSP DAT PHT3DGCG DAT PHT3DSSM DAT PHT3D_PH DAT PHT3D_DATAB DAT INSTRUCT DAT PESTCTL DAT BCFTPL DAT DRNTPL DAT EVTTPL DAT GHBTPL DAT RCHTPL DAT RIVTPL DAT WELTPL DAT STRTPL DAT IBSTPL DAT filename GRD BORELIST DAT BORECOOR DAT 395 396 6 Supplementary Information 6 4 Using MODPATH with PM PM supports two versions version 1 x and 3 x of MODPATH and MODPATH PLOT Since MODPATH and MODPATH PLOT reads the binary model result files from MODFLOW these programs needed to be compiled with the same Fortran Compiler to ensure the binary compatibility between them The MODFLOW pro grams which come with pmp are compiled with Lahey Fortran 95 To run MOD PATH or MODPATH PLOT with PM these programs need to be compiled the same compiler too The users can however use their own compiler to compile the MOD FLOW MODPATH and MODPATH PLOT for using with pmp See Section 1 2 for details MODPATH or MODPATH PLOT must be started within a DOS Box of Win dows or in the DOS Environment When using MODPATH version 1 x released prior to September 1994 type path PATHFILE at the prompt ENTER NAME OF FILE CONTAINING NAMES AND UNITS OF DATA FILES Where path is the path to the directory of your model data PATHFILE contains the IUNIT assignments and paths and names of input data files generated by PMWIN The names of the input files for MODFLOW and MO
176. Menu This menu is used to input time initial hydraulic head values and aquifer parameters such as HK or VK Depends on the settings of the layer properties Section 2 4 2 it is possible that an aquifer parameter is required only for certain model layers or is not required for any of the model layers In the latter case the corresponding menu item will be dimmed In the former case the Data Editor will display a short indicative message data of this layer will be used in the simulation or data of this layer will NOT be used in the simulation on the status bar to indicate whether an aquifer parameter is required for the layer being edited 2 5 1 Time Selecting this menu item to display a Time Parameters dialog box The appearance of this dialog box is affected by the setting of the Modflow version Section 2 3 4 When the Modflow Version is set to gt MODFLOW 2000 MODFLOW 2005 the Transient column appears in the table of this dialog box and the Simulation Flow Type group of this dialog box is dimmed and deactivated Fig 2 16 since MODFLOW 2000 allows individual stress periods in a single simulation to be either transient or steady state instead of requiring the entire simulation to be either steady state or transient Steady state and transient stress periods can occur in any order Commonly the first stress period is steady state and produces a solution that is used as the initial condition for subsequent transient stress peri
177. N constant head boundary h 8 m eee SSS eee EZ eonetont head boundary no flow boundary Em constant head baundary h no flaw boundary 2m constant head boundery h no flaw beundary conatant head boundary h B m 5 8 Miscellaneous Topics 373 Realization 1 Safety Criterion 85 Mean Safety Criterion 85 Realization 2 Safety Criterion 87 Mean Safety Criterion 86 Realization 3 Safety Criterion 97 Mean Safety Criterion 89 7 Realization 4 Safety Criterion 48 Mean Safety Criterion 79 3 Realization 5 Safety Criterion 93 Mean Safety Criterion 82 Fig 5 61 Calculation of the mean safety criterion by the Monte Carlo method 6 Supplementary Information 6 1 Limitation of PM This section gives the size limitation of PM Refer to the documentation of individual packages for their assumptions applicability and limitations 6 1 1 Data Editor Maximum number of layers 300 Maximum number of stress periods 1000 Maximum number of cells along rows or columns 2000 Maximum number of cells in a layer 1000000 Maximum number of polygons in a layer 20 Maximum number of vertex nodes of a polygon 40 Maximum number of stream segments 1000 Maximum number of tributary segments of each stream segment 10 Maximum number of reservoirs 20 Maximum number of observed stages of each reservoir 200 Max
178. No 2 No 3 0 738 ion No 3 No 4 0 644 No 4 No 5 No 5 No 6 No 6 No 7 No 7 No 8 No 8 No 9 No 3 No 10 No 10 No 11 No 11 No 12 No 12 No 13 No 13 No 14 No 14 No 15 No 15 No 16 No 16 No 17 No 17 No 18 No 18 No 19 No 19 No 20 No 20 No 21 No 21 No 22 No 22 No 23 No 23 No 24 Fig 2 45 The Stoichiometry tab of the Simulation Settings MT3DMS SEAWAT dialog box surement unit can be used for solute concentration provided DRHODC and the reference fluid density DENSEREF see below are set properly CRHOREF This item is used by SEAWAT only CRHOREF is the reference concentration for the species For most simulations CRHOREF should be specified as zero e Stoichiometry tab Fig 2 45 is used to specify yield coefficients or stoichiomet ric ratios between species pairs A yield coefficient Y j between two species means consuming of one mass unit of species 1 will yield Y 2 mass units of species 2 For example if Y 2 3 then consuming of 1 g of species 1 will yield 3 g of species 2 The stoichiometric ratio Fip between species 1 and species k means one mass unit of species 1 reacts with Flk mass units of species k For example if F14 3 then g of species 1 will react with 3 g of species 4 e SEAWAT tab Fig 2 46 is used to specify SEAWAT simulation control parame ters The available settings are
179. OW even without the wetting capability but problems are more likely to occur when the wetting capability is used Symptoms of a problem are slow convergence or divergence combined with the frequent wetting and drying of the same cells It is normal for the same cell to con vert between wet and dry several times during the convergence process but frequent conversions are an indication of problems As a matter of fact situations exist where the real solution oscillates such as in the case of a well causing a drawdown which makes the well cells fall dry This in turn switches off the well and leads to a rise of the water table and wetting of the well cell etc The user can detect such situations by examining the model run record file OUTPUT DAT a message is printed each time a cell converts The basic tools at hand to combat convergence problems are Choose vertical discretization such that only few cells will fall dry Choose wetting from below only i e set THRESH lt 0 Change to a different preconditioner if the PCG2 solver is used Change to a different solver Increase the modulus of THRESH Increase WETIT Decrease pumping rates of wells 2 6 1 13 MODFLOW Solvers To calculate heads in each cell in the finite difference grid MODFLOW prepares one finite difference equation for each cell expressing the relationship between the head at a node and the heads at each of the six adjacent nodes at the end of a time step Because each equat
180. P 18 000 m Adjoining Recharge hillside Zone 1 Recharge Confining unit Fig 5 30 Physical system for test case 1 Adapted from Hill and others 63 5 3 Parameter Estimation and Pumping Test 335 Stresses on the system include 1 areal recharge to aquifer 1 in the area near the stream zone 1 and in the area farther from the stream zone 2 and 2 groundwater abstraction from wells in each of the two layers The pumping rates from aquifers 1 and 2 are assumed to be the same Modeling Approach and Simulation Results For the finite difference method the system is discretized into square 1 000 m by 1 000 m cells so that the grid has 18 rows and 18 columns Three model layers are used Layers 1 and 3 represent aquifers 1 and 2 respectively Layer 2 represents the confining unit A fairly small value of 1 x 107 m s is assigned to horizontal hydraulic conductivity of layer 2 so that the groundwater flows vertically through the confining unit Time discretization for the model run is specified to simulate a period of steady state conditions with no pumping followed by a transient state period with a constant rate of pumping The steady state period is simulated with one stress period having one time step The transient period is simulated with four stress periods the first three are 87162 261486 and 522972 seconds long and each has one time step the fourth is 2 356745 x 107 seconds long and has 9 time steps a
181. Proportions table is not used here because the subsidence is the sum of the compactions in all model layers The specified subsidence values are solely for display purposes and not used by PEST or MODFLOW 2000 for parameter estimation 2 6 1 17 MODFLOW Compaction Observations Select this menu item to open a Compaction Observation dialog box The use of this dialog box is identical to the Head Observation dialog box except the Layer Pro portion table The layer Proportions values are used as a flag here When displaying compaction time curves or a compaction scatter diagram the sum of the compaction 74 2 Modeling Environment values of the layers which have a positive layer proportion value is assign to the observation borehole The specified compaction values are solely for display purposes and not used by PEST or MODFLOW 2000 for parameter estimation 2 6 1 18 MODFLOW Output Control The primary output file of MODFLOW is the run listing file OUTPUT DAT MOD FLOW calculates a volumetric water budget for the entire model at the end of each time step and saves it in the run listing file The volumetric water budget provides an indication of the overall acceptability of the numerical solution In numerical so lution techniques the system of equations solved by a model actually consists of a flow continuity statement for each model cell Continuity should therefore also exist for the total flows into and out of the entire model or a
182. Run MT3D MT3D96 dialog box Fig 2 73 are de scribed below e The File Table has three columns Generate Prior to running a transport simulation PM uses the user specified data to generate input files for MT3D An input file will be generated if it does not exist or if the corresponding Generate box is checked The user may click on a box to check or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs 134 2 Modeling Environment Run MT3D MT3D96 x Destination File v Basic Transport Package c program filesseitspmwinsexamplesSsample1 mtbtn1 Vv Advection Package c program files eit pmwin examples sample mtady1 Vv Dispersion Package c program files eit pmwin examplessample1 mtdsp1 Vv Chemical Reaction Package c program files eit pmwin examples sample1 mtrct1 Vv Sink and Source Mixing Package c program files eit pmwin examples sample1 mtssm1 Options J Regenerate all input files I Generate input files only don t start MT3D Fig 2 73 The Run MT3
183. Run RT3D dialog box Fig 2 62 are described below Run RT3D Generate Destination File Basic Transport Package c simcore pmwin8 examples transport transportd it3d Advection Package c simcore pmwin8 examples transport transport4 it3d Dispersion Package c simcore spmwin8 examples transport transport4 t3d Chemical Reaction Package c simcore pmwin8 examples transport transport4 rtad Generalized Conjugate Gradient Solver F c simcore pmwin8 examples transport transport4 t3d Sink and Source Mixing Package c simcore pmwin8 examples transport transport4 it3d Options I Regenerate all input files I Generate input files only don t start RT3D Fig 2 62 The Run RT3D dialog box e The File Table has three columns 118 2 Modeling Environment Generate Prior to running a transport simulation PM uses the user specified data to generate input files for RT3D An input file will be generated if it does not exist or if the corresponding Generate box is checked The user may click on a box to check or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This
184. S SEAWAT Mass Loading Rate 103 2 6 2 10 MT3DMS SEAWAT Solver GCG 103 2 6 2 11 MT3DMS SEAWAT Concentration Observations 104 2 6 3 2 6 4 2 6 5 2 6 6 2 6 7 Contents 2 6 2 12 MT3DMS SEAWAT Output Control 2 6 2 13 MT3DMS SEAWAT Run 2 6 2 14 MT3DMS SEAWAT View 2 6 4 1 RT3D Simulation Settings 2 6 4 2 RT3D Initial Concentration 2 6 4 3 RT3D Advection 2 6 4 4 RT3D Dispersion 2 6 4 5 RT3D Sorption Layer by Layer 2 6 4 6 RT3D Sorption Cell by Cell 2 6 4 7 RT3D Reaction Parameters Spatially Constant 2 6 4 8 RT3D Reaction Parameters Spatially Variable 2 6 4 9 RT3D Sink Source Concentration 2 6 5 1 MOC3D Subgrid 2 6 5 2 MOC3D Initial Concentration 2 6 5 3 MOC3D Advection 2 6 5 4 MOC3D Dispersion amp Chemical Reaction 2 6 5 5 MOC3D Strong Weak Flag 2 6 5 6 MOC3D Observation Wells 2 6 5 7 MOC3D Sink Source Concentration 2 6 5 8 MOC3D Output Control 2 6 5 9 MOC3D Concentration Observation 2 6 5 10 MOC3D Run 2 6 6 1 MT3D Initial Concentration 2 6 6 2 MT3D Advection 2 6 6 3 MT3D Dispersion 2 6 6 4 MT3D Chemical Reaction Layer by Layer 2 6 6 5 MT3D Chemical Reaction Cell by Cell 2 6 6 6 MT3D
185. ST 172 RT3D 117 run listing file MOC3D 126 MODFLOW 78 MODFLOW 2000 147 MT3D 134 MT3DMS SEAWAT 108 pest 174 rt3d 118 Save Plot As 26 SCALE 154 scatter diagram MOC3D 126 MODFLOW 78 MODFLOW 2000 148 MT3D 134 MT3DMS SEAWAST 108 PEST 175 RT3D 118 SEAWAT 4 26 84 Examples 368 Prescribed Fluid Density 102 seepage 342 344 semi analytical particle tracking method 204 semivariance 180 sensitivity composite observation 175 composite parameter 175 composite scaled 148 dimensionless scaled 147 one percent scaled 148 sensitivity analysis MODFLOW 2000 141 sensitivity arrays one percent scaled 148 Sensitivity Process 1 Simulation Settings MODFLOW 2000 136 MT3DMS SEAWAT 85 PEST 151 PHT3D 109 113 sink source concentration MT3D 131 MT3DMS SEAWAT 102 RT3D 116 SIP solver package 67 solution methods comparison 62 solvers 61 DE45 63 GCG 103 GMG 68 PCG2 65 SIP 67 SSOR 67 sorption distribution coefficient 99 first order kinetic 98 Freundlich isotherm 98 Langmuir isotherm 98 linear equilibrium isotherm 98 SOSC 140 specific storage 38 specific yield 38 SSOR solver package 67 stochastic modeling 372 stoichiometry 87 storage coefficient 30 38 Streamflow routing package 53 subgrid 118 subsidence 75 351 subsidence observations 73 subsidence scatter diagram MODFLOW 81 SURFER 177 TECKONEM 177 telescoping flow model 22 Theis Solution 328 time 33 time
186. ST the observation times and the associated HOBS Weight and Statistic values are linearly interpolated to the simulation times at the end of each stress period or time step The interpolated values are then used for parameter estimation When running MODFLOW 2000 the specified observation times and values are used for parameter estimation directly without interpolation HOBS The hydraulic head observed at the observation time Weight The Weight of an observation gives a relative confidence level of the observed value The higher the value the better is the measurement The weight can be set at zero if needed meaning that the observation takes no part in the calculation of the objective function during a param eter estimation process but it must not be negative Refer to the docu ments of PEST 33 34 36 for the function of weights in the parameter estimation process Statistic MODFLOW 2000 reads statistics from which the weights are calculated The physical meaning of Statistic is controlled by the Options tab see below 2 6 The Models Menu 73 The Options Tab This tab is only used by MODFLOW 2000 for parameter estimation There are two options e Parameter Estimation Option When the option temporal changes in hydraulic heads are used as observations is selected the temporal change is calculated as a specified hydraulic head minus the first hydraulic head specified for that location The first hydraulic head at a loc
187. Simcore Software Processing Modflow An Integrated Modeling Environment for the Simulation of Groundwater Flow Transport and Reactive Processes September 13 2010 Contents A MntroductiOn secs ii ts cee Rete aes hohe ened ae ieee 1 1 1 Supported Computer Codes 0 eee ee 1 1 2 Compatibility Issues sennu eeunenn eee eee ee 5 2 Modeling Environment 0 eee ee 7 21 Phe Gnd Editor perne tiee eee ieee teh a oe 8 2 2 The Data Editor o5 6 esiasitee gS Fx SDA ATS BE RS See A Went hs 13 2 2 1 The Cell by Cell Input Method 0 16 2 2 2 The Polygon Input Method 0 eee ee ee 17 2 2 3 The Polyline Input Method 00 19 2 2 4 Specifying Data for Transient Simulations 20 223 Phe File Menus si 24c acy eee ectiene yet n yeee Sola Male aE wee beste 21 23k New Model rre 0 ona eb te INARA oe CaN eS 21 2 3 2 Open Model sea sates ata an she oe BA ee oO 21 2 3 3 Convert Model miese cis to aid ee RON ed ee es 21 253 4 Preferences seu sisted Geis Adee tase os MRED gt hea Rls E 23 2 335 Save PlOtAS i e Added ened Seid iw a s as 26 23 6 Print Plotesc33 seere is hata E ee Saas pls ha ae a s 26 2 357 Animation e seneese Cases eea TEE heii Wen Maier es 27 24 The Grid Menu oie 20sec eels Gan bee ea ah eae ae weds 27 ZAT MESH SIZE Bess e e Boe Fad Meee Sees E ee te hee 27 2 42 Layer Property suedia
188. T3DMS The Output Control MT3D Family dialog box The Run MT3DMS dialog box 0 00 e eee ee eee ee Contours of the concentration values at the end of the simulation The Time Series Curves Concentration dialog box The Chart tab of the Time Series Curves Concentration dialog box The Subgrid for Transport MOC3D dialog box The Parameters for Advective Transport MOC3D dialog box The Dispersion Chemical Reaction MOC3D dialog box The Output Control MOC3D dialog box 0 The Run Moc3d dialog box 0 0 2 ee eee eee Contours of the concentration values at the end of the simulation The Time Series Curves Concentration dialog box The Chart tab of the Time Series Curves Concentration dialog box The Head Observation dialog box 0c eee ee eee The List of Parameters PEST dialog box 00005 The Run PEST dialog box 0 0 2 ee eee The Scatter Diagram dialog box 0 The Chart tab of the Scatter Diagram dialog box The Animation dialog box 00 0 2 eee eee ee Configuration of the hypothetical model The Model Grid and Coordinate System dialog box Model grid after the refinement 00 0 000008 Model Boundaries 0 e a E A O SE E Steady state head distribution
189. The available Result Types are concentration and velocity terms The simulation time from which the result is read can be selected from the Total Elapsed Time drop down box This drop down box is empty if the selected simulation result does not exist MT3D The primary result of MT3D is concentration When using MT3D96 two additional result types i e solute mass and sorbed mass can be selected The simulation time from which the result is read can be selected from the Total Elapsed Time drop down box This drop down box is empty if the selected simulation result does not exist MT3DMS The primary result of MT3DMS is concentration When using MT3D99 122 two additional result types i e solute mass and sorbed mass can be selected The species number and simulation time from which the re sult is read can be selected from the Species Number and Total Elapsed Time drop down boxes These drop down boxes are empty if simulation results do not exist RT3D The primary result of RT3D is concentration The species number and simulation time from which the result is read can be selected from the Species Number and Total Elapsed Time drop down boxes These drop down boxes are empty if simulation results do not exist Save and Read To extract a certain result type simply click the Read button The spreadsheet is saved by clicking the Save button and specifying the file name and the file type in a Save Matrix As dialog box There are four
190. The bottom of the excavation is 3 m above the aquifer bottom The task is to calculate the inflow into the pit and show head contours and catch ment area of the pit Modeling Approach and Simulation Results The aquifer is simulated using a grid of one layer 40 columns and 19 rows A regular grid spacing of 50 m is used for each column and row The layer type is 1 uncon fined To simplify the simulation use of symmetry is made by modeling only half the domain The river and the pit are modeled as fixed head boundaries with hydraulic heads of h 5 m and 3 m respectively All other boundaries are no flow boundaries The distance between the eastern no flow boundary and the pit is not known a pri ori and must be selected large enough so that the pit does not influence it Whether the choice was adequate can be easily checked by increasing the sizes of the last few columns and calculating again If the results do not change appreciably the first computation was fine Fig 5 33 shows the head contours the catchment area of the excavation and two cross sections Using the Water budget calculator the inflow into the pit is calculated at 2 x 0 0129 m s 0 0258 m 3 s 5 4 Geotechnical Problems 341 Plane view sa sy no flow boundary gt y 900 m excavation pit 200 x 100 m h 3m River water level h 5m A A A Cross section tion ay am meee hert
191. To specify the initial hydraulic head 1 Select Parameters Initial amp Prescribed Hydraulic Heads to display the model grid Move the grid cursor to the first layer Select Value Reset Matrix or press Ctrl R and enter 8 in the dialog box then click OK Move the grid cursor to the cell 1 1 1 and press the Enter key or the right mouse button to display a Cell Value dialog box Enter 9 into the Cell Value dialog box then click OK Now turn on duplication by clicking on the duplication button Pal Move the grid cursor from the upper left cell 1 1 1 to the lower left cell 1 30 1 of the model grid The value of 9 is duplicated to all cells on the west side of the model Turn on layer copy by clicking the layer copy button Move to the second layer and the third layer by pressing PgDn twice The cell values of the first layer are copied to the second and third layers Select File Leave Editor or click the leave editor button w gt To specify the horizontal hydraulic conductivity i Select Parameters Horizontal Hydraulic Conductivity PM displays the model grid Move the grid cursor to the first layer Select Value Reset Matrix or press Ctrl R enter 0 0001 in the dialog box then click OK Move the grid cursor to the second layer Select Value Reset Matrix or press Ctrl R enter 0 0005 in the dialog box then click OK Move the grid cursor to the third layer
192. User Specified Calculated CTransmissivity varies Horizontal Vertical Anisotr Anisotri Storage Transmissivity Leakance Coefficient 3 Confined Unconfined 1 w Calculated User Specified Transmissivity varies 0 Confined 1 VK Calculated User Specified 0 Confined fa VK Calculated User Specified 0 Confined 1 Calculated User Specified 0 Confined fi p Calculated User Specified 0 Confined Calculated User Specified 0 Confined Calculated User Specified Fig 2 14 The Layer Property dialog box 2 4 The Grid Menu 29 Note that the LPF package uses only two layer types confined and convertible Layer type 0 will be interpreted by the LPF package as confined and all other layer types will be interpreted as convertible layers i e the layers are convertible between confined and unconfined Horizontal Anisotropy The ratio of the horizontal hydraulic conductivity along columns to hydraulic conductivity along rows The latter is specified by selecting Parameters Horizontal Hydraulic Conductivity When the LPF package is used a positive Horizontal Anisotropy value indi cates that horizontal anisotropy is constant for all cells in the layer and the anisotropy is the specified value A negative value indicates that horizontal anisotropy can vary at each cell in the layer The cell by cell anisotropy val ues are specified by selecting
193. When sharp concentration fronts are present the advection term is solved by MOC through the use of moving particles dynamically distributed around each front Away from such fronts the advection term is solved by MMOC The criterion for controlling the switch between the MOC and MMOC schemes is given by DCHMOC see below Particle Tracking Algorithm MT3D provides three particle tracking options a first order Euler algorithm a fourth order Runge Kutta algorithm and a combi nation of these two Using the first order Euler algorithm numerical errors tend to be large unless small transport steps are used The allowed transport step t of a particle is determined by MT3D using equation 2 35 on page 91 The basic idea of the fourth order Runge Kutta method is to calculate the particle velocity four times for each tracking step one at the initial point twice at two trial midpoints and once at a trial end point A weighted veloc ity based on values evaluated at these four points is used to move the parti cle to a new position The fourth order Runge Kutta method permits the use of larger tracking steps However the computational effort required by the fourth order Runge Kutta method is considerably larger than that required by the first order Euler method For this reason a mixed option combining both methods is introduced in MT3D The mixed option is implemented by automatic selection of the fourth order Runge Kutta algorithm for particles lo
194. Y fon 292 4 Tutorials Z TUTORIAL3 PMS Processing Modflow Pro See Ele Value Options Heip 3 ESEA e T n ea mn a Well2 Se Ss S a Well1 Well3 South Granite Hills Fig 4 53 Define the river using a polyline River Parameters x m Layer Option apply to the selected polyline Assign layer number manually 7 m Parameters apply to the selected vertex Vv Active Hydraulic Conductivity of Riverbed L T fe ALL Headin the River Li fis4 ALL Elevation of the Riverbed Bottom L 17 4 au Width ofthe River L 100 au Thickness of Riverbed Li ALL Parameter Number j0 CALL Layer Number CALL Cancel Help Fig 4 54 Parameters of the upstream vertex 8 Right click on the last vertex of the polyline on the downstream side to open a River Parameters dialog box and enter the values as shown in Fig 4 55 then click OK to close the dialog box The parameters specified to the vertices are used to calculated the cell properties along the trace of the polyline Refer to Section 2 6 1 8 page 51 for details 9 Select File Leave Editor or click the leave editor button E 4 3 Aquifer System with River 293 x r Layer Option apply to the selected polyline Assign layer number manually Parameters apply to the selected vertex M Active Hydraulic Conductivity of Riverbed L T R tC A Headinthe Rivert i74 ALL Elevation of the Riverbed Bottom L15
195. _2 Parabolic Relative T E Parabolic Relative T Parabolic Relative T G Parabolic Relative r vays Parabolic Relative Y i Parabolic Relative Y Parabolic Relative X E Parabolic Relative T E Parabolic Relative Always_ Parabolic Relative T Parabolic Relative M bi Parabolic Relative Parabolic Relative Parabolic s Save OK Cancel Help Fig 2 80 The Parameter Groups tab of the Simulation Settings PEST dialog box Number is the group number The maximum number of parameter groups is 150 Description A text describing the estimated parameter can be entered here op tional for example Transmissivity Group 1 A maximum of 120 characters is allowed 156 2 Modeling Environment INCTYP and DERINC INCTYP defines the type of parameter increment per turbation used for forward difference calculation of derivatives with respect to any parameter belonging to the group INCTYP can be Relative Absolute or Rel_to_max INCTYP Relative The parameter increment is calculated as a fraction of the current value of that parameter that fraction is specified in DERINC A DERINC value of 0 01 is often appropriate INCTYP Absolute The parameter increment is fixed at the value of DER INC No suggestion for an appropriate DERINC value can be provided for this option the most appropriate increment will depend on the parameter magnitudes
196. a tion problem is possible Furthermore this simplification is carried out in a way that is mathematically optimal with respect to the dataset available for calibration Thus it effectively allows the estimation of parameter combinations rather than parame ters themselves these combinations being such as to be most receptive to the data at hand In this way the problem simplification necessary to achieve numerical stability of the parameter estimation process is undertaken by the process itself Furthermore the inclusion of many parameters in the model calibration process can be justified by observing that the inclusion of such parameterization detail allows the truncated SVD mechanism more flexibility in determining an appropriate simplification strat egy than by undertaken preemptive simplification through reducing the number of model parameters externally to the parameter estimation process The required settings for using PEST s SVD functionality are given in the SVD Truncated Singular Value Decomposition group of Fig 2 82 and are explained below e Activate SVD for solution of inverse problem Check this box to activate PEST s SVD functionality e Set PEST variables RLAMBDAI to zero and NUMLAM to one Check this box to set Marquardt lambda RLABMDA1 and the number of trial lambdas NUM LAM to the values recommended by the PEST manual e Create complete SVD output file uncheck this box to save only eigenvalues to the output file
197. a per sector 1 Per Sector points are found in a sector the program uses the other nearest points found in the entire model The valid range of Data Per Sector is SIMPLE 3 lt Data Per Sector lt 30 QUADRANT 1 lt Data Per Sector lt 7 OCTANT 1 lt Data Per Sector lt 3 The search method defaults to OCTANT search Octant or quadrant searches are usually used when the measurement points are grouped in clusters These search methods force the interpolation programs to use measurement data points radially distributed around the model cell They usually introduce more smoothing than a SIMPLE search Note that the entries in Search Method are ignored when Renka s triangulation algorithm is used 2 7 The Tools Menu 183 Output file name c eagle model eagle we m Parameters Number of Realizations 1 to 999 fo Mean Value 0910 30t0 30 2 Standard Deviation log10 Oto 30 5 Correlation Length Field width along rows 0to1 1 Correlation Length Field Width along columns 0 to 1 1 Number of Rows 2 to 500 154 Number of Columns 2 to 500 179 Help Close Go Fig 2 90 The Field Generator dialog box 2 7 3 The Field Generator The Field Generator Frenzel 47 can generate fields with heterogeneously dis tributed transmissivity or hydraulic conductivity values This allows the user to perform stochastic modeling by considering parameter distributions within PM In stochastic mode
198. a ref erence pressure of zero Minimum Fluid Density DENSEMIN If DENSEMIN gt 0 If the computed fluid density is less than DENSEMIN the density value is set to DENSEMIN If DENSEMIN 0 The computed fluid density is not limited by DENSEMIN Maximum Fluid Density DENSEMAX If DENSEMAX gt 0 If the computed fluid density is greater than DENSE MAX the density value is set to DENSEMAX 2 6 The Models Menu 89 Tf DENSEMAX 0 The computed fluid density is not limited by DENSEMAX Density Options uncoupled mode When the all Density On boxes in the Species tab are cleared i e SEAWAT runs in a uncoupled mode the user has the option to determine the density of the source fluid at wells river and general head boundaries If Reference Fluid Density is selected then density value of the source fluid is equal to DENSEREF otherwise the user specified density values to the respective packages will be used Simulation Settings MT 3DMS SEAWAT Simulation Mode Variable Density Flow and Transport with SEAWAT Type of Reaction No kinectic reaction is simulated Species T3099 SEAWAT SEAWAT Simulation Controls I Activate the variable density water table corrections IWTABLE Method for calculating intermodal density values upstream weighted Flow and transport coupling procedure Non Linear Iterative Maximum Number of Non linear Coupling Iterations 50 Density change convergen
199. above the stream the upper aquifer and confining unit are missing Under natural conditions recharge flows through the system to the stream Under stressed conditions two wells with draw water from the lower aquifer If enough water is pumped cells in the upper aquifer will desaturate Removal of the stresses will then cause the desaturated areas to resaturate The task is to construct a model to compute the natural steady state head distri bution and then calculate the head distribution under the stressed condition When solving for natural conditions the top aquifer initially is specified as being entirely dry and many cells must convert to wet When solving for pumping condition the top aquifer is initially specified to be under natural conditions and many cells must convert to dry Modeling Approach and Simulation Results The model consists of two layers one for each aquifer Since horizontal flow in the confining bed is small compared to horizontal flow in the aquifers and storage is not a factor in steady state simulations the confining bed is not treated as a separate model layer The effect of the confining bed is incorporated in the value for vertical leakance Note that if storage in the confining bed were significant transient simula tions would require that the confining layer be simulated using one or more layers The confining layer must also be simulated if you intend to calculate pathlines with PMPATH or to simulate sol
200. ace are entered explicitly or in m mol when the amount of surface sites is coupled to a pure phase or a kinetic reactant Mass defines the mass of solid and is used to calculate the surface area Al though a value must always be specified here it is only used when the number of sites and mass are defined explicitly i e when not coupled to a pure phase or kinetic reactant Phase Reactant Switch Phase Reactant is an optional argument to define a pure phase or kinetic reactant to which the surface binding site must be coupled The number of moles of surface sites will be calculated from the number of moles of the phase reactant SWITCH is an optional argument to define whether a pure phase is used Phase Reactant equilibrium phase or a kinetic reactant Phase Reactant kinetic reactant Phase Reactant only works in conjunction with Phase Reactant that is there is no need to specify it unless Phase Reactant is defined If no value is specified the default is equilibrium phase e Options Simulation Options Temperature of the aqueous solution is is the temperature in Celsius used in chemical reactions for which a temperature dependence is defined in the database file The default value is 25C Output File Format determines ASCII files extension ACN and or Bi nary files UCN that contain the computed concentrations for all grid cells and for all output times that are defined in the PHT3D Output Control CB_OFFSET i
201. active cell and the four hori zontally adjacent cells can cause the cell to become wet A dry cell or an inactive cell can be turned into an active cell if the head from the previous iteration in a neighboring cell is greater than or equal to the turn on threshold TURNON TURNON BOT THRESH 2 29 where BOT is the elevation of the bottom of the cell To improve the stability of the numerical solution a neighboring cell cannot become wet as a result of a cell that has become wet in the same iteration only variable head cells either immediately below or horizontally adjacent to the dry cell can cause the cell to become wet When a cell is wetted its IBOUND value is set to 1 which indicates a variable head cell vertical conductance values are set to the orig inal values and the hydraulic head h at the cell is set by using one of the following equations h BOT WETFCT hn BOT 2 30 h BOT WETFCT THRESH 2 31 where hn is the head at the neighboring cell that causes the dry cell to wet and WET FCT is a user specified constant called the wetting factor The user may select between equations 2 30 and 2 31 in the Wetting Capability dialog box Fig 2 29 This dialog box appears after selecting Models MODFLOW Flow Packages Wetting Capability The dialog box allows the user to specify the iteration interval for attempting to wet cells IWETIT Wetting is attempted every IWETIT iterations When using the PCG2 solver
202. along the trace of the polyline and the value Cg is obtained by Ca K L 2 5 where L is the length of the drain within a cell The discharge rate to a drain cell Qa is calculated by Qa Ca h d 2 6 where h is the hydraulic head in a drain cell By default MODFLOW saves the calculated discharge rates in the BUDGET DAT Parameter Number Since Cg is usually unknown it must be estimated Parameter Number is used to group cells where the C4 values are to be es timated by the parameter estimation programs MODFLOW 2000 Section 2 6 7 or PEST Section 2 6 8 Refer to the corresponding sections for pa rameter estimation steps The value of Parameter Number is assigned to all model cells downstream from a vertex until the next vertex redefines the pa rameter number Drain Bottom Elevation L This value is used by SEAWAT to calculate reference head considering the density effect to to accurately simulate the flow of variable density ground water to a drain The ALL button Click the ALL button of a property to copy the property value to all other active vertices e When using the Cell by cell or Polygon input methods the following values are to be assigned to model cells of a drain system See the explanations above for the definition of the input values Drain hydraulic conductance Ca L T Elevation of the Drain d L Parameter Number and Drain Bottom Elevation L 2 6 The Models Menu 41 2 6 1 2 MO
203. an active remediation can be simulated Simula tions could potentially be applied to scenarios involving contaminants such as heavy metals explosives petroleum hydrocarbons and or chlorinated solvents PHT3D 96 97 PHT3D couples MT3DMS 123 for the simulation of three dimensional advec tive dispersive multi component transport and the geochemical model PHREEQC 2 91 for the quantification of reactive processes PHREEQC 2 in its original version is a computer program written in the C programming language that is designed to perform a wide variety of low temperature aqueous geochemical cal culations PHT3D uses PHREEQC 2 database files to define equilibrium and ki netic e g biodegradation reactions For the reaction step PHT3D simulations might include 1 Equilibrium complexation reaction speciation within the aque ous phase 1 Kinetically controlled reactions within the aqueous phase such as biodegradation 3 Equilibrium dissolution and precipitation of minerals 4 Kinetic dissolution and precipitation of minerals 5 Single or multi site cation exchange equilibrium and 6 Single or multi site surface complexation reac tions SEAWAT 51 76 77 SEAWAT is designed to simulate three dimensional variable density saturated groundwater flow and transport The original SEAWAT program was devel oped by Guo and Langevin 51 based on MODFLOW 88 and an earlier ver sion of MT3DMS 121 The program has subsequently been modi
204. and MODELRUN BAT in the model folder When all files are generated PM automatically runs PEST BAT in a Command Prompt window DOS box PEST BAT will call the other batch file MODELRUN BAT During a parameter estimation process PEST prints the estimated parameter values to the run record file PESTCTL REC in the model folder and writes the estimated parameter values to the corresponding input files of MODFLOW BCE DAT WEL DAT etc So after a parameter process the simulation results of MODFLOW are updated by using the most recently estimated parameter values PEST does not modify the original model data This provides a greater security to the model data since a parameter estimation process does not necessarily lead to a success 2 6 8 5 PEST Parameter Estimation View PEST Parameter Estimation View Run Record File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run record file PESTCTL REC which contains the optimized value of each adjustable parameter together with that parameter s 95 confidence interval It tabulates the set of field measurements their optimized model calculated counterparts the difference between each pair and certain functions of these differences 174 2 Modeling Environment PEST Parameter Estimation View Forward Run Listing File During a parameter estimation process forward runs are repeated and the run record is saved in the listing file OUTPUT DAT Listing
205. and tops 3 2 PMPATH Modeling Environment The PMPATH modeling environment Fig 3 4 consists of the Worksheet the cross section windows the tool bar and the status bar They are described in the following sections 3 2 1 Viewing Window and cross section windows PMPATH as well as PM use the same spatial discretization convention as MOD FLOW An aquifer system is discretized into mesh blocks or cells An K I J indexing system is used to describe the locations of cells in terms of layers rows and columns The K I and J axes are oriented along the layer row and column directions respectively The origin of the cell indexing system is located at the upper top left cell of the model MODFLOW numbers the layers from the top down an increment in the K index corresponds to a decrease in elevation z PMPATH always displays the model grid parallel to the Viewing Window while the user may shift and rotate a model grid by giving the rotation angle A and the coordinates Xo Yo of the upper left corner of the grid The relation between the model grid and the real world x y z coordinate system is illustrated in Fig 3 4 The Viewing Window displays the plan view of the current model layer and the pro jection of pathlines on the horizontal plane The cross section windows display the projection of pathlines on the IK and JK planes The Environment Options dialog 3 2 PMPATH Modeling Environment 209 local vertical coordinate for s
206. ange Stress Period button EH to open a Temporal Data dialog box select Period 2 then click the Edit Data button The status bar displays Period 2 indicating that you are entering data for stress period 2 6 Use the above procedure to change the recharge flux for the entire grid to 0 00075 the values for the layer indicator and recharge option remain the same 7 Select File Leave Editor or click the leave editor button ee Before running a transient simulation it is necessary to specify storage terms which account for the amount of water stored or released from aquifer matrix due to changes in hydraulic heads For an unconfined layer MODFLOW requires the storage term specific yield gt To specify the specific yield 1 Select Parameters Specific Yield 2 Select Value Reset Matrix to set the entire grid to 0 06 3 Select File Leave Editor or click the leave editor button w gt To run the transient model 1 Select Models MODFLOW Run 2 Click OK to accept the warning regarding the Effective Porosity 3 Click OK in the Run Modflow dialog box to generate the required data files and to run MODFLOW you will see a DOS window open and MODFLOW performs the iterations required to complete the flow simulation By default the simulation results at the end of each time step are saved Refer to Section 2 6 1 18 page 74 for more about Output Control 4 Press any key to exit the DOS Window gt To create head cont
207. arame ters Horizontal Hydraulic Conductivity The menu item Horizontal Anisotropy is dimmed and cannot be used with the Block Centered Flow BCF package The cell by cell horizontal anisotropy values of a layer are used only when the Horizontal Anisotropy value of the layer in the Layer Options dialog box Fig 2 14 page 28 is negative 2 5 The Parameters Menu 37 2 5 5 Vertical Leakance and Vertical Hydraulic Conductivity The BCF package uses the vertical leakance VCONT values to formulate the flow rate equation between two vertically adjacent cells As discussed in Section 2 4 2 the user may either specify the vertical leakance values directly or specify the vertical hydraulic conductivity values and let PM calculate the required VCONT values When Vertical Leakance of a layer in the Layer Property dialog box Fig 2 14 is User specified the user specified vertical leakance values of that layer are used in the simulation When Vertical Leakance is calculated PM calculates the VCONT values and uses them in the simulation Refer to Section 2 4 2 for details 2 5 6 Vertical Anisotropy and Vertical Hydraulic Conductivity The Layer Property Flow LPF package supports the use of the cell by cell ver tical hydraulic conductivity or vertical anisotropy which is the ratio of horizontal hydraulic conductivity along rows to vertical hydraulic conductivity for the model layer The menu item Vertical Anisotropy is dimmed and cannot be used wi
208. arameter PARVALI is the parameter s starting value which together with the starting values of all other adjustable parameters it is successively improved during the optimization process To enhance optimization efficiency the user should choose an initial parameter value which is close to the guessed optimized value The user should note the following repercussions of choosing an initial parameter value of zero Limitation of the parameter adjustment is not possible see the discussion on RELPARMAX and FACPARMAX during the first optimization iteration if the starting value of a parameter is zero Furthermore FACORIG cannot be used to modify the action of RELPARMAX and FACPARMAX for a particu lar parameter throughout the optimization process if that parameter s original value is zero A relative increment for derivatives calculation cannot be evaluated during the first iteration for a parameter whose initial value is zero If the parameter belongs to a group for which derivatives are in fact calculated as Relative see INCTYP and DERINC below a non zero DERINCLB variable must be provided for that group 154 2 Modeling Environment Ifa parameter has an initial value of zero the parameter can be neither a tied nor a parent parameter as the tied parent parameter ratio cannot be calcu lated PARLBND and PARUBND are a parameter s lower and upper bounds respec tively For adjustable parameters the initial parameter val
209. asic basic7 Overview of the Problem This example is adapted from the second test problem of the STR1 package 98 The function of the STR1 package that computes the head in the stream as well as changes in flows to and from the aquifer was compared to an analytical solution developed by Cooper and Rorabaugh 28 The model grid used in the previous example was also used in this model The aquifer properties and assumptions are the same as those used in the previous example except for assumptions 8 10 which are replaced with the following assumptions 1 The recharge to the aquifer is only from the river as river stage increases with time and 2 The discharge from the aquifer is only to the river as river stage decreases with time The analytical solution from Cooper and Rorabaugh 28 pp 355 358 is applicable for the case where the lateral boundary is at infinity referred to by Cooper and Rorabaugh as semi infinite The impermeable boundary assigned at 4 000 ft for this model is of sufficient distance from the river in order not to interfere with the results A flood in the river was simulated for a 30 day period The procedure used to calculate the distribution of streamflow for the 30 day period and for 60 days following the flood was first to calculate a distribution of river stage using equation 71 in Cooper and Rorabaugh 28 p 355 assuming a maximum flood stage of 4 ft above the initial river stage The streamflow distri
210. at all cells during a inner iteration is less than or equal to this value iteration stops When it takes only one inner iteration to converge the solution is considered to have converged and the simulation proceeds to the next transport step e Concentration Change Printout Interval The maximum concentration changes are printed out whenever the iteration number is an even multiple of this printout interval Set it to zero for printing only at the end of each stress period e Include full dispersion tensor memory intensive This is a flag for treatment of dispersion tensor cross terms If this option is not used all dispersion cross terms will be lumped to the right hand side of the system of transport equations Omitting the cross terms represents a method of approximation which is highly efficient It must be noted however that for critical applications the full disper sion tensor should be included 2 6 2 11 MT3DMS SEAWAT Concentration Observations Select this menu item from the MT3DMS menu or from MOC3D MT3D or RT3D to specify the locations of the concentration observation boreholes and their associ ated observed measurement data in a Concentration Observations dialog box Its use is identical to the Head Observation dialog box see Section 2 6 1 14 The only difference is that the head observations are replaced by concentration observations 2 6 2 12 MT3DMS SEAWAT Output Control Use the Output Control MT3D MT3DMS dialo
211. ata Editor the following properties of interbeds are specified to model cells e Preconsolidation Head or preconsolidation stress He L Preconsolidation head is the previous minimum head value in the aquifer For any model cells in which the specified preconsolidation head is greater than the initial hydraulic head the value of the preconsolidation head will be set to that of the initial hydraulic head When compressible fine grained sediments are stressed beyond a previous max imum stress preconsolidation stress compaction is permanent inelastic e Elastic Storage Factor Spe For a confined aquifer the elastic compaction or expansion of sediments is proportional or nearly proportional to changes in hydraulic head values in the aquifer The IBS package uses the following equation to calculate the change in the thickness Ab L of the interbed positive for compaction and negative for expansion Ab Ah Spe Ah She bo 2 11 where Ah L is change in hydraulic head positive for increase Sske Lt is the skeletal component of elastic specific storage bo is the thickness of the interbed For an unconfined aquifer the elastic compaction or expansion of sediments can be expressed as Ab Ah Spe Ah 1 n nu Sere bo 2 12 where n is porosity and n is moisture content above water table as a fraction of total volume of porous medium e Inelastic Storage Factor Sf For a co
212. ater recharge is treated as distributed source within the model cells 0 0 ccc cece eee eens 299 Particles are tracked back to the groundwater surface by applying the groundwater recharge on the groundwater surface 3D approach 299 Catchment area of the pumping well 3D approach 300 Plan view of the model area 0 0 2 eee ee ee eee 301 Calculated head contours for the west part of the aquifer 302 Calculated head contours for the entire aquifer 302 Configuration of the hypothetical model after McDonald and others BOP ices Si ee eos wai et ee dane eA Ee ek ees 304 Hydrogeology and model grid configuration 306 Simulated water table along row 1 beneath a leaking pond after 190 708 2630 days and steady state conditions 307 Hydrogeology and model grid configuration 309 Simulated steady state head distribution in layer 1 310 Configuration of the model grid and the location of the observation Wellin s4 c8 eo deustiet E E E dune ESE 311 Distribution of recharge used for analytical solution and the model after Prudic 98 05 5 00 9 ne we ae et pene See eee 312 Comparison of simulation results to analytical solution developed by Oakes and Wilkinson 90 0 0 0 cece eee eee ee eee eens 313 Distribution of streamflow for a 30 day flood event used for the simulation after Prudic 98 0 2 0
213. ation Settings The available settings of the Reaction Definition RT3D dialog box Fig 2 59 are described below e Reaction Module Currently seven pre programmed reaction modules are avail able Their purposes taken from the RT3D manual are described briefly below Refer to Clement 25 for their reaction algorithms No Reaction tracer transport chemical reaction is not simulated Instantaneous aerobic decay of BTEX Simulates aerobic degradation of BTEX using an instantaneous reaction model The reaction simulated are similar to those simulated by BIOPLUME II 102 Instantaneous degradation of BTEX using multiple electron acceptors Sim ulates instantaneous biodegradation of BTEX via five different degradation Simulation Settings RT3D Reaction Module faca ca ea 08 1002 TAAS Oleg gr Sorption Parameter Use Cell by Cell mode RT3D 2 0 and later only Me Convergence Criteria for iterative solver Absolute Tolerance atol Relative Tolerance rtol 0 00001 0 00001 TCE mobile DCE mobile 0 00001 0 00001 0 00001 0 00001 WC mobile 0 00001 0 00001 ETH mobile CI mobile 0 00001 0 00001 0 00001 0 00001 Cancel Help Fig 2 59 The Reaction Definition RT3D dialog box 114 2 Modeling Environment pathways aerobic respiration O2 denitrification NO3 iron reduction Fe sulfate reduction S077 and methanogenesis C H4 Kinetic l
214. ation from the Operation Mode drop down box assign appropriate control parameters to the Regularization tab of of the Simulation Settings PEST dialog box Fig 2 81 You must also de fine at least one prior information equation see above and set the observation group Obgnme of the prior information equation to regul Refer to chapter 7 of the PEST manual 37 for further details about regularization e Target measurement objective function PHIMLIM This is the upper limit of the measurement objective function i e the upper level of model to measurement misfit that is tolerable when trying to minimize the regularization objective function In some cases a PEST regularization run will postdate a normal parameter estimation run If the latter run was successful it will have informed the user of how low the measurement objective function can be if all parameters are adjusted without reference to any regularization con ditions PHIMLIM should be set somewhat above this for the imposition of reg 160 2 Modeling Environment Simulation Settings PEST Operation Mode Regularization Parameters Parameter Groups Prior Information SVD SVD Assist Control Data Target measurement objective function PHIMLIM 10 Acceptable measurement objective function PHIMACCEPT FRACPHIM optional Initial regularization weight factor WFINIT Minimum regularization weight factor WFMIN Maximum regularization weight factor
215. ation is included in the regression The advantage of matching temporal changes in hydraulic head is that errors that are constant in time such as well elevation are expunged 63 e Statistic Option This option defines the physical meaning of Statistic specified in the Head Observation s table It also defines how the weights are calculated Refer to Hill 62 for more details about the role of statistics and weights in solving regression problems Note The PEST interface of PM can only handle single layer observation boreholes Multilayer boreholes are ignored when using PEST However multilayer boreholes will be used when using PEST ASP MODFLOW 2000 2 6 1 15 MODFLOW Drawdown Observations Select Drawdown Observations from the MODFLOW menu or from the PEST menu to specify the locations of the drawdown observation boreholes and their as sociated observed measurement data in a Drawdown Observations dialog box Its use is identical to the Head Observation dialog box The only difference is that the head observations are replaced by drawdown observations Note that MODFLOW 2000 does not use drawdown observations for parameter estimation Instead the temporal changes in specified hydraulic heads are used 2 6 1 16 MODFLOW Subsidence Observations Select this menu item to open a Subsidence Observation dialog box Except the Layer Proportion table the use of this dialog box is identical to the Head Observation dialog box The Layer
216. ations see Section 2 6 1 14 or flow observations Section 2 6 7 3 have been defined Select this menu item to open a Time Series Curves dialog box which is identical as the Time Series Curves Hy draulic Head dialog box as described in Section 2 6 1 20 The only exception is that the user specified observation times and observed values are given in the columns Simulation Time and Observed value directly without interpolating to the times at the end of each stress period or time step The Calculated Value column contains the values calculated by MODFLOW 2000 i e the values are not calculated by PM using equation 2 34 page 79 2 6 8 PEST Parameter Estimation This menu provides an interface between PM MODFLOW and PEST All versions of MODFLOW can be used with PEST The parameters and or excitations which may be estimated by regression are listed in Table 2 9 The adjustable aquifer pa rameters depend on the selection of BCF or LPF package and layer types During a parameter estimation process PEST searches optimum parameter values for which the sum of squared deviations between model calculated and observed values of hydraulic heads or drawdowns at the observation boreholes is reduced to a minimum The coordinates of the observation boreholes and observed values are given in PEST Parameter Estimation Head Observations or Drawdown Obser vations Note that a simultaneous fit of highly correlated parameters for example transmissi
217. ayer have the same thickness In practice variable layer thickness is often preferred 208 3 The Advective Transport Model PMPATH for approaching varying thickness of stratigraphic geohydrologic units In order to calculate approximate groundwater paths for this kind of discretization PMPATH uses a local vertical coordinate instead of the real world z coordinate The local ver tical coordinate is defined for each cell as Zr z 21 z2 21 3 7 where z and z3 are the elevations of the bottom and top of the cell respectively According to this equation the local vertical coordinate zz is equal to 0 at the bottom of the cell and is equal to 1 at the top of the cell For water table layers z2 is set equal to the head in the cell In MODFLOW model layers of type 1 unconfined are always water table layers model layers of type 2 or 3 confined unconfined are water table layers when the hydraulic head in the cell is beneath the elevation of the cell top When a particle moves laterally from one cell to another the exit point in the one and the entry point in the other cell have the identical local vertical coordinates This causes vertical discontinuities of pathlines if bottoms and tops of cells of the neigh boring cells are different This discontinuity does not introduce error it is merely unesthetic It can be kept small if the discretization is kept fine enough to have rela tively small cell to cell variations of bottoms
218. b A flow observation is commonly represented by a group of cells with the same Group Number For each cell group MODFLOW 2000 compares the simulated flow rate gain or loss with the observation data specified in the Flow Observation tab The simulated flow rate of a cell group y LTT is calculated by nqel f fnn 2 58 n 1 where nqcl is the number of cells in the cell group fn is a user specified mul tiplicative factor qn L3T 1 is the simulated flow rate at one cell Generally fn 1 0 However if a gauging site is located within a cell instead of at the edge of the cell f needs to be less than 1 0 so that only part of the simulated flow for the cell is included in y The Flow Observation Tab The Flow Observation tab Fig 2 76 is used to specify the names of cell groups and their associated observed measurement data The options of this tab are described below 2 6 The Models Menu Flow Observation River xi Group Number r Cell Group _ Time Observation Values HOBS STATISTIC ro 4 0507 04 jenen 33371 0 38 _ 2 44396 07 2 2719 021 Fig 2 76 The Flow Observation tab of the Flow Observation River dialog box 143 1 Cell Group Each row of the table pertains to a group of cells The name OB SNAM and the associated group number Group Number of each cell group are to be specified in the table A cell group is active if the
219. b of the Output Control MT3D MT3DMS dialog DOR exe ck BERR Ae ed fA ORR ae BERR TE Se ae 106 The Run MT3DMS dialog box 0 00 eee ee eee 106 The Run SEAWAT dialog box 0 eee ee eee 107 The Chemical Reaction Module PHT3D dialog box 110 The Simulation Settings PHT3D dialog box 110 The Reaction Definition RT3D dialog box 113 The Sorption Parameters RT3D dialog box 115 The Reaction Parameters for RT3D Spatially Constant dialog box 116 The Run RT3D dialog box 0 ce eee 117 List of Figures XV 2 63 The Subgrid for Transport MOC3D dialog box 119 2 64 The Parameter for Advective Transport MOC3D dialog box 120 2 65 The Dispersion Chemical Reaction MOC3D dialog box 122 2 66 The Source Concentration Constant Head dialog box 123 2 67 The Output Control MOC3D dialog box 0 124 2 68 The Run Moc3d dialog box 2 0 2 eee eee eee 125 2 69 The Advection Package MTADV1 dialog box 127 2 70 The Chemical Reaction Package MTRCT1 dialog box 131 2 71 The Output Control MT3D MT3DMS dialog box 132 2 72 The Output Times tab of the Output Control MT3D MT3DMS dial g box sheesh eR eee Oa ahd wee abe ibs 133 2 73 The Run MT3D MT3D96 dialog box 0 00088 134 2 74 The Simulation Settings MODFLOW 2000
220. because the simulation time is normally very short and the extent of the model domain is relative large so that at the end of a transient flow simulation the drawdown values at the model boundaries are acceptable low If the vertical hydraulic conductivity of the aquitard is known we can use PEST to estimate the horizontal hydraulic conductivity and storage coefficient of the leaky aquifer by defining them as estimated parameters Click Models PEST Run to see how the parameter estimation programs work Because the analytical drawdown values were used as the observations the results from the parameter estimation pro grams must be horizontal hydraulic conductivity 2 3 x 1074 m s and storage coefficient 0 00075 If the vertical hydraulic conductivity is unknown and needs Table 5 4 Analytical solution for the drawdown with time Time seconds Drawdown m Time seconds Drawdown m 123 0 0067 4932 0 336 247 0 03 12330 0 449 352 0 052 24660 0 529 493 0 077 35228 0 564 1233 0 168 49320 0 595 2466 0 25 123300 0 652 3523 0 294 5 3 Parameter Estimation and Pumping Test 333 Drawdown Co en analytical solution CoU T O numerical solution M 0 1 0 0 0 10000 20000 30000 40000 50000 Time Fig 5 29 Configuration of the leaky aquifer system and the aquifer parameters to be estimated we will need additional drawdown values in the overlying aquifer during the pumping test 334 5 Exa
221. ber of Layers 3 Model Thickness 20 Model Top Elevation 0 r Row I Dimension Number of Rows 20 Model Extent 5000 Column J Dimension Number of Columns 27 Model Extent feso r Cross Sectional Display Vertical Exaggeration 25 Load Help Cancel OK Fig 4 49 The Model Grid and Coordinate System dialog box You are now in the Grid Editor To help visualize the problem we can overlay a DXF file as a map which gives us the locations of the boundaries and the pumping wells gt To load a map 1 Select Options Map to open the Map Options dialog box 2 Right click on the first DXF File field to bring up the Map Files dialog box and then select the file BASEMAP DXF from the folder examples tutorials tutorial3 3 Check the box at the front of the DXF File field The map will be displayed only if the box is checked 4 Click OK to close the Map Options dialog box You will see that it does not match the grid that you have generated So we need to move the grid to the proper position gt To move the grid 1 Select Options Environment to open the Environment Options dialog box 2 In the Coordinate System tab enter Xo 200 and Yo 6000 then click OK to close the dialog box 3 Select File Leave Editor or click the leave editor button w 4 3 1 3 Step 3 Refine the Model Grid gt To refine the model grid 1 Select Grid Mesh Size to open the Grid Editor 4 3 Aquifer Sy
222. ble contains a list of species for the selected reaction module Reaction solvers of RT3D use absolute tolerance atol and relative tolerance rtol values to control convergence errors The fol lowing rule of thumb may be used to set the atol and rtol values If m is the num ber of significant digits required in a solution component set rtol 107 and set atol to a small value at which the absolute value of the component is essentially insignificant Note that the values of atol and rtol should always be positive 2 6 4 2 RT3D Initial Concentration At the beginning of a transport simulation RT3D requires the initial concentration of each active species at each active concentration cell i e ICBUND gt 0 2 6 4 3 RT3D Advection Select this menu item to open an Advection Package RT3D dialog box The use of this dialog box is identical to the Advection Package MT3DMS dialog box Fig 2 47 on page 90 2 6 The Models Menu 115 Sorption Parameters RT3D Description PCE mobile TCE mobile DCE mobile VC mobile ETH mobile CI mobile Kdis the distribution coefficient L 3 M SP2 is not used OK Cancel Help Fig 2 60 The Sorption Parameters RT3D dialog box 2 6 4 4 RT3D Dispersion Select this menu item to open a Dispersion Package dialog box Its use is identical to the Dispersion Package of MT3DMS see Section 2 6 2 4 for details 2 6 4 5 RT3D Sorption
223. booted Gh GaGa aes aes Beds 29 384 6 2 9 Polygon File sc senei eee eh bat Seas tS eee 385 O2I0 XYZ Filen ot poets a ie alee canes 387 6 2 41 Pathline Pile seges ly pee ern en OOO Aaa VRE Fs 387 6 2 11 1 PMPATH Format 0005 387 6 2 11 2 MODPATH Format 0 388 6 2 12 Particles Files 00sec bee E E e Pe whee oes we 388 6 3 Input Data Files of the supported Model 389 63 1 Name File 5 523 e cad ache tw db eke gee Sanne e 389 6 3 2 MODFLOW 96 woes eee ahaa ea ee dee eee it 392 6 3 3 MODFLOW 2000 2005 2 0 eee eee eee 393 6 3 4 MODPATH and MODPATH PLOT version 1 x 393 6 3 5 MODPATH and MODPATH PLOT version 3 x 394 6 3 0 MOC3D ss pio 2h nw ate as bias ieee deeds 394 XII Contents E3 MRD are a we i i a a Riot let ase Ak 394 6 3 8 MT3DMS SEAWAT 0002 ccc eee 394 63 9 u RTS Dees o a a a a e Pad a Ratan 395 6310 PHTI Do ecco scape a a a e ae OU p Aaa Webee be 395 Eo PA EI PAA Eg eA BATA sale ae oe aon ee 395 6 4 Using MODPATH with PM 0 396 6 5 Define PHT3D Reaction Module 0 000 e eee eee 397 RefEPEN COS 0 24 5 isc od o Bee Seed tube be eWeek hare ok Ea de ies des 399 List of Figures 2 1 2 2 2 3 2 4 2 6 2 7 2 8 2 9 2 10 2 11 2 12 2 13 2 14 2 15 2 16 2 17 2 18 2 19 2 20 2 21 2 22 2 23 2 24 2 25 2 26 2 27 Spatial discretization of an aquifer syst
224. boundary conditions The boundaries at the upstream and downstream of the weir are modeled as fixed head boundaries with h 12 m and h 10 m above reference level respectively The aquifer bottom and the weir itself are modeled as no flow boundaries Fig 5 36 shows the flow net for the isotropic case The head values range from 10 to 12 m with a head increment of 0 1 m The flux through the aquifer per meter width of the weir is 3 65 x 1074 m3 s m 31 56 m3 day m Fig 5 37 shows the flow net for the aquifer in the anisotropic case The flux through the aquifer is now only 2 5 x 1074 m3 s m 21 6 m3 day m Note that in a homogeneous and anisotropic medium flowlines intersect head contours at right angle only where flow is parallel to one of the principal directions of hydraulic conductivity 5 4 Geotechnical Problems 343 Embedded weir j_ Water table h 12 m s l aquifer 3m TEE 7 water table h 10 m no flow boundary Fig 5 34 Configuration of the physical system Embedded weir water table h 12 m water table h 10 m i th Fig 5 35 Model grid and the boundary conditions Fig 5 36 Flowlines and calculated head contours for isotropic medium
225. bove the groundwater surface went dry To calculate inflow into the mining pit we select Tools Water Budget to calculate the water budget by assigning zone to the fixed heads cells within the mining pit The water budget for zone in layer 4 should look like Table 5 1 8 The inflow rate to the constant head cells mining pit is 1 9428713E 00 m s For task 2 all cells within the mining pit are set as active cells The wetting capability of MODFLOW is turned on by selecting Models Modflow Wetting Ca pability The wetting iteration interval is 1 wetting factor is 0 5 and THRESH is 1 for all cells The specific yield and effective porosity of all cells within the mining pit Table 5 1 Volumetric budget for the entire model written by MODFLOW Flow Term In Out In Out STORAGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 CONSTANT HEAD 0 0000000E 00 1 9428709E 00 1 9428709E 00 HORIZ EXCHANGE 1 1840475E 00 0 0000000E 00 1 1840475E 00 EXCHANGE UPPER 0 0000000E 00 0 0000000E 00 0 0000000E 00 EXCHANGE LOWER 7 5882387E 01 0 0000000E 00 7 5882387E 01 WELLS 0 0000000E 00 0 0000000E 00 0 0000000E 00 DRAINS 0 0000000E 00 0 0000000E 00 0 0000000E 00 RECHARGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 ET 0 0000000E 00 0 0000000E 00 0 0000000E 00 5 1 Basic Flow Problems 319 lake are set to 1 Compared to the specific yield the influence of the elastic storage coefficient within the lake is insignificant Therefore the specific storage coeffici
226. brium Freudlich isotherm nonlinear equilibrium and Langmuir isotherm nonlinear equilibrium See Section 2 6 2 6 for details e Simulate the radioactive decay or biodegradation Check this box to simulate the effect of the first order irreversible rate reactions See the description of the reaction type First order irreversible reaction on page 100 for details 2 6 The Models Menu 131 Chemical Reaction Package MTRCT1 ilibriumn 0 000125 0 000125 0 000125 Kd is the distribution coefficient L 3 M SP2 is not used RC1 is the first order rate constant for the dissolved phase 1 T RC2 is the first order rate constant for the sorbed phase 1 T OK Cancel Help Fig 2 70 The Chemical Reaction Package MTRCT1 dialog box 2 6 6 5 MT3D Chemical Reaction Cell by Cell Using the Data Editor chemical reaction coefficients may be entered on a three di mensional cell by cell basis This option provides the ability to have different reaction coefficients for different areas in a single model layer 2 6 6 6 MT3D Sink Source Concentration The use of this menu is the same as MT3DMS SEAWAT Sink Source Concentration except the use of the menu item Time Variant Specified Concentration A time variant specified concentration cell is defined by specifying the following data in the Data Editor Note that Time Variant Specified Concentration may not be supported by some earlier version of MT
227. bution Fig 5 16 was calculated from the river stage distribution The river has a width of 100 ft a dimensionless roughness coefficient of 0 02377 and a slope of 0 0001 A constant C 1 486 should be used for the simulation see Equation 2 26 Modeling Approach and Simulation Results Streamflow for the first 30 days was divided into 1 day periods for simulation Fig 5 17 shows the computed river stage The simulation results are the same as the manually calculated river stage values using equation 71 of Cooper and Rorabaugh 28 p 355 Detailed discussion on the analytical and numerical results can be found in Prudic 98 Results of varying both the number of columns and the length of stress periods used to simulate the flood wave indicate that both the number of columns and the length of the time step are important in exactly duplicating the analytical solution A groundwater flow model with the Streamflow Routing package has an advan tage over analytical solutions because it can be used to simulate complex systems An example Folder pmdir examples basic basic7a containing a stream system Fig 5 18 is used to illustrate most of the features of the Stream flow Routing package The example assumes that an aquifer of 6 000 ft wide by 6 000 ft long is divided into six equally spaced rows and columns The transmissivity of the aquifer is 0 08 ft s Recharge to the aquifer occurs only from stream leakage The example in 315 5 1
228. cated in cells which contain or are ad jacent to sinks or sources and automatic selection of the first order Euler algorithm for particles located elsewhere Maximum number of total moving particles MXPART is the number of particles allowed in a simulation Courant number PERCEL is the number of cells or a fraction of a cell any particle will be allowed to move in any direction in one transport step Generally 0 5 lt PERCEL lt 1 Concentration weighting factor WD lies between 0 and 1 The value of 0 5 is normally a good choice This number can be adjusted to achieve better mass 2 6 The Models Menu 129 balance Generally it can be increased toward 1 as advection becomes more dom inant Negligible relative concentration gradient DCEPS is a criterion for placing par ticles A value around 10 is generally adequate If DCEPS is greater than the relative cell concentration gradient DCCELL equation 2 36 on page 92 the higher number of particles NPH is placed in the cell k i j otherwise the lower number of particles NPL is placed see NPH and NPL below Pattern for initial placement of particles NPLANE is used to select a pattern for initial placement of moving particles NPLANE 0 the random pattern is selected for initial placement Particles are distributed randomly in both the horizontal and vertical directions Fig 2 48b on page 93 This option generally leads to smaller mass balance dis crepa
229. cceleration Parameter ACCL 1 Convergence Criterion Head Change L 001 Fig 2 33 The Slice Successive Overrelaxation Package dialog box e JPRSOR is the printout interval for SSOR A positive integer is required The maximum head change positive or negative is saved in the run record file OUT PUT DAT for each iteration of a time step whenever the time step is an even multiple of JPRSOR This printout also occurs at the end of each stress period regardless of the value of JPRSOR e ACCLis the acceleration parameter usually between 1 0 and 2 0 e Head Change is the head change criterion for convergence When the maximum absolute value of head change from all cells during an iteration is less than or equal to Head Change iteration stops MODFLOW Solvers GMG MODFLOW 2000 Only The required parameters for the GMG package 115 are specified in the Geometric Multigrid Solver dialog box Figure 2 34 The parameters are described below e Iteration Control Maximum Number of Outer Iteration MXITER MXITER is the maximum number of outer iterations For linear problems MXITER can be set to 1 Fornonlinear problems MXITER needs to be larger but rarely more than 100 Head Change Closure Criterion HCOLOSE HCLOSE is the head change convergence criterion for nonlinear problems After each linear solve in ner iteration themaximum head change is compared against HCLOSE HCLOSE can be set to a large number for linear
230. ce criterion for coupling iterations M L 3 0 Length of the first transport timestep FIRSTDT 0 Reference fluid density DENSEREF 1000 Minimum fluid density DENSEMIN 0 Maximum fluid density DENSEMAX 0 Source Density Options Uncoupled Mode when density effects of all species are off Density of Injected Fluid of Wells Reference Fluid Density Density of River Fluid Density of Model Cell Density of General Head Boundary Fluid Density of Model Cell Fig 2 46 The Variable Density tab of the Simulation Settings MT3DMS SEAWAT dialog box 2 6 2 2 MT3DMS SEAWAT Initial Concentration At the beginning of a transport simulation MT3DMS and SEAWAT require the initial concentration of each active species at each active concentration cell i e ICBUND gt 0 2 6 2 3 MT3DMS SEAWAT Advection The available settings of the Advection Package MT3DMS dialog box Fig 2 47 are described below 90 2 Modeling Environment Advection Package MT 3DMS Solution Scheme Hybrid MOC MMOC HMOC X Particle Tracking Algorithm Hybrid 1st order Euler and 4th order Runge Kutte v Simulation Parameters Max number of total moving particles MXPART 500000 Courant number PERCEL 0 75 Concentration weighting factor wD Negligible relative concentration gradient DCEPS Pattern for initial placement of particles NPLANE No of particles per cell in case of DCCELL lt DCEPS NPL No of
231. ch a model run by simply clicking on the Update button to import the estimated base parameter values from PESTCTL PAR to the Parameter tab set Operation Mode Fig 2 82 to Forward Model Run using PARVAL values given in the Parameters tab and then run PEST Save Multiple JCO files If this box is checked PEST will write a Jacobian matrix file i e a JCO file at the end of each optimization iteration this containing the Jacobian matrix em ployed for that particular iteration Save Multiple REI files If this box is checked PEST will write a residuals file i c a REI file at the end of each optimization iteration The Control Data Tab The control data are used to set internal array dimensions of PEST and tune the optimization algorithm to the problem at hand The items of the Control Data tab Fig 2 83 are described in detail below When in doubt the user should use the default values RLAMBDAL is the initial Marquardt lambda PEST attempts parameter improve ment using a number of different Marquardt lambdas during any optimization it 168 2 Modeling Environment Simulation Settings PEST Parameters Parameter Groups Prior Information Regularization SYD SYD Assist Control Data PHIREDLAM NUMLAM RELPARMAX FACPARMAX FACORIG IPHIREDSWH INOPTMAX IPHIREDSTP INPHISTP INPHINORED RELPARSTP NRELPAR Output Options I Write covariance matrix White
232. ch and Modify Cell Yalues x Parameter Initial Hydraulic Heads x Value J 105 Search Range Options s C Replace Min J 105 C Add eel Cancel Max 105 C Multiply Display Only Help Fig 2 9 The Search and Modify Cell Values dialog box e Shift left mouse button or Ctrl Q Open the Cell Information dialog box Fig 2 8 which displays the user specified data of the cell pointed to by the grid cursor e Ctrl left mouse button Open the Search and Modify Cell Values dialog box Fig 2 9 This allows you to display all cells that have a value located within the Search Range to be specified According to the user specified Value and the operation Options you can easily modify the cell values For example if Add is used the user specified value will be added to the cell value The Parameter drop down box shows the available parameter type s The user may select the parameter to which the subsequent Search and Modify operation will be applied e Select Value Search and Modify or press Ctrl S Open a Search and Modify dialog box for more advanced data manipulation fea tures See Section 2 8 5 for details 2 2 2 The Polygon Input Method The Polygon Input Method allows the user to assign parameter values to model cells with the help of polygons This input method is not allowed in the cross sectional view To activate this method click on the button or the button to switch to Grid View or Map View an
233. ck Execute backward particle tracking for a user specified ward step by step particle tracking step length Stop particle tracking Stop the particle tracking or stops drawing particles a E Run particles forward Execute forward particle tracking for a user specified step by step particle tracking step length F Run particles forward Execute forward particle tracking for a time length The product of the number of particle tracking steps and the particle tracking step length defines the time length 3 2 3 2 Set particle Use the following two methods to place particles in the current layer The current layer is shown in the tool bar Fig 3 4 Change it first if particles need to be placed in another layer Note that particles cannot be placed in inactive cells or fixed head cells constant head cells gt To place a group of particles 1 Click the Set particle button 2 Move the mouse pointer to the active model area The mouse pointer turns into crosshairs 3 Place the crosshairs where the user wants a corner of the Set Particle window 4 Drag the crosshairs until the window covers the sub region over which particles will be placed then release the mouse button 212 3 The Advective Transport Model PMPATH The Add New Particles box appears Fig 3 5 Where NK NI and NJ are the number of particles in layer row and column directions respectively Particles can be placed either on cell faces or within cel
234. ck OK 3 Select File Leave Editor or click the leave editor button w The last step before performing the flow simulation is to specify the location of the pumping well and its pumping rate In MODFLOW an injection or a pumping well is represented by a node or a cell The user specifies an injection or a pumping rate for each node It is implicitly assumed that the well penetrates the full thickness of the cell MODFLOW can simulate the effects of pumping from a well that penetrates more than one aquifer or layer provided that the user supplies the pumping rate for each layer The total pumping rate for the multilayer well is equal to the sum of the pumping rates from the individual layers The pumping rate for each layer Qx can be approximately calculated by dividing the total pumping rate Qtota1 in proportion to the layer transmissivity McDonald and Harbaugh 1988 Tk Qiotal 4 1 Qk Qiotal Fp 4 1 where Tj is the transmissivity of layer k and XT is the sum of the transmissivities of all layers penetrated by the multi layer well Unfortunately as the first layer is unconfined we do not exactly know the saturated thickness and the transmissivity of this layer at the position of the well Equation 4 1 cannot be used unless we assume a 4 1 Your First Groundwater Model with PM 237 saturated thickness for calculating the transmissivity Another possibility to simulate a multi layer well is to set a very large vertical hy
235. confined layer The top and bottom of the model layer are at an elevation of 10 m and 0 m respectively To simulate the groundwater seepage velocity of 1 3 m day fixed head boundaries with h 11 m and h 10 m are as signed to the west and east side of the model The horizontal hydraulic conductivity is 45 m day The flow field was first calculated by MODFLOW The third order TVD scheme was used in the simulation for the advection term and the GCG solver is used to solve the system equations The contour map of the concentration field at the end of the 365 day simulation period obtained for this example is shown in Fig 5 49 An analytical solution for this problem is given by Wilson and Miller 116 The analytical solution is applicable only under the assumption that 1 the aquifer is relatively thin so that instantaneous vertical mixing can be assumed 2 the injection rate is insignificant compared with the ambient uniform flow Fig 5 50 shows the breakthrough curves at an observation well located 60 m downstream of the injection well The analytical solution is obtained by using the computer program by Rausch 99 included in the folder Source analytical solu tion of the companion CD ROM Fig 5 51 compares the analytical solution with the numerical solution obtained by using the upstream finite difference method The 5 5 Solute Transport 357 numerical dispersion is significant when the upstream finite difference method is used to
236. contour The contour is visible if LVISIBLE is TRUE LSIZE is the appearance height of the label text in the same unit as the model LDIS is the distance between two contour labels in the same unit as the model 378 6 Supplementary Information 6 2 3 Grid Specification File The grid specification file provides the grid geometry and location details File Format 1 Data NROW NCOL 2 Data X Y ANGLE 3 Data DELR NCOL 4 Data DELC NROW 5 Data X1 Y1 6 Data X2 Y2 7 Data NLAY The following data contains the top elevations of each layer This data record repeats NLAY times if the layer top elevation has been specified 8 Data TOP The following data contains the bottom elevations of each layer This data record repeats NLAY times if the layer bottom elevation has been specified 9 Data BOTTOM Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NROW is the number of model rows NCOL is the number of model columns X is the x coordinate of the top left corner of the model grid Y is the y coordinate of the top left corner of the model grid ANGLE is the rotation angle expressed in degrees and measured counterclock wise from the positive x axis DELR is the cell width along rows Read one value for each of the NCOL columns This is a single array with one value for each column DELC is the cell width al
237. correlation coefficient matrix Save data for a possible restart IV Write normalized eigenvectors of covariance matrix Include decimal point even if redundant Load Save OK Cancel Help Fig 2 83 The Control Data tab of the Simulation Settings PEST dialog box eration In the course of the overall parameter estimation process the Marquardt lambda generally gets smaller An initial value of 1 0 to 10 0 is appropriate for many models though if PEST complains that the normal matrix is not positive definite you will need to provide a higher initial Marquardt lambda For high values of the Marquardt parameter and hence of the Marquardt lambda the pa rameter estimation process approximates the gradient method of optimization While the latter method is inefficient and slow if used for the entire optimization process it often helps in getting the process started especially if initial parameter estimates are poor PEST reduces lambda if it can However if the normal matrix is not positive definite or if a reduction in lambda does not lower the objective function PEST has no choice but to increase lambda e RLAMFAC is the factor by which the Marquardt lambda is adjusted RLAMFAC must be greater than 1 0 When PEST reduces lambda it divides by REAMFAC when it increases lambda it multiplies by RLAMFAC e PHIRATSUF is the first criterion for moving to the next optimization iteration During any optimization iterati
238. crease or decrease the magnification level of the display e To move a part of the image to the center of the display simply click the desired position e To zoom in hold down the Shift key and click the image e To zoom out hold down the Ctrl key and click the image e To display entire map hold down the Alt key and click the image 3 Follow the steps below to set geo reference points a Click the Set button from the Point 1 or Point 2 group The mouse pointer turns into a crosshairs b Place the crosshairs at a point with known x y real world coordinates and press the left mouse button c Enter the x y coordinates into the corresponding edit fields of the group Point or Point 2 d Repeat the previous steps to set the other reference point Note that the geo reference points must not lie on a vertical or horizontal line e g the x and y coordinates of the points must not be the same 2 9 2 Environment The Environment Options dialog box Fig 2 104 allows the user to configure the coordinate system and modify appearance of the model grid Available settings are grouped under three tabs Appearance Coordinate System and Contours which are described below The checkbox Display zones in the cell by cell mode is used to force PM to display the user specified polygons when using the cell by cell input method s Xz X s Y3 Y X3 Y3 XY Xa Yo S X4 X S Y s X X s Y3 Y a triangle before scaling
239. d The aquifer is homogeneous and isotropic with a measured horizontal hydraulic conductivity of 0 0005 m s and an effective porosity of 0 1 The elevations of the aquifer top and bottom are 15 m and 0 m re spectively The aquifer is bounded by a no flow zone to the west To the east exists a river which is in direct hydraulic connection with the aquifer and can be treated as fixed head boundary The river width is 50 m and stage is 10 m The mean ground water recharge rate is 8 x 107 m s A pumping well is located at a distance of 1000 m from the river The task is to calculate the catchment area of the well and the 365 days capture zone under steady state flow conditions 298 5 Examples and Applications Well Q 005 m s 1475 m 1000 m No flow boundary fixed head boundary 2525 m OO SS Fig 5 1 Plan view of the model area Modeling Approach and Simulation Results The west boundary of the model is impervious and the river to the east is simulated by the fixed head boundary condition BOUND 1 with the initial hydraulic head at 10 m There are no natural boundaries to the South and North so we have to use streamlines as impervious boundaries The distance of the selected streamline from the well must be large enough so that the hydraulic head at these boundaries are not affected by the pumping well This is the case if the total recharge in the chosen strip is considerably larger than the pumpin
240. d at the Command Prompt DOS box by executing the batch file PESTMF2K BAT Check the model data If this option is checked PM will check the geometry of the model and the consistency of the model data as given in Table 2 6 page 77 before creating data files The errors if any are saved in the file CHECK LIS located in the same folder as the model data Let PEST ASP calculate Derivatives Although the derivatives calculated by MODFLOW ASP using the sensitivity equation method is more accurate sometimes the slight loss of numerical precision incurred through the use of derivatives calculated by PEST ASP using the perturbation finite difference method appears to abet rather than hinder the parameter estimation process This option should be tried if a parameter estimation process fails to con verge e OK Click OK to generate the input files In addition PM creates a batch files PESTMF72K BAT in the model folder When all files are generated PM automat ically runs PESTMF2K in a Command Prompt window DOS box After com pleting the parameter estimation process PEST ASP MODFLOW 2000 prints the optimized parameter values to the file MF2KOUT _B in the model folder The model results after the parameter estimation process are calculated by using the optimized parameter values During a parameter estimation process PEST ASP x V Basic Package c program files eit pmwin examples mf2k ex1
241. d in the center of the contaminated area is 8 m Furthermore the duration until the steady state is reached should be calculated Modeling Approach and Simulation Results The condition is simulated using a grid of one layer 31 columns and 31 rows The layer type is 1 unconfined Fig 5 23 shows the model grid and the selected boundary conditions The extent of the model is fairly large to ensure that the changes in hy draulic heads at the boundaries are not affected by the remedial measure To obtain the hydraulic gradient of 0 05 the west and east sides of the model are assumed to be fixed head boundaries with hydraulic head values of 9 8925 m and 9 m re spectively The steady state condition is simulated using one stress period and one time step Although the length of the stress period is not relevant for a steady state solution we set the length to 1 so the computed head values can be compared with observed values For this example an observation borehole is set at the center of the contaminated area The observed head at time 1 is set at 8 m the objective using the Head Observation dialog box see Section 2 6 1 14 The configuration of the remedial measures is shown in Fig 5 24 The pumping rates of the wells are defined as an estimated parameter by assigning the parameter number to all four wells Using PEST the pumping rate of each well is estimated at about 7 9 x 107 m3 s 326 5 Examples and Applications no
242. d run record saved by MODFLOW MODFLOW View Head Scatter Diagram This menu item is available only if Head Observations have been defined see Section 2 6 1 14 Select this menu item to open the Scatter Diagram Hydraulic Head dialog box Fig 2 38 The options are grouped under two tabs Data and Chart as described below e The Data Tab contains a table showing the observed and calculated values at ac tive observation boreholes see Section 2 6 1 14 for the definition of observation boreholes The columns of this table are listed Plot A borehole will be displayed on the scatter diagram only when its Plot box is checked Color Defines the plot color for each borehole Click the 2J button to change the color OBSNAM Displays the name of each observation borehole specified in the Head Observation dialog box Section 2 6 1 14 Calculated value Displays simulated head values at observation boreholes If a borehole lies in an inactive or dry cell the default value for dry cells Scatter Diagram Hydraulic Head xj Data Chart SimulationTime 100 225 100 225 126 9377 126 9377 1 1 157 1459 157 1459 1 126 9377 126 9377 1 140 8625 140 8625 1 1 1 1 1 127 1486 127 1486 101 2353 101 2354 157 1331 157 1331 176 946 176 946 140 9725 140 9724 1 100 225 100 225 87163 126 9328 126 9328 87163 154 5827 154 5827 87163 126 929 126 929 87163 140 842 140 842 87163 127 1423 12
243. d then click on the J button or choose Options Input 18 2 Modeling Environment Method Polygon The use of this input method is straightforward First you draw a polygon and then assign parameter values to the polygon Finally press the El button to apply the parameter values to model cells that lie within the polygon Note Polygon data is not used by PM for model computation directly If poly gon data is not applied to the model cells the original values in the cells are used gt To draw a polygon 1 If the display mode is not Grid View or Map View click the J button or the button to switch to the Grid View or Map View Click the assign value button LH and click the 4 button Click the mouse pointer on a desired position to anchor one end of a line Move the mouse pointer to another position then press the left mouse button again Repeat steps 3 and 4 until the polygon is closed or press the right mouse button to abort gt To delete a polygon 1 If the display mode is not Grid View or Map View click the J button or the button to switch to the Grid View or Map View Click the assign value button L J and click the 4 button Move the mouse pointer into a polygon The boundary of the polygon will be highlighted Press the Delete key gt To assign value s to polygons 1 If the display mode is not Grid View or Map View click the J button or the button to switch to the Grid View
244. d to approximate the advection relevant average concentration at the cell where the particle is placed The MMOC technique is free of artificial oscillations if implemented with a lower order velocity interpolation scheme such as linear interpolation used in MT3D and MT3DMS However with a lower order velocity interpo lation scheme the MMOC technique introduces some numerical dispersion especially for sharp front problems The hybrid method of characteristics HMOC attempts to combine the strengths of the MOC and MMOC schemes by using an automatic adap tive scheme conceptually similar to the one proposed by Neumann 89 The fundamental idea behind the scheme is automatic adaptation of the solution process to the nature of the concentration field When sharp concentration fronts are present the advection term is solved by MOC through the use of 2 6 The Models Menu 91 moving particles dynamically distributed around each front Away from such fronts the advection term is solved by MMOC The criterion for controlling the switch between the MOC and MMOC schemes is given by DCHMOC see below The finite difference method is implicit with the Generalized Conjugate Gra dient solver GCG package see Section 2 6 2 10 Due to the problems of numerical dispersion and artificial oscillation the up stream finite difference method is only suitable for solving transport problems not dominated by advection When the grid Peclet number P
245. de Flowlines use the flow field from the current time step Pathlines use transient flow fields r Stop Condition IV Particles stop when they enter cells with internal sinks P Particles stop when the simulation time limit is reached Fig 3 12 The Particle Tracking Time dialog box particles will move backward or forward for a time length defined by the product of Step length and Maximum steps e Time Mark PMPATH places a time mark on pathlines for each n th tracking step where n is given in Interval Check the corresponding Visible boxes to see time marks on the Viewing Window or the cross section windows The appearance size of the time marks is defined by Size in pixels The default value of Size is 10 for the Viewing Window and 3 for the cross section windows The sizes can be ranged from 1 to 2 147 483 647 e Simulation Mode PMPATH can be used to calculate flowlines or pathlines Flow lines indicate the instantaneous direction of flow throughout a system at all times of a steady state flow simulation or at a given time step of a transient flow simula tion Pathlines map the route that an individual particle of water follows through a region of flow under steady state or transient conditions In a steady state flow system pathlines will coincide with flowlines In this case only the option Flow line use the flow field from the current time step is available In the case of a transient flow simulati
246. deling Environment 1 Click the Stage button from the Reservoir Package dialog box Fig 2 23 A Stage Time Table of Reservoirs dialog box appears Fig 2 24 2 Select a reservoir number a row from the first table The reservoir number is corresponding to the number Ips see above The description column is a place for the user to take notes 3 Type the observation time and the corresponding stage into the second table The observation time is measured from the start of the model simulation to which the measured stage pertains Reservoir Package Reservoir Number Land Surface Elevation L fs Reservoir bed vertical hydr Conductivity L T fs Thickness of the Reservoir bed L3 LayerIndicator IRESL HIO Parameter Number 0 F Connection Options Reservoir connected to the top layer Reservoir connected to highest active cell Vertical distribution of reservoir is specified in IRESL Current Position Layer Row Column 1 12 25 The connection option is applied to the entire matrix IRESL is only required if the third connection option is selected Fig 2 23 The Reservoir Package dialog box bs Stage Time Table of Reservoirs Reservoir _ Description au First Reservior Output Options IV Make a stage volumn area table for reservoirs Number of values in the stage volumn area table NPTS 10 Load Save Clear Cancel Help Fig 2 24 Th
247. ditor Cross sectional View 2 2 1 The Cell by Cell Input Method To activate this method click the L button or select Options Input Method Cell By Cell gt To assign new value s to a cell 1 Click the assign value button E It is not necessary to click this button if the button is already depressed 2 Move the grid cursor to the desired cell by using the arrow keys or by clicking the mouse on the cell The value s of the current cell is are displayed in the status bar 3 Press the Enter key or press the right mouse button once The Data Editor shows a dialog box 4 In the dialog box type new value s then click OK Since groundwater model data are often very complex PM provides several possi bilities for checking or modifying cell by cell model data as listed below e Double click a cell All model cells with the same value will appear in the same color The color can be changed by repeated double clicks 2 2 The Data Editor 17 xi Cell position 8 53 50 Top of layer 17 33625 Bottom of layer 1 813999 Initial Head 105 Initial Concentraton l Horizontal K 8 64 Transmissiv Vertical K 00001 Vertical leakance 2 Specific storage Storage Coefficient _ Horizontal Anisotropy Effective porosity 2 Vertical Anisotropy Specific Yield l 4 only used by transient flow simulations not to be used for the current layer Fig 2 8 The Cell Information dialog box 43 Sear
248. draulic conductivity or vertical leakance e g 1 m s to all cells of the well The total pumping rate is assigned to the lowest cell of the well For the display purpose a very small pumping rate say 1 x 10 m3 s can be assigned to other cells of the well In this way the exact extraction rate from each penetrated layer will be calculated by MODFLOW implicitly and the value can be obtained by using the Water Budget Calculator see below Since we do not know the required pumping rate for capturing the contaminated area shown in Fig 4 1 we will try a total pumping rate of 0 0012 m s gt To specify the pumping well and the pumping rate 1 Select Models MODFLOW Well 2 Move the grid cursor to the cell 1 15 25 and press the Enter key or the right mouse button to display a Cell Value dialog box 3 Type 1E 10 in the dialog box then click OK Note that a negative value is used to indicate a pumping well 4 Move the grid cursor to the cell 2 15 25 and press the Enter key or the right mouse button to display a Cell Value dialog box 5 Type 1E 10 in the dialog box then click OK 6 Move the grid cursor to the cell 3 15 25 and press the Enter key or the right mouse button to display a Cell Value dialog box 7 Type 0 0012 in the dialog box then click OK 8 Select File Leave Editor or click the leave editor button w 9 Now select Parameters Vertical Hydraulic Conductivity and change the vertical hydrau
249. dual is cal culated as A x b for each inner iteration When the maximum absolute value of the residual at all cells during an iteration is less than or equal to Residual and the criterion for Head Change is satisfied see above iteration stops Printout From the Solver Printout Interval requires a positive integer If the op tion All available information is selected the maximum head change and residual positive or negative are saved in the run listing file OUTPUT DAT for each it eration of a time step whenever the time step is an even multiple of Printout Interval If the option The number of iterations only is checked the printout of maximum head change and residual is suppressed Select the option None to sup press all printout from the solver Damping Parameter The Damping Parameter is a multiplier for the computed head change for each iteration Normally this value is 1 A value smaller than 1 may be useful for unstable systems 2 6 The Models Menu 67 Strongly Implicit Procedure Package Allowed Iteration Number MXITER 200 Printout From the Solver Help Interval IPRSIP 1 No of Iteration Parameters Cancel NPARM 5 Acceleration Parameter ACCL 1 Convergence Criterion Head Change L 001 Fig 2 32 The Strongly Implicit Procedure Package dialog box MODFLOW Solvers SIP The required parameters for the SIP package are specified in the Strongly Implicit Procedure Pac
250. dy State Flow Simulation 229 4 1 2 1 Step 1 Create a New Model 229 4 1 2 2 Step 2 Assign Model Data 229 4 1 2 3 Step 3 Perform the Flow Simulation 237 4 1 2 4 Step 4 Check Simulation Results 238 4 1 2 5 Step 5 Calculate subregional water budget 239 4 1 2 6 Step 6 Produce Output 00 242 4 1 3 Simulation of Solute Transport 0 004 249 4 1 3 1 Perform Transport Simulation with MT3DMS 250 4 1 3 2 Perform Transport Simulation with MOC3D 257 4 1 4 Parameter Estimation 0 0 0 eee ee eee 263 4 1 4 1 Parameter Estimation with PEST 265 4 1 3 Animato 5032 ce es Gees AS se LE RE EES 269 4 2 Unconfined Aquifer System with Recharge 271 4 2 1 Overview of the Hypothetical Problem 271 4 2 2 Steady state Flow Simulation 000 272 4 2 2 1 Stepl Create a New Model 272 4 2 2 2 Step2 Generate the Model Grid 272 4 2 2 3 Step 3 Refine the Model Grid 273 4 2 2 4 Step 4 Assign Model Data 274 4 2 2 5 Step 5 Perform steady state flow simulation 279 X Contents 4 2 2 6 Step 6 Extract and view results 279 4 2 3 Transient Flow Simulation 0 004 280 4 3 Aquifer System with River 0 e
251. e porosity Storage coefficient specific May not be negative storage or specific yield River package 1 A river cell may not be a fixed head cell and should not be an inactive cell 2 Elevation of the riverbed should be higher than the ele vation of the cell bottom 3 The river stage must be higher than elevation of the riverbed Streamflow Routing package A STR cell may not be a constant head cell and should not be an inactive cell Drain package 1 A drain cell may not be a fixed head cell and should not be an inactive cell 2 Elevation of the drain should be higher than the eleva tion of the cell bottom General head boundary A GHB cell may not be a fixed head cell and should not be an inactive cell Well package A well cell may not be a fixed head cell and should not be an inactive cell are generated PM automatically runs MODFLOW BAT in a Command Prompt window DOS box During a flow simulation MODFLOW writes a detailed run record to the file OUTPUT DAT saved in the model folder MODFLOW saves the simulation results in various unformatted binary files only if a flow simulation has been successfully completed See MODFLOW Output Control page 74 for details about the output terms of MODFLOW 78 2 Modeling Environment 2 6 1 20 MODFLOW View MODFLOW View Run Listing File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run list file OUTPUT DAT which contains a detaile
252. e grid respectively Pattern for initial placement of particles NPLANE is used to select a pattern for initial placement of moving particles NPLANE 0 the random pattern is selected for initial placement Parti cles are distributed randomly in both the horizontal and vertical directions Fig 2 48b This option generally leads to smaller mass balance discrep ancy in nonuniform or diverging converging flow fields NPLANE gt 0 the fixed pattern is selected for initial placement The value of NPLANE serves as the number of planes on which initial par ticles are placed within each cell Fig 2 48a This fixed pattern may work better than the random pattern only in relatively uniform flow fields For two dimensional simulations in plan view set NPLANE 1 For cross 2 6 The Models Menu 93 sectional or three dimensional simulations NPLANE 2 is normally ad equate Increase NPLANE if more resolution in the vertical direction is desired coe Fig 2 48 Initial placement of moving particles adapted from Zheng 117 a Fixed pattern 8 particles are placed on two planes within a cell b Random pat tern 8 particles are placed randomly within a cell No of particles per cell in case of DCCELL lt DCEPS NPL is the num ber of initial particles per cell to be placed at cells where the relative cell concentration gradient DCCELL is less than or equal to DCEPS Generally NPL can be set to zero since advection i
253. e 5 2 River data Row Column Stage ft Riverbed Elevation ft 4 1 100 0 90 0 4 2 100 0 90 0 4 3 100 0 90 0 4 4 99 0 89 0 4 5 99 0 89 0 5 6 98 0 88 0 6 7 97 0 86 0 7 8 96 0 86 0 8 9 95 0 85 0 9 10 94 0 84 0 9 11 94 0 84 0 9 12 94 0 84 0 9 13 94 0 84 0 9 14 93 0 83 0 9 15 93 0 83 0 5 3 Parameter Estimation and Pumping Test 323 Table 5 3 Measurement data Borehole X Y Head ft Borehole X Y Head ft 1 250 750 124 0 7 4750 2250 108 5 2 1750 2250 119 9 8 4750 2250 111 7 3 6250 1250 113 9 9 6750 4250 107 6 4 250 3750 116 1 10 3750 6250 111 3 5 5750 5750 113 0 11 7250 6750 115 6 6 2750 3250 114 0 Modeling Approach and Simulation Results The aquifer is simulated using a grid of one layer 15 columns and 15 rows A regular grid spacing 500 ft is used for each column and row The layer type is 0 confined and the Transmissivity flag in the Layer Property dialog box is user specified Transmis sivity and recharge are defined as estimated parameters Note that the names of these two parameters are t_1 and rch_2 The optimized parameter values and the correlation coefficient matrix calculated by PEST are listed below Parameter Estimated 95 percent confidence limits value lower limit upper limit tat 1 000282E 02 9 902461E 03 1 010419E 02 rch_2 1 996080E 08 1 983990E 08 2 008169E 08 Note confidence limits provide only an indication of parameter uncertainty They rely on a linearity assumption which may not extend as far in
254. e Command Prompt DOS box by executing the batch file MF2K BAT Check the model data If this option is checked PM will check the geometry of the model and the consistency of the model data as given in Table 2 6 page 77 before creating data files The errors if any are saved in the file CHECK LIS located in the same folder as the model data e OK Click OK to generate MODFLOW 2000 input files In addition to the input files PM creates a batch file MF2K BAT in the model folder When all files are generated PM automatically runs MF2K BAT in a Command Prompt window DOS box During the parameter estimation process the user will notice that the parameter names PARNAM of time varying parameters e g RCH WEL are further combined with the stress period number to which the parameter pertains For example parameter number 2 of recharge in stress period 3 is indicated by RCH_2_3 For steady state simulations the string 1 is used After completing the parameter estimation process MODFLOW 2000 prints the optimized parameter values to the file MF2KOUT _b in the model folder The model results after the parameter estimation process are calculated by us ing the optimized parameter values During a parameter estimation process MODFLOW 2000 does not modify the original model data This provides a greater security for the model data because a parameter estimation process does not necessarily lead to a success PEST ASP MODFLOW 2
255. e MTRCT1 DAT Dispersion Package MTDSP1 DAT Sink amp Source Mixing Package MTSSM1 DAT 6 3 8 MT3DMS SEAWAT Advection Package MTMSADV1 DAT Basic Transport Package MTMSBTN1 DAT Chemical Reaction Package MTMSRCT1 DAT Dispersion Package MTMSDSP1 DAT Generalized Conjugate Gradient Solver MSMSGSG1 DAT Sink amp Source Mixing Package MTMSSSM1 DAT Variable Density Flow Package SEAWAT Only SW2KVDF1 dat 6 3 Input Data Files of the supported Model 6 3 9 RT3D Advection Package Basic Transport Package Chemical Reaction Package Dispersion Package Generalized Conjugate Gradient Solver Sink amp Source Mixing Package 6 3 10 PHT3D Advection Package Basic Transport Package Chemical Reaction Package Dispersion Package Generalized Conjugate Gradient Solver Sink amp Source Mixing Package PHREEQC Interface File PHREEQC Style Database File 6 3 11 PEST Instruction File Control File Block Centered Flow Package Template File Drain Package Template File Evapotranspiration Package Template File General Head Boundary Package Template File Recharge Package Template File River Package Template File Well Package Template File Stream Routing Flow Package Template File Interbed Storage Package Template File Grid Specification File used by MODBORE EXE Borehole Listing File used by MODBORE EXE Borehole Coordinates File used by MODBORE EXE filename is the name of the model MTMSADV1 DAT MTMSBTN1 DAT MTMSRCT1 DAT MT
256. e Stage Time Table of Reservoirs dialog box 2 6 The Models Menu 51 The Reservoir package requires the input of the starting and ending stages for each stress period These stage values are linearly interpolated to the beginning of each time step to determine whether the reservoir boundary is activated at that time point The stage values for each stress period are obtained by linear interpolation using the values specified in the Stage Time Table of Reservoirs dialog box If the starting time of a stress period is earlier than the earliest observation time in the table the earliest observed stage is used as the starting stage for that stress period Similarly if the ending ending time of a stress period is beyond the latest observation time the latest observed stage is used gt Output Option 1 Make a stage volume area table for reservoirs If this option is checked reser voir stage area and volume will be printed to the Run Listing File of MOD FLOW each time step 2 Number of values in the stage volume area table NPTS NPTS is the number of values in printed table of stage volume and area for each reservoir First and last stage value are minimum and maximum elevations within area of potential inundation A value of 15 or greater is recommended for detailed representation of stage volume and stage area relations 2 6 1 8 MODFLOW Flow Packages River The purpose of the River package is to simulate the effect of flow between
257. e Zoom In button XI 2 Move the mouse pointer to where the user wants a corner of the Zoom window 3 Drag the mouse pointer until the window covers the model area to be displayed 4 Release the mouse button 3 2 3 5 Zoom Out Clicking on the Zoom Out button forces PMPATH to display the entire model grid 214 3 The Advective Transport Model PMPATH 3 2 3 6 Particle Color Clicking on the Particle color button allows the user to select a color for new particles from a Color dialog box Particles with different colors are useful for de termining the capture zones of various pumping wells In this case particles with a certain color are placed around or on the cell faces of each pumping well Through backward tracking capture zones of each pumping well can be recognized by their different colors 3 2 3 7 Run Particles Backward Click J to execute backward particle tracking for a specified time length The time length is the product of the number of particle tracking steps and the particle tracking step length given in the Particle Tracking Time Properties dialog box See Section 3 3 2 for details 3 2 3 8 Run Particles Backward Step by Step Click to move particles backward a single particle tracking step The particle tracking step length is defined in the Particle Tracking Time Properties dialog box See Section 3 3 2 for details 3 2 3 9 Stop Particle Tracking Click E to stop particle tracking or stop redrawing
258. e been defined see Section 2 6 2 11 on page 104 Select this menu item to open a Scatter Diagram Concentration dialog box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 on page 78 except the concentration values replace the head values MT3DMS SEAWAT View Concentration Time Curves 2 6 The Models Menu 109 This menu item is available only if Concentration Observations have been defined see Section 2 6 2 11 on page 104 Select this menu item to open a Time Series Curves Concentration dialog box which is identical to the Time Series Curves Hydraulic Head dialog box Fig 2 41 on page 82 except the concentration values replace the head values 2 6 3 PHT3D With the exception of user definable reaction modules that use PHREEQC 2 as the reaction simulator the PHT3D interface of PM is identical to the MT3DMS SEAWAT interface with the Simulation Mode setting to Constant Density Transport with MT3DMS see Section 2 6 2 1 As is the case with MT3DMS the composition of a PHT3D model starts with Simulation Settings and PHT3D simulations are carried out on the basis of flow fields computed beforehand by MODFLOW Thus as given by Prommer and others 97 PHT3D cannot reproduce the potential impact of reactive processes on the ground water flow field and the model is not suitable to predict for example the impact of bioclogging or mineral precipitation on the hydraulic properties of an aquifer The s
259. e been defined see Section 2 6 4 10 on page 117 Select this menu item to open a Time Series Curves Concentration dialog box which is identical to the Time Series Curves Hydraulic Head dialog box Fig 2 41 on page 82 except the concentration values replace the head values 2 6 The Models Menu 119 2 6 5 MOC3D 2 6 5 1 MOC3D Subgrid Within the finite difference grid used to solve the flow equation in MODFLOW the user may specify a window or subgrid over which MOC3D will solve the solute transport equation This feature can significantly enhance the overall efficiency of the model by avoiding calculation effort where it is not needed However MOC3D requires that within the area of the transport subgrid row and column discretization must be uniformly spaced that is x and y must be constant although they need not be equal to each other The spatial discretization or rows and columns beyond the boundaries of the subgrid can be nonuniform as allowed by MODFLOW to permit calculations of head over a much larger area than the area of interest for transport simulation Vertical discretization defined by the cell thickness can be variable in all three dimensions However large variability may adversely affect numerical ac curacy For details refer to Konikow et al 74 for the model assumptions that have been incorporated into the MOC3D model The subgrid is defined in the Subgrid for Transport MOC3D dialog box Fig 2 63 MOC3D as
260. e calculated and mea surement data if any The Chart tab displays the time series curves Refer to Section 2 6 1 20 for details about these tabs 2 Click the Chart tab to display the curves Fig 4 35 3 Use the button Save Plot As to save the chart to a file or use Copy to Clipboard to copy the chart to the Windows Clipboard An image in the clipboard can be pasted into most word or graphics processing software by using Ctrl V 4 Click OK to close the Time Series Curves Concentration dialog box 4 1 4 Parameter Estimation The process of estimating unknown parameters is one of the most difficult and crit ical steps in the model application The parameter estimation often referred to as model calibration of a flow model is accomplished by finding a set of parameters hydrologic stresses or boundary conditions so that the simulated values match the measurement values to a reasonable degree Hill 62 gives methods and guidelines for model calibration using inverse modeling To demonstrate the use of the parameter estimation program PEST within PM we assume that the hydraulic conductivity in the third layer is homogeneous but its Time Series Curves Concentration x OBSNAM Simulation Time Calculated Value Observed Value 0 0 0 0 O 0 0 0 0 0 0 0 2912900 7 0026E 06 2912900 1 7839E 15 2912900 2 6144E 04 2912900 8 225101E 14 2912900 7 7791E 05 2912900 2 6645E 14 5825800 7 8247E 04 5825800 1 63526 11
261. e calculated values and observed values pertain Save Table Press this button to save the data of OBSNAM Calculated Value Observed Value and Simulation Time in an ASCII file This button is enabled only when the Data tab is chosen The Chart Tab Fig 2 40 displays the scatter diagram using the calculated and observed data Scatter diagrams are often used to present the quality of cali bration results The observed values are plotted on one axis against the corre sponding calculated values on the other If there is an exact agreement between 80 2 Modeling Environment Scatter Diagram Hydraulic Head E x Data r Label I Display observation name s Comparison of Calculated and Observed Heads 5 TLAS I Display simulation time s 124 r Observation Use results of all observations 1227 Use results of the following OBSNAM 1204 OBSNAM 1 z T 2 r Simulation Time Use results from all simulation time s C Use results from the following Calculated Values a 4 simulation time 114 5 Time 1 z nat i Axes Bounds T J Fix Bounds aer p Upper Bound 124 0134 19 Lower Bound 107 6 108 110 112 114 116 118 120 122 124 Observed Values Reset Bounds Variance 5 72389999999862E 04 Copy to Clipboard Save Plot As OK Cancel Help Fig 2 40 The Chart tab of the Scatter Diagram Hydraulic Head dialog box measurement and simulatio
262. e cross sectional display the coordinate system the horizontal extent of the Viewing Window and the position of the model grid to fit the condition of the study area Regardless of the display modes the mouse pointer position x y z is always expressed in the world coordinates according to the user defined coordinate system and K I J is expressed in Layer Row Column cell indices The position of the grid cursor is shown in the tool bar The grid cursor can be moved by using the arrow keys clicking the mouse on the desired position using J J buttons in the tool bar or typing the new position in the layer row column edit fields and pressing the Enter key The parameter values of the cell pointed to by the grid cursor are displayed from left to right in the status bar A summary of the tool bar buttons of the Data Editor is given in Table 2 4 14 2 Modeling Environment File Value Options Help B i t ofe alfa colle eme al apr ee position of the grid cursor k J mouse pointer grid cursor Viewing Window Position of the mouse pointer x y z Position of the mouse pointer K J Period number if the data is time dependent Current parameter or package 1486286 14696 36 085 745 1 7108 Time independent E foizontal Hi Conductivity IL TT CO a a i Value s of the cell pointed by the grid cursor Fig 2 5 The Data Editor Grid View I MIRO_GRO PMS EIT Processing Modflow Pro
263. e difference method is reasonably accurate It is advisable to use the upstream finite difference method anyway for obtaining first approximations in the initial stages of a modeling study The method of characteristics MOC scheme was implemented in the trans port models MOC 73 and MOC3D see Section 2 6 5 3 and has been widely used One of the most desirable features of the MOC technique is that it is virtually free of numerical dispersion which creates serious diffi culty in many numerical schemes The major drawback of the MOC scheme is that it can be slow and requires a large amount of computer memory when a large number of particles is required Also the computed concentrations sometimes tend to show artificial oscillations The modified method of characteristics MMOC uses one particle for each finite difference cell and is normally faster than the MOC technique At each new time level a particle is placed at the nodal point of each finite difference _ Advection Package MTADV1 Solution Scheme Hybrid MOC MMOC HMOC Particle Tracking Algorithm Hybird 1st order Euler and 4th order Runge Kutta v Simulation Parameters Max number of total moving particles MXPART 12500 Courant number PERCEL 0 75 Concentration weighting factor WD 0 5 Negligible relative concentration gradient DCEPS 0 00001 Pattern for initial placement of particles NPLANE 1 No of particles per cell in case of DCCELL lt DCEPS NPL 0
264. e following messages 1 Current position of the mouse pointer in both x y z coordinates and K I J indices Hydraulic head at the cell K I J Average horizontal pore velocity at the center of the cell K I J Average vertical pore velocity at the center of the cell K I J Current stress period of the flow simulation Current time step of the flow simulation and Number of particles ADNKWN See Particle Tracking Time Properties dialog box Section 3 3 2 for how to change the current stress period and time step The hydraulic heads at the current stress period and time step are calculated by MODFLOW The x and y components of the average horizontal pore velocity at the center of a cell is obtained by averaging the velocities vz1 Vz2 and Vy1 Vy2 respectively Equation 3 3 The average vertical pore velocity at the center of a cell is the average of the velocities v1 vz2 Equation 3 3 The vertical velocity is defined as positive when it points in the K direction 3 2 3 Tool bar The tool bar provides quick access to commonly used commands in the PMPATH modeling environment You click a button on the tool bar once to carry out the action represented by that button To change the current layer or the local vertical coordi nate click the corresponding edit field in the tool bar and type the new value then press ENTER See equation 3 7 for the definition of the local vertical coordinate Table 3 1 summa
265. e insensitive prior information label The label must be no more than twenty characters in length and must be unique to each prior information article e Pifacand Parnme Pifac is a parameter factor Parnme is parameter name Both are required To the left of the sign there are one or more combinations Pifac and Parnme with a log prefix to Parnme if appropriate Pi fac and Parnme are separated by a character signifying multiplication All param eters referenced in a prior information equation must be adjustable parameters i e you must not include any fixed or tied parameters in an article of prior in formation Furthermore any particular parameter can be referenced only once in any one prior information equation however it can be referenced in more than one equation 158 2 Modeling Environment e Pival Pival is the value of the right side of the prior information equation e Weight Weight is the weight assigned to the article of prior information in the parameter estimation process The prior information weight should ideally be inversely proportional to the standard deviation of Pival it can be zero if you wish but must not be negative In practice the weights should be chosen such that the prior information equation neither dominates the objective function or is dwarfed by other components of the objective function In choosing observa tion and prior information weights remember that the weight is multiplied by its
266. e locations within the cell J I K are specified using local coordinates LJ LI LK Local coordinates vary within a cell from zero to one as shown in Fig 6 1 J 0 1 K 0 1 1 Z y 0 X Fig 6 1 Local coordinates within a cell 6 3 Input Data Files of the supported Model 6 3 1 Name File The name file contains the names of most input and output files used in a model sim ulation and controls the parts of the model program that are active The format of the name file for MODFLOW 88 96 is identical to that of MODFLOW 2000 except the latter has some additional file types marked with the character see Ftype below The name file contains one record similar to the following line for each input and output file used in a MODFLOW model simulation All variables are free format The length of each record must be 199 characters or less Ftype Nunit Fname Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space 390 6 Supplementary Information Ftype is the file type which must be one of the following character values Ftype may be entered in all uppercase all lowercase or mixed case LIST for the simulation listing file BAS for the Basic Package of MODFLOW BCF for the Block Centered Flow Package of MODFLOW CHD for the Time Variant Specified Head Package DE4 for the Direct Solver Package DRN for the Drain Package EYT for the E
267. e meth ods to calculate the effects of other processes For improved efficiency the user can apply MOC3D to a subgrid of the primary MODFLOW grid that is used to solve the flow equation However the transport subgrid must have uniform grid spacing along rows and columns Using MODFLOW as a built in function MOC3D can be modified to simulate density driven flow and transport MT3D 117 120 MT3D is a single species transport model uses a mixed Eulerian Lagrangian approach to the solution of the three dimensional advective dispersive reactive transport equation MT3D is based on the assumption that changes in the con centration field will not affect the flow field significantly This allows the user to construct and calibrate a flow model independently After a flow simulation is complete MT3D simulates solute transport by using the calculated hydraulic heads and various flow terms saved by MODFLOW MT3D can be used to simu late changes in concentration of single species miscible contaminants in ground water considering advection dispersion and some simple chemical reactions The chemical reactions included in the model are limited to equilibrium controlled linear or non linear sorption and first order irreversible decay or biodegradation Since most developers focus their efforts on supporting its successor MT3DMS 121 MT3D is considered to be obsolete in terms of further development MT3DMS 121 123 MT3DMS is a further development of MT3D
268. e of the pores and water moves faster at the internal points between soil grains than on the solid surface This spreading is often referred to as mechanical dispersion and it occurs in all three spatial directions The coeffi cient of mechanical dispersion is defined by a vi where a is the dispersivity and v is the average linear velocity in the i direction The sum of mechanical dispersion and molecular diffusion is called hydrodynamic dispersion Values of dispersivity used for simulations generally depend on the scale of a concentration plume being considered While a plume grows it will not only undergo the microscopic mechanical dispersion but also the dispersion caused by macroscopic heterogeneities This results in a trend of increasing dispersivity values with the scale of observation Summaries of the scale dependent disper sivity values can be found in Anderson 6 7 Gelhar et al 49 50 and Spitz and Moreno 109 Note that all heterogeneity which is not explicitly represented in the model should be incorporated into the dispersion coefficients TRPV is the ratio of the vertical transverse dispersivity to the longitudinal dis persivity DMCOEFF is the effective molecular diffusion coefficient D L T71 equation 2 38 DMCOEF describes the diffusive flux of a solute in water from an area of greater concentration toward an area where it is less concentrated The mass flux is pro portional to the concentration gradien
269. e performed in a steady state flow simulation Create a new model Assign model data Perform the flow simulation Check simulation results Calculate subregional water budget Produce output NnBWN 4 1 2 1 Step 1 Create a New Model The first step in running a flow simulation is to create a new model gt To create a new model 1 Select File New Model A New Model dialog box appears Select a folder for saving the model data such as C Models tutorial1 and type the file name TU TORIALI as the model name A model must always have the file extension PM5 All file names valid under MS Windows with up to 120 characters can be used It is a good idea to save every model in a separate folder where the model and its output data will be kept This will also allow PM to run several models simultaneously multitasking 2 Click OK PM takes a few seconds to create the new model The name of the new model name is shown in the title bar 4 1 2 2 Step 2 Assign Model Data The second step in running a flow simulation is to generate the model grid mesh specify cell status and assign model parameters to the model grid PM requires the use of consistent units throughout the modeling process For example if you are using length L units of meters and time T units of seconds hydraulic conductivity will be expressed in units of m s pumping rates will be in units of m s and dispersivities will be in units of m
270. e that there is no space between log and the following opening bracket Thus in the above example if parameter par1 is log transformed the prior information article should be rewritten as pil 1 0 log parl 362671 1 0 pr_info Note that logs are taken to base 10 Though not illustrated you will also need to review the weight which you attach to this prior information article by comparing the extent to which you would permit the log of parl to deviate from 0 362671 with the extent to which model generated observations are permitted to deviate from their corresponding measurements The left side of a prior information equation can be comprised of the sum and or difference of a number of factor parameter pairs of the type already illustrated these pairs must be separated from each other by a or sign with a space to either side of the sign For example 2 6 The Models Menu 159 pi2 1 0 par2 3 43435 x par4 2 389834 x par3 1 09e3 3 00 group_pr Prior information equations which include log transformed parameters must express a relationship between the logs of those parameters For example if you would like the ratio between the estimated values of parameters par1 and par2 to be about 40 0 the prior information article may be written as pis 1 0 log parl 1 0 x log par2 1 60206 2 0 group_pr The Regularization Tab Tikhonov regularization is the most commonly used method of regula
271. e the method of characteristics MOC to simulate the advective transport in which dissolved chemicals are repre sented by a number of particles and the particles are moving with the flowing ground water Besides the MOC method the MT3DMS model provide several other methods for solving the advective term see Section 2 6 2 3 for details The hydrodynamic dispersion can be expressed in terms of the dispersivity L and the coefficient of molecular diffusion L T for the solute in the porous medium The types of reactions incorporated into MOC3D are restricted to those that can be represented by a first order rate reaction such as radioactive decay or by a retardation factor such as instantaneous reversible sorption desorption reactions governed by a linear isotherm and constant distribution coefficient K4 In addition to the linear isotherm MT3DMS supports non linear isotherms i e Freundlich and Langmuir isotherms Prior to running MT3DMS or MOC3D you need to define the observation bore holes for which the breakthrough curves will be calculated gt To define observation boreholes 1 Select Models MT3DMS Concentration Observations or Models MOC3D Concentration Observations A Concentration Observation dialog box appears Enter the coordinates of the observation boreholes into the dialog box as shown in Fig 4 18 For boreholes 1 and 2 set the proportion value of the first layer to 250 4 Tutorials 1 and other layers
272. e values for RELPARMAX and FACPARMAX can vary enormously from case to case If you are unsure of how to set these parameters a value of 5 for 170 2 Modeling Environment each of them is often suitable For highly non linear problems these values are best set low If they are set too low however the estimation process can be very slow An inspection of the PEST run record by pressing the ESC key will often show whether you have set these values too low for PEST records the maxi mum parameter factor and relative changes are recorded on this file at the end of each optimization iteration If these changes are always at their upper limits and the estimation process is showing no signs of instability it is quite possible that RELPARMAX and or FACPARMAX are too low and could be increased Note that FACPARMAX can never be less than 1 RELPARMAX can be less than 1 as long as no parameter s upper and lower bounds are of opposite sign If necessary use OFFSET to shift the parameter domain so that it does not include zero FACORIG is a criterion for modifying RELPARMAX and FACPARMAX If in the course of an estimation process the absolute value of a parameter falls below the product of FACORIG and its original value then the product is substituted for the denominators of equation 2 62 or equation 2 63 to prevent the denomina tors becoming zero or too small FACORIG is not used to adjust limits for log transformed parameters FACORIG must be g
273. eave Editor or click the leave editor button ee gt To specify the boundary flux 1 Select Models MODFLOW Well Since MODFLOW does not have a separate package for a specified flux bound ary condition we use the Well package to simulate this boundary condition 2 Make sure the cell selected is 1 36 1 Since the width of this cell is 500 m the inflow rate through this cell is 500m x 0 0672m3 day m 33 6m day Press Enter or right click to open the Cell Value dialog box enter 33 6 then click OK to exit the dialog box A positive value means that water enters the system 3 Specify the value 33 6 to the cell 1 36 2 the value 16 8 to the cells 1 36 3 and 1 36 4 and the value 11 2 to the rest of the South boundary 4 2 Unconfined Aquifer System with Recharge 279 4 Select File Leave Editor or click the leave editor button w 4 2 2 5 Step 5 Perform steady state flow simulation You are just about ready to run the flow model Quickly review the data that you have entered for each of the parameters by checking the values of various cells Correct any data that does not look right by redoing the appropriate sections above gt To run the flow simulation 1 Select Models Modflow Run 2 Click OK to accept the warning regarding the Effective Porosity 3 Click OK in the Run Modflow dialog box to generate the required data files and to run MODFLOW you will see a DOS window open and MODFLOW perform the it
274. ecause model cells of this layer type do not convert between dry and wet Therefore layer type 3 should be used for all layers impervious SX lt 10 m gt Fig 5 38 Seepage surface through a dam 346 5 Examples and Applications no flow boundary TF i D a 5 e 5 D 5 5 D x fixed head boundary no flow boundary Fig 5 39 Model grid and the boundary conditions Cells in the J direction 5 6 8 9 Si CE J A p e E A O e A a aa Seo 8 77 8 54 8 31 8 08 7 86 7 66 7 46 7 27 7 10 6 94 6 80 6 68 6 58 6 51 6 46 9 01 21 8 77 8 53 8 30 8 07 7 86 7 65 7 45 7 26 7 08 6 92 6 78 6 66 6 56 648 6 43 6 40 7 84 763 7 42 7 23 7 05 6 89 6 74 6 62 6 51 6 43 6 38 6 35 7 60 7 39 719 7 01 6 84 6 69 655 644 6 36 6 30 6 27 7 14 6 95 6 77 6 61 6 47 6 35 6 26 6 19 6 16 6 87 6 68 6 51 6 36 6 23 6 13 6 05 6 02 6 40 623 6 08 5 96 5 88 5 83 5 91 5 77 5 67 5 61 5 41 Cells in the I direction Fig 5 40 Calculated hydraulic heads after one iteration step elevation of the cell bottom m 5 4 Geotechnical Problems 347 3 a a Toy 95 oc or a hs a i E i Hy na i i Hi H Lid ial Fig 5 41 Calculated hydraulic heads distribution and the form of the seepage surface 95 as p o
275. eck or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start PEST Check this option if the user does not want to run PEST The program can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file PEST BAT Perform PESTCHEK prior to running PEST PESTCHEK reads the PEST input files generated by PM making sure that every item is consistent with every other item and writes errors to the file PEST CHK It is recommended to use PESTCHEK as PM and PEST do not carry out consistency checks of all user specified control data and parameters Check the model data If this option is checked PM will check the geometry of the model and the consistency of the model data as given in Table 2 6 before creating data files The errors if any are saved in the file CHECK LIS located in the same folder as the model data e OK Click OK to generate MODFLOW and PEST input files In addition to the input files PM creates a batch files PEST BAT
276. ed head at time t MODFLOW View Subsidence Scatter Diagram This menu item is available only if Subsidence Observations have been defined see Section 2 6 1 16 Select this menu item to open a Scatter Diagram Subsidence dia log box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 except the subsidence values replace the head values MODFLOW View Compaction Scatter Diagram This menu item is available only if Compaction Observations have been defined see Section 2 6 1 17 Select this menu item to open a Scatter Diagram Compaction dialog box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 except the compaction values replace the head values MODFLOW View Head Time Curves This menu item is available only if Head Observations have been defined see Section 2 6 1 14 Select this menu item to open the Time Series Curves Hydraulic Head dialog box Fig 2 41 The options are grouped under two tabs Data and Chart as described below e The Data Tab The Data tab contains two tables The table to the left shows the names OBSNAM of the observation boreholes and their Plot and Color set 82 2 Modeling Environment tings The table to the right shows the Observation Time Calculated Values and Observed Values OBSNAM This column displays the name of each observation borehole spec ified in the Head Observation dialog box Fig 2 35 Plot The t
277. ed on the size of the current row or col umn will be copied to all rows or columns passed by the grid cursor Duplication is on when this button is depressed When this button is depressed Layer row column copy is on and the following rules apply 1 If the display mode is Grid View or Map View when moving to another layer the zones and cell values of the current layer will be copied to the desti nation layer 2 If the display mode is Row View when mov ing to another column the cell values of the current row cross section will be copied to the destination row cross section 3 If the display mode is Column View when moving to another column the cell values of the current column cross section will be copied to the destination column cross section Manage model data for transient simulations 16 2 Modeling Environment HH HITT UI HUT TTT LLL HTHH AII tI u peu 1007003 9825973 88 10528 12 53 72 Time independent intial Hydrauic Heads L 15 Fig 2 7 The Data E
278. ed such that the con taminated area lies within the capture zone of the well When different realizations of the heterogeneous distribution of hydraulic conductivity are introduced it is obvi ous that the capture zone not always covers the entire contaminated area The safety criterion for the measure can be defined as the percentage of the covered area in re lation to the entire contaminated area The expected value of the safety criterion can be obtained from stochastic simulation Modeling Approach and Simulation Results Using the Field Generator log normal distributions of the horizontal hydraulic con ductivity are generated and stored in ASCII Matrix files First each generated re alization is imported into the horizontal hydraulic conductivity matrix then a flow simulation is performed The capture zone of the pumping well as well as pathlines are computed with PMPATH The resulting safety criterion is obtained by a Monte Carlo simulation This implies that many realizations of the parameter field are pro duced and used in the flow simulation Fig 5 61 shows results of five realizations and the calculated mean safety crite rion The mean safety criterion is the sum of safety criteria divided by the number of realizations A large number of realizations may be required for the mean safety criterion to converge no flow boundary no ilow boundary h 8m constant hea 7 7 e n f g Ji g 8 2 8
279. ed to undergo A parameter is denoted as either relative limited or factor limited through PARCHGLIM see page 154 Ifa parameter b is relative limited the relative change of the parameter value between optimization iterations i 1 and i is defined as b _1 bi 2 62 7A 2 62 The absolute value of this relative change must be less than RELPARMAX If a parameter upgrade vector is calculated such that the relative adjustment for one or more relative limited parameters is greater than RELPARMAX the magnitude of the upgrade vector is reduced such that this no longer occurs If parameter b is factor limited the factor change between optimization iter ations i 1 and i is defined as bi 1 bi if b 1 gt b bi bi if Jbl lt Jbl 2 63 This factor change must be less than FACPARMAX If a parameter upgrade vector is calculated such that the factor adjustment for one or more factor lim ited parameters is greater than FACPARMAX the magnitude of the upgrade vector is reduced such that this no longer occurs It is important to note that a factor limit will not allow a parameter to change sign If a parameter must be free to change sign during an optimization process it must be relative limited furthermore RELPARMAX must be set at greater than unity or the change of sign will be impossible Similarly if a parameter s upper or lower limit is zero it cannot be factor limited and RELPARMAX must be at least unity Suitabl
280. ee eee eee 284 4 3 1 Overview of the Hypothetical Problem 284 4 3 1 1 Step 1 Create a New Model 285 4 3 1 2 Step 2 Generate the Model Grid 285 4 3 1 3 Step 3 Refine the Model Grid 286 4 3 1 4 Step 4 Assign Model Data 287 4 3 1 5 Step 5 Perform steady state flow simulation 293 4 3 1 6 Step 6 Extract and view results 293 5 Examples and Applications 0 0 0 0 cece eee eee 297 5 1 Basic Flow Problems 0 0 0 cece eee eee eens 297 5 1 1 Determination of Catchment Areas 297 5 1 2 Use of the General Head Boundary Condition 301 5 1 3 Two layer Aquifer System in which the Top layer Converts between Wet and Dry 0 0 eee eee 303 5 1 4 Water Table Mount resulting from Local Recharge 305 5 1 5 Perched Water Table 0 0 308 5 1 6 An Aquifer System with Irregular Recharge and a Stream 311 5 1 7 Flood im a River soi sts es tees eae ee iape 314 5 1 8 Simulation of Lakes 0 0 eee eee eee 317 5 2 EPA Instructional Problems 0 00 00 e eee eee 320 5 3 Parameter Estimation and Pumping Test 321 5 3 1 Basic Parameter Estimation Skill 0 321 5 3 2 Estimation of Pumping Rates 00 325 5 3 3 The Theis Solution Transient Flow to a Well in a Confined Aquif
281. effective porosity ne 0 2 which overlies a confined aquifer of a variable thickness HK 2 m day VK 1 m day specific storage Ss 5 x 1075 ne 0 25 A silty layer thickness 2 m KH 0 5 m day VK 0 05 m day ne 0 25 separates the two aquifers The elevations of the aquifer tops and bottoms are known and saved in ASCII Matrix files Three pump ing wells pumping at 500m day each abstracts water from the confined aquifer The river has the following properties River stage 19 4 m on the upstream boundary River stage 17 m on the downstream boundary river width 100 m Granite Hills upstream fixed head boundary 5000 m downstream fixed head boundary South Granite Hills 6750 m Fig 4 48 Configuration of the hypothetical model 4 3 Aquifer System with River 285 riverbed hydraulic conductivity 2 m day riverbed thickness 1 m Riverbed bottom elevation 17 4 m on the upstream boundary Riverbed bottom elevation 15 m on the downstream boundary The task is to construct a 3 layer groundwater flow model of the area including the river and the pumping wells and to determine the capture zone of the wells Seven main steps need to be done in this tutorial NN WN Create a new model Generate the model grid Refine the model grid Assign the model data Perform steady state flow simulation Extract and view results 4 3 1 1 Step 1 Create a New Mode
282. efficiency on scalar computers occur for three dimensional non linear problems For these types of problems it may be well worth the time and effort to try more than one solver Note The GMG solver 115 is only implemented in MODFLOW 2000 The MODFLOW version gt MODFLOW Density package from KIWA does not support the Direction Solution package 2 6 The Models Menu 63 MODFLOW Solvers DE45 Although a direct solver requires more memory and typically requires more compu tational effort than iterative solvers it may execute faster than an iterative solver in some situations The Direct Solution package 53 uses Gaussian elimination with an alternating diagonal equation numbering scheme that is more efficient than the standard method of equation numbering It is the most efficient when solving small linear problems Use the Direct Solution DE45 dialog box Fig 2 30 to specify required param eters as described below e Maximum iterations external or internal is the maximum number of iterations in each time step Set this number to 1 if iteration is not desired Ideally iteration would not be required for direct solution however it is necessary to iterate if the flow equation is non linear see Problem type below or if computer precision limitations result in inaccurate calculations as indicated by a large water budget error For a non linear flow equation each iteration is equally time consuming because the coefficient mat
283. el h2 Yh C h EXP 5 Co 2 69 Exponential model h Yay C j exe Co 2 70 a Where C is the variance of measurement data and is calculated by the program a is the correlation length co the nugget variance a the slope and w the power factor of the power model w 1 yields the linear model Fig 2 88 The Search Method Tab The interpolation algorithms use three search methods to find a certain number of the measurement data points to interpolate a cell value The search methods are called SIMPLE QUADRANT and OCTANT The search radius is assumed to be infinitely large The SIMPLE search method finds the data points nearest to the model cell The QUADRANT or OCTANT search methods find closest data points from each quad rant or octant around a model cell Figures 2 89a and 2 89b The number of data points used in a search is defined by the Data Per Sector value If fewer than Data x m Variogram Model m Parameters Correlation Length a fos Nugget Variance Co fos Power Factor wy ni Slope nu Cancel OK Fig 2 87 The Variogram dialog box 182 2 Modeling Environment Yh Y h 087 linear 0 8 logarithmic 0 6 0 6 0 4 amp 0 4 E ower 02 P 0 2 Co 1 2 3 4 h 2 5 10 2030 Fig 2 88 Linear Power and logarithmic models a b Fig 2 89 Search patterns used by a the Quadrant Search method Data per sec tor 2 and b the Octant Search method Dat
284. elect a model and the type of result that you want to display then click OK MODFLOW mocan MT3p MT30MS SEAWAT PHT3D AT3D Result Type Hydraulic Head z Fig 4 57 Steady state hydraulic head distribution in the first model layer NN Click on the L button and drag a small box around the cell containing Well 1 by holding down the left mouse button and moving the mouse When you release the mouse button the Add New Particles dialog box appears In the Particles on circles group set the number of particles to 15 the radius R 80 and the number of planes NK 3 Click the Properties tab and change the color of new particles to Blue Click OK to close the Add New Particles dialog box Use a similar procedure to add particles around Well 2 and Well 3 Assign a different color say Green and Black to each of these particle groups Select Options Environment to open the Environment Options dialog box for setting up the display of the hydraulic heads contours and cross sections Click the Contours tab check the Visible box and click the Restore Defaults button to get standard settings Click the Cross Sections tab check the Visible and Show grid boxes and set Exaggeration 25 Projection Row 15 and Projection Column 9 4 3 Aquifer System with River 295 Click OK to close the Environment Options dialog box The hydraulic head contours for layer 3 and cross sections sho
285. elected Flag 0 For each time step within a period the package lin early interpolates prescribed hydraulic heads h for each time variant specified head boundary cell by using the equation PERTIM PERLEN h h he hs 2 27 where PERTIM is the starting time of a time step within a stress period and PERLEN is the length of the stress period The interpolated head values remain constant during a time step If a cell is specified as a time variant specified head boundary for a stress period and omitted in the specification for a subsequent period it remains a fixed head boundary with a head equal to that at the end of the previous period 2 6 The Models Menu 59 2 6 1 11 MODFLOW Flow Packages Well An injection or a pumping well is defined by using the Cell by Cell or Polygon input methods of the Data Editor to assign the following parameters to model cells The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress periods the input parameters can be different from period to period e Recharge rate of the well Qu L T Negative values are used to indicate pumping wells while positive cell values indicate injection wells The injection or pumping rate of a well is independent of both the cell area and the hydraulic head in the cell MODFLOW assumes that a well penetrates the full thickness of the cell To simulate wells that penetrate more than
286. electing Transmissivity Vertical Leakance or Storage Coefficient from the Parameters menu regardless whether the Calculated or User Specified settings are used 2 To estimate the conductance values of head dependent cells e g drain general head boundary river or stream cells or pumping rates of wells a non zero con ductance value or pumping rate must be assigned to those cells with adjustable parameters Conductance values or pumping rates will not be adjusted if the user specified cell values are zero Table 2 9 Adjustable parameters through PEST within PM Packages Abbreviation Adjustable Parameters Block Centered Flow BCF Layer type 0 T S and VCONT Layer type 1 HK Sy and VCONT Layer type 2 T S Sy and VCONT Layer type 3 HK S Sy and VCONT Layer Property Flow LPF All layer types HK HANI VANI VK Ss and Sy Drain DRN Conductance of drain cells Evapotranspiration EVT Maximum evapotranspiration rate General Head Boundary GHB Conductance of GHB cells Horizontal Flow Barrier HFB6 Hydraulic characteristic of barrier Interbed Storage IBS Inelastic storage factor Recharge RCH Recharge flux Reservoir RES Conductance of RES cells River RIV Conductance of RIV cells Stream Flow Routine STR Conductance of STR cells Well WEL Pumping or injection rates of WEL cells 2 6 The Models Menu 151 2 6 8 1 PEST Parameter Estimation Simulation Settings The required inputs and options for running PEST are specified in the
287. ells 2 Select File Leave Editor or click the leave editor button w gt To assign the input rate of contaminants 1 Select Models MT3DMS Sink Source Concentration Recharge 2 Assign 12500 g m to the cells within the contaminated area This value is the concentration associated with the recharge flux Since the recharge rate is 8 x 107 m m s and the dissolution rate is 1 x 1074 252 4 Tutorials 3 gt 1 2 gt 1 2 ug s m the concentration associated with the recharge flux is 1 x 1074 8 x 107 12500 ug m Select File Leave Editor or click the leave editor button E To assign the transport parameters to the Advection Package Select Models MT3DMS Advection The Advection Package MT3DMS dialog box appears Enter the values shown in Fig 4 20 into the dialog box select Method of Characteristics MOC for the solution scheme and First order Euler for the particle tracking algorithm Click OK to close the dialog box To assign the dispersion parameters Select Models MT3DMS Dispersion The Dispersion Package MT3D dialog box appears Enter the ratios of the transverse dispersivity to longitudinal dispersivity as shown in Fig 4 21 Click OK PM displays the model grid At this point you need to specify the longitudinal dispersivity to each cell of the grid Click the 1 button if the display mode is not Grid View Select Value Reset Matrix or press Ctrl R ty
288. em and the cell incides The Model Dimension dialog box 0 0000000 The Grid Editi sereen soe pet cae Reyer ake oo ge R bbe eg SOE fas The Grid Size dialog box 0 0 0 eee eee The Data Editor Grid View 1 0 0 0 00 cece cece eee eee The Data Editor Map View 000 cece cee eee e ene The Data Editor Cross sectional View 0 000 cee eee The Cell Information dialog box 0 0 02000 The Search and Modify Cell Values dialog box The Temporal Data dialog box 00 cee eee ee ee nee The Convert Model dialog box 0 00 e eee eee eee ee Telescoping a flow model using the Convert Model dialog box The Preferences dialog box 0 cee cece cee eee eens The Layer Property dialog box 00 cece eee eee eee Grid configuration used for the calculation of VCONT The Time Parameters dialog box for MODFLOW 2000 MODFLOW 2005 0 0 ee eee ee eee The Time Parameters dialog box for MODFLOW 96 The Drain Parameters dialog box 0 eee eee eee eee The General Head Boundary Parameters dialog box The Horizontal Flow Barrier dialog box 0002 0 e eee Types of fine grained beds in or adjacent to aquifers Beds may be discontinuous interbeds or continuous confining beds Adapted from Leake and Prudic 78 0 ccc ccc ccc eee eee The Recharge Package dialog box
289. ement between measurement and simu lation all points lie on a 45 line The narrower the area of scatter around this line the better is the match gt To create a scatter diagram for head values 1 Select Models PEST View Head Scatter Diagram The Scatter Diagram Hydraulic Head dialog box appears Fig 4 39 This dia log box has two tabs The Data tab displays the calculated and observed values The Chart tab displays the scatter diagram Refer to Section 2 6 1 20 for details about these tabs 2 Click the Chart tab to display the scatter diagram Fig 4 40 268 4 Tutorials Scatter Diagram Hydraulic Head Fig 4 40 The Chart tab of the Scatter Diagram dialog box 3 Use the button Save Plot As to save the chart to a file or use Copy to Clipboard to copy the chart to the Windows Clipboard An image in the clipboard can be pasted into most word or graphics processing software by using Ctrl V 4 Click OK to close the Scatter Diagram Hydraulic Head dialog box 4 1 Your First Groundwater Model with PM 269 4 1 5 Animation You already learned how to use the 2D Visualization tool to create and print con tour maps of calculated head and concentration values The saved or printed images are static and ideal for paper based reports or slide based presentations In many cases however these static images cannot ideally illustrate the motion of concen tration plumes or temporal variation of
290. en click OK Note that a strong sink or source is indicated by the cell value of 1 When a fluid source is strong new particles are added to replace old particles as they are advected out of that cell Where a fluid sink is strong particles are removed after they enter that cell Repeat steps 2 and 3 to assign the value 1 to the cells 2 15 25 and 3 15 25 Select File Leave Editor or click the leave editor button E gt To specify the output terms and times 1 Select Models MOC3D Output Control An Output Control MOC3D dialog box appears The options in the dialog box are grouped under five tabs Concentration Velocity Particle Locations Disp Coeff and Misc In the Concentration tab select the option These data will be printed or saved every Nth particle moves and enter N 20 Click OK to accept all other default values and close the Output Control MOC3D dialog box Fig 4 31 gt To perform the transport simulation 1 2 Select Models MOC3D Run The Run MOC3D dialog box appears Fig 4 32 Click OK to start the transport computation Prior to running MOC3D PM uses user specified data to generate input files for MOC3D as listed in the table of the Run MOC3D dialog box An input file will be generated only if the corresponding Generate box is checked You can click on the box to check or uncheck Normally we do not need to worry about these boxes since PM will take care of t
291. ent Ss 0 0001 is assigned to all cells A transient flow simulation is performed for a stress period with the length of 3 15576E 08 seconds 100 time steps and a time step multiplier of 1 0 The temporal development curve of the water table at a measure ment point located in the fourth layer within the lake is shown in Fig 5 21 The final stage in the lake is about 97 1 m j i 7 i DIT 2 3 Ey N3 E l 9 4 5 El 4 S 8 a ad ira Fe He BEANN fi APNA TLEN AOA l ia 2 a8 ih HHR L L H J aCe ATARIM Q o 2 WE ow amp a Bl y g a JN P g 3 d Fi g 5 20 Steady state hydraulic head contours in layer 4 100p eee T E Hydraulic Head 1 00E 08 2 00E 08 3 00E 08 Time Fig 5 21 Time series curve of the water stage in the lake 320 5 Examples and Applications 5 2 EPA Instructional Problems Folder pmdir examples EPA Instructional Problems Overview of the Problem The manual of instructional problems for MODFLOW Andersen 5 is intended to allow the student to have hands on experience with the practical application of mod els Twenty documented problems complete with problem statements input data s
292. eological Survey Open File Report 01 177 Moench AF and Ogata A 1981 A numerical inversion of the Laplace transform solu tion to radial dispersion in a porous medium Water Resour Res 17 1 250 253 Neumann SP 1984 Adaptive Eulerian Lagrangian finite element method for advection dispersion Int J Numerical Method in Engineering 20 321 337 Oakes BD and Wilkinson WB 1972 Modeling of ground water and surface water systems I Theoretical relationships between ground water abstraction and base flow Reading Great Britain Reading Bridge House Water Resources Board 16 37 pp Parkhurst DL and Appelo C 2000 PHREEQC Version 2 A computer program for speciation batch reaction one dimensional transport and inverse geochemical calcula tions U S Geological Survey Water Resources Investigations report 99 4259 Pannatier Y 1996 Variowin Software for spatial data analysis in 2D Springer Berlin Heidelberg New York ISBN 0 387 94679 9 Pollock DW 1988 Semianalytical computation of path lines for finite difference mod els Ground Water 26 6 743 750 Pollock DW 1989 MODPATH version 1 x Documentation of computer programs to compute and display pathlines using results from the U S Geological Survey modular three dimensional finite difference ground water model U S Geological Survey Open file report 89 381 Pollock DW 1994 User s Guide for MODPATH MODPATH PLOT Version 3 A par ticle tracking post processing pac
293. er 0 0 0 cece eee ee eee 328 5 3 4 The Hantush and Jacob Solution Transient Flow to a Well in a Leaky Confined Aquifer 004 331 5 4 39 5 3 5 Parameter Estimation with MODFLOW 2000 Test Case 1 334 5 3 6 Parameter Estimation with MODFLOW 2000 Test Case 2 337 Geotechnical Problems 0 0 cc cece eee eee eee 340 5 4 1 Inflow of Water into an Excavation Pit 340 5 4 2 Flow Net and Seepage under a Weir 342 5 4 3 Seepage Surface through a Dam 344 DAA oCutotk Wall coaie nd soe ee Ae oes Beta eee ER 348 5 4 5 Compaction and Subsidence 000000 351 Solute Transport vcs tiei eni igs seb bow E wee ees ee ob 354 5 5 1 One dimensional Dispersive Transport 354 5 5 2 Two dimensional Transport in a Uniform Flow Field 356 5 5 3 Monod Kinetics 0 cee eee eee eee 359 5 5 4 Instantaneous Aerobic Biodegradation 361 5 5 5 First Order Parent Daughter Chain Reactions 363 Contents XI 5 5 6 Benchmark Problems and Application Examples from Literature neea a A Sa tne eet E EEK 365 5 6 PHT3D Examples 05 eo2c pee e EEE S EE aS 367 5 7 SEAWAT Examples 0 00 eee eee 368 5 8 Miscellaneous Topics 0 eee eee 369 5 8 1 Using the Field Interpolator 00 369 5 8 2 An Example of Stochastic Modeling
294. er vation boreholes gt To generate the concentration time series curves at the observation boreholes 1 Select Models MT3DMS View Concentration Time Curves A Species dialog box appears 2 In the Species dialog box select the first species and click OK PM displays the Time Series Curves Concentration dialog box Fig 4 26 This dialog box has two tabs The Data tab displays the calculated and measurement data if any The Chart tab displays the time series curves Refer to Section 2 6 1 20 for details about these tabs 3 Click the Chart tab to display the curves Fig 4 27 I SAMPLEI PMS Processin Fie Value Optio Simulation Time lt gt Period Step 1 Time 9 467E 07 E tions Help ol lt lt fo anaes no flow boundary 9 m contaminated area A2 r pumping z well E constant head boundary h 8 m constant head boundary h no flow boundary 457 4899 207 4494 8 1 16 23 2D Visualization Solute Concentration MT 3DMS Species 1 T02516E16 Fig 4 25 Contours of the concentration values at the end of the simulation 4 1 Your First Groundwater Model with PM 257 Time Series Curves Concentration E Data Chast __ OBSNAM_ Plot Color OBSNAM Simulation Time Calculated Value Observed Value _ a 1 v 0 3000000 9 545736E 06 3000000 9 484143E 16 3000000 2 639631E 04 3000000 7 791829E 14 3000000 8 614525
295. er has a constant thickness of 10 m The task is to calculate the head contours for the case that only the west part of the aquifer is modeled The east boundary of the modeled part should be approached by using the general head boundary Modeling Approach and Simulation Results The aquifer is simulated using a grid containing 1 layer 10 rows and 16 columns A regular grid spacing of 100 m is used for each column and row The layer type is 0 confined and the Transmissivity flag in the Layer Options dialog box is User specified The initial hydraulic head is 12 m everywhere While the west model boundary is simulated by the fixed head boundary condition BOUND 1 with 12m 10m 1000 m S gz c gt 2 a amp o S i o c o Loz fixed head boundary h fixed head boundary h 1550 m 1000 m Fig 5 5 Plan view of the model area 302 5 Examples and Applications the initial head at 12 m the east boundary is simulated by the general head bound ary GHB condition with the head h 10 m Analogous to the riverbed hydraulic conductance equation 2 19 the hydraulic conductance term of each GHB cell is Coens Keune A L where Keyp is the horizontal hydraulic conductivity L is the distance from the actual fixed head boundary to the modeled GHB cell and A is the area of the cell face which is perpendicular to the groundwater flow in the unmodeled area For this example Cexp T 10 100 10 1000
296. er be tracked back to the ground surface where the groundwater recharge from the precipitation occurs Note that pathlines can be drawn in 3 dimensions in PMPATH even if you build a 2D model See Section 5 1 1 for an example PMPATH can create time related capture zones of pumping wells The 100 days capture zone shown in Fig 4 16 is created using the settings in the Particle Tracking Time Properties dialog box Fig 4 17 and clicking El To open this dialog box select Options Particle Tracking Time Refer to Section 3 3 2 for details about this Eile Bun Opis Help ialf x 8 8 lt gt oe contaminated area pumping well E constant head boundary h 9 m constant head boundary h 8 m no flow boundary 4749E 02 3 242E 02 7 038E 00 24141 80763E 00 7 9990E 06 1 7199E 07 1 1 Oo Fig 4 12 The model loaded in PMPATH 4 1 Your First Groundwater Model with PM 247 A Add New Particles contaminate 4 284E 02 5 306E 02 1 500E 00 22 4 3 8 3339E 00 3 9778E 06 6 3382E 09 1 1 48 Fig 4 14 The capture zone of the pumping well vertical exaggeration 1 dialog box Note that the capture zone in the first layer is smaller than those in the other layers due to lower hydraulic conductivity and thus lower flow velocity of the first layer 248 4 Tutorials File Bun Opis Help al xa ala si no flow boundary 8m contaminated area
297. erate Description Destination File bS i Basic Transport Package c program files wt360 pmwin examplessample1 mtrn Advection Package c program files wt360 pmwin examples sample1 mtm Vv Dispersion Package c program files wt360 pmwin examples sample mtm M Chemical Reaction Package __ e Sprogram files wt360 pmwin examples sample1 smtm Vv Generalized Conjugate Gradient Solver F c program files wt360 pmwinexamples sample mtm Vv Sink and Source Mixing Package c program files wt360 pmwin examples sample1 mtm Options J Regenerate all input files J Generate input files only don t start MT3DMS Fig 4 24 The Run MT3DMS dialog box or uncheck Normally we do not need to worry about these boxes since PM will take care of the settings gt Check simulation results and produce output During a transport simulation MT3DMS saves a detailed run record path OUT PUT MTM where path is the folder in which the model data is saved In addition MT3DMS saves the simulation results in various files The output options are con trolled by selecting Models MT3DMS Output Control To check the quality of the simulation results MT3DMS calculates a mass budget at the end of each transport step and accumulated to provide summarized informa tion on the total mass into or out of the groundwater flow system The discrepancy between the in and outflows of mass serves as an indicator of the accuracy of the simulation results It
298. erations required to complete the flow simulation 4 Press any key to exit the DOS Window 4 2 2 6 Step 6 Extract and view results It is now time to view the results of your efforts but first it is necessary to understand how the Results Extractor operates On occasions it is necessary to view some of the various sorts of output such as hydraulic heads and cell by cell flows generated by a MODFLOW simulation This layer wise data is accessed using 2D Visualization tool It is quite a simple procedure to load and save any of the output generated by MODFLOW gt To generate contour maps of the calculated heads 1 Select Tools 2D Visualization to display a Result Selection dialog box 2 Click OK to select the default result type Hydraulic Head PM displays the model grid and head contours By default PM sets 10 contour levels ranging from the minimum to the maximum value You can customize the appearance of the contour lines by using the Environment Options dialog box 3 Select Options Environment to open the Environment Options dialog box to customize the appearance of the contours Click the Contours tab and make sure the Visible box is checked Click on the header Level of the table to change the contour minimum to 12 5 maximum to 19 and the contour interval to 0 5 It is also possible to change contour color if you desire If Fill Contours is checked the contours will be filled with the colors given in the Fill column of the tab
299. erred to as fixed head cell constant head cell or time varying specified head cell or 3 no flow takes place within the cell referred to as inactive cell Use 1 for an active cell 1 for a constant head cell and 0 for an inactive cell For this example 232 4 Tutorials the value 1 needs to be assigned to the cells on the west and east boundaries and the value 1 to all other cells Any outer boundary cell which is not a constant head cell is automatically a zero flux boundary cell Flux boundaries with non zero fluxes are simulated by assigning appropriate infiltration or pumping wells in the corre sponding active cell via the well package Head dependent boundary conditions are modeled on active cells by means of the general head boundary package or the river package gt To define the layer properties 1 Select Grid Layer Property A Layer Options dialog box appears 2 Click a cell of the Type column a drop down button will appear within the cell By clicking the drop down button a list containing the available layer types Fig 4 5 will be displayed 3 Select 1 Unconfined for the first layer and 3 Confined Unconfined for the other layers then click OK to close the dialog box gt To assign the cell status to the flow model 1 Select Grid Cell Status IBOUND Modflow The Data Editor of PM appears and displays the model grid Fig 4 6 A grid cursor is located over the current cell The value of the current ce
300. ersion 12 Water mark Computing Australia Downloaded from http www pesthomepage org Doherty J 2010 Addendum to the PEST Manual Watermark Computing Australia Downloaded from http www pesthomepage org Domenico PA 1972 Concepts and Models in Groundwater Hydrology McGraw Hill New York 405 pp Domenico PA and Schwartz FW 1990 Physical and Chemical Hydrogeology John Wiley amp Sons New York 709 pp Englund E and Sparks A 1991 User s guide of GEO EAS Geostatistical environ mental assessment software EPA 600 8 91 008 Fenske J P Leake SA and Prudic DE 1996 Documentation of a computer program RES 1 to simulate leakage from reservoirs using the modular finite difference ground water flow model MODFLOW U S Geological Survey Open File Report 96 364 Fetter CW 1994 Applied Hydrogeology 3rd Edition Macmillan College New York 691 pp Franke R 1982 Scattered data interpolation Tests of some methods Mathematics of computation 38 157 181 200 Freeze RA and Cherry JA 1979 Groundwater Prentice Hall Inc Englewood Cliffs New Jersey Frenzel H 1995 A field generator based on Mejia s algorithm Institut fr Umwelt physik University of Heidelberg Germany Gelhar LW and Collins MA 1971 General analysis of longitudinal dispersion in nonuniform flow Water Resour Res 7 6 1511 1521 Gelhar LW Mantaglou A Welty C and Rehfeldt KR 1985 A review of field scale physical solute transport processes
301. es Misc M Concentration unformatted IV Cell by Cell mass unformatted only MT3D96 MT3D99 I Concentration ASCII I Number of particles ASCII I Ratardation factor ASCII I Dispersion coefficient ASCII Cancel Help Fig 2 71 The Output Control MT3D MT3DMS dialog box 2 6 The Models Menu 133 E Output Control M13D MT3DMS Output Terms f Misc Output Frequency 33 Out i a 3000000 36000000 Method 1 L 4 9000000 gt Type in Output Frequency then Press TAB 1 2E 07 gt Specify the Output Time s 1 5E 07 1 BE 07 Method 2 2 1E 07 gt Click on the column header Output Time 2 4E 07 gt Specify Min Max output times and interval 2 7E 07 3E 07 3 3E 07 3 6E 07 3 9E 07 4 2E 07 ARE ma gt Cancel Help Fig 2 72 The Output Times tab of the Output Control MT3D MT3DMS dialog box CINACT is the predefined concentration value for an inactive concentration cell CBUND 0 This value is a marker for these cells only and has no physical meaning THKMIN is the minimum saturated thickness in a cell expressed as the deci mal fraction of the model layer thickness below which the cell is considered inactive THKMIN is only used by MT3D96 or later NPRMAS indicates how frequently the mass budget information should be saved in the mass balance summary file MT3D MAS 2 6 6 9 MT3D Run The available settings of the
302. es are multiplied by the user specified value e Parameter drop down box For particular packages in which a cell has more than one value e g the River package of MODFLOW this drop down box contains the available parameter type s Choose the parameter type for which the Search and Modify operation will apply e Ignore Inactive Cells If this box is checked the Search and Modify operation will only be applied to active cells e Maps The user may display background maps DXF or Line Map by using the Maps Options dialog box See Section 2 9 1 for details e Save and Load The entries in the Trace Table can be saved or loaded in trace files The format of the trace file is given in Section 6 2 8 2 8 6 Import Results To import the model results select this menu item to open the Import Results dialog box Fig 2 100 The dialog box contains several tabs each corresponds to a sim ulation model Use these tabs to select the desired result type simulation time and click the OK button to import Depends on the selected model simulation time is expressed in terms of stress period time step or elapsed time 2 8 7 Import Package When editing flow packages of MODFLOW the user may select this menu item to import existing input files saved in the MODFLOW 88 96 format Refer to McDon ald and others 85 or Harbaugh and others 54 for input file format The following packages are supported Drain Package Evapotranspiration Package Gene
303. es derived from it are not cal culated by PEST at regular intervals during the parameter estimation process for recording in the matrix file case mtt nor are these matrices calculated at the end of the inversion process for recording in the run record file case rec Because the covariance matrix is unavailable parameter uncertainties cannot be calculated and hence are also not recorded in the run record file In a regularization context these have little meaning anyway Some avenues for increasing the efficiency of regularization calculations are no longer available under the leaner storage regime that prevails when mem ory conservation is active including the benefits gained through the LINREG variable and through the placing of regularization observations behind other observations involved in the parameter estimation process This can lead to significant run time penalties in problems involving many parameters unfor tunately these are the very contexts in which memory conservation is most likely to be warranted e All regularization constraints are linear LINREG If this box is checked the variable LINREG of the PEST control data file will be set to linreg As is discussed in chapter 7 of the PEST manual 37 regularization constraints can be supplied through observations through prior information or through both of these mechanisms Prior information relationships are always linear Regulariza tion constraints supplied a
304. es dry MODFLOW will stop the flow simulation and write a message gt CONSTANT HEAD CELL WENT DRY SIMULATION ABORTED into the run listing file OUTPUT DAT 2 5 3 Horizontal Hydraulic Conductivity and Transmissivity Horizontal hydraulic conductivity is required for layers of types 1 or 3 Transmis sivity is required for layers of types 0 or 2 Horizontal hydraulic conductivity is the hydraulic conductivity along model rows It is multiplied by an anisotropy fac tor specified in the Layer Property dialog box Section 2 4 2 to obtain the hydraulic conductivity along model columns Typical values and ranges of horizontal hydraulic conductivity for different types of soils are given in many groundwater textbooks for example Freeze and Cherry 46 Spitz and Moreno 109 and Fetter 44 For layers of types 0 or 2 PM uses the horizontal hydraulic conductivity and layer thickness to calculate transmissivity if the corresponding Transmissivity set ting in the Layer Property dialog box Section 2 4 2 is set to Calculated The user specified transmissivity values of a model layer are used in the simulation if the Transmissivity setting of that layer is set to User specified 2 5 4 Horizontal Anisotropy The Layer Property Flow LPF package supports the use of the cell by cell horizon tal anisotropy which is the ratio of horizontal hydraulic conductivity along columns to hydraulic conductivity along rows The latter is specified by selecting P
305. es for different soil types can be found in Zheng and Bennett 118 or Domenico and Schwartz 41 38 2 Modeling Environment 2 5 8 Specific Storage Storage Coefficient and Specific Yield For transient flow simulations MODFLOW requires dimensionless storage terms specified for each layer of the model For a steady state simulation these menu items are not used and are therefore dimmed In a confined layer the storage term is given by storativity or confined storage coefficient specific storage L71 x layer thickness L The storativity is a func tion of the compressibility of the water and the elastic property of the soil matrix The specific storage or specific storativity is defined as the volume fraction of water that a unit column of aquifer releases from storage under a unit decline in hydraulic head The specific storage ranges in value from 3 3 x 1076 m of rock to 2 0 x 107 mt of plastic clay Domenico 40 Layers of types 0 2 and 3 require the confined storage coefficient PM uses spe cific storage and the layer thickness to calculate the confined storage coefficient if the corresponding Storage Coefficient setting in the Layer Property dialog is Cal culated By setting the Storage Coefficient setting to User Specified and selecting Parameters Storage Coefficient you can specify the confined storage coefficient directly In a phreatic aquifer Layers of types 2 and 3 the storage term is given by spe cific yield
306. eter and once you become familiar with the commands and menus it is very easy to enter and change the model data The values of the particular data being edited or entered and the selected cell are displayed in the status bar on the bottom of the screen The model data for task 1 steady state water level with recharge no pumping includes layer properties model boundaries aquifer geometry aquifer parameters initial conditions time parameters and recharge rates 4 2 Unconfined Aquifer System with Recharge 275 gt To define the layer properties 1 Select Grid Layer Property A Layer Options dialog box appears 2 In the Layer Options dialog box click on Type and select Unconfined it is okay to browse through the rest of this dialog box but leave all the values as the default ones 3 Click OK to close the Layer Options dialog box gt To define the model boundaries 1 Select Grid Cell Status IBOUND Modflow MODFLOW uses a cell status array called the IBOUND array to determine if a particular cell is active inactive no flow or a constant head cell Cell values within IBOUND are as follows active or other positive integers inactive 0 fixed head 1 or other negative integers These values are assigned to cells as required in the Data Editor By default and
307. eter values often reduces execution time PEST Parameter Estimation View Composite Parameter Sensitivities Select this menu item to use the Text Viewer see Section 2 3 4 to display the Param eter Sensitivity file PESTCTL SEN which contains composite parameter sensitivity values The composite sensitivity of a parameter is defined in Equation 5 1 of the PEST manual 34 As given in the PEST manual composite parameter sensitivities are useful in identifying those parameters which may be degrading the performance of the parameter estimation process through lack of sensitivity to model outcomes PEST Parameter Estimation View Composite Observation Sensitivities Select this menu item to use the Text Viewer see Section 2 3 4 to display the Ob servation Sensitivity file PESTCTL SEO which contains all observation values and corresponding model calculated values as well as composite sensitivities for all ob servations The composite sensitivity of an observation is a measure of the sensitivity of that observation to all parameters involved in the parameter estimation process A high value of composite observation sensitivity normally indicates that an observa tion is particularly crucial to the inversion process Refer to Section 5 1 6 of the PEST manual 34 for more details PEST Parameter Estimation View Head Scatter Diagram This menu item is available only if Head Observations have been defined see Sec tion 2 6 1 14
308. ets and discussion of results are presented in that manual The problems are de signed to cover modeling principles specifics of input output options available to the modeler rules of thumb and common modeling mistakes You can find an elec tronic version of this manual in the folder Document Instructional Problems for MODFLOW EPA on the companion CD ROM Modeling Approach and Simulation Results Most of the models described in the manual of instructional problems have been re built by using PM You can find the models in sub folders under path examples EPA Instructional Problems Although these models are ready to run it is suggested to construct the models by yourself because you will learn more through exercises and mistakes 5 3 Parameter Estimation and Pumping Test 321 5 3 Parameter Estimation and Pumping Test 5 3 1 Basic Parameter Estimation Skill Folder pmdir examples calibration calibration1 Overview of the Problem Groundwater models are usually applied to conceptualize and understand a hydro logic system or to predict the outcome of a future change to the system In order to provide some assurance that the model reflects the behavior or appearance of the flow system it must be calibrated prior to use as a predictive tool Model Calibra tion is accomplished by finding a set of model parameters boundary conditions and excitations or stresses that produce simulated heads or drawdowns and fluxes that match measurement
309. etting particles current layer is PMPATH example pm5 File Bun Options Help alf xR lt J A a 7 DA e J p Worksheet plan view Co Ds Projection of pathlines l K cross section e T Projection of pathines i i J K cross section number of particles current time step current stress period vertical pore velocity at the cell K J horizontal pore velocity at the cell K J head at the cell K 1 J position of the mouse pointer K J layer row column position of the mouse pointer in real world coordinates x y Z Fig 3 4 The PMPATH modeling environment box of PMPATH see Section 3 3 1 allows the user to change the appearance of these windows The projection of pathlines on the cross sections is useful when running PM PATH with a three dimensional multi layer flow field The user should always keep in mind that only the projections of pathlines are displayed The projection of a path line may be intersected by another or even itself particularly if a three dimensional flow field or a transient flow field is used 210 3 The Advective Transport Model PMPATH 3 2 2 Status bar The Status bar displays th
310. exa OO 1 a C C w fo Jo H mj fa h R a fo Wo Wh m Line Map File Filename x Factor n T La wI p Jo h mj fo fo R ae on the filename fields to select files Cancel Help Fig 2 101 The Map Options dialog box 2 9 The Options Menu 195 A Line Map consists of a series of polylines Each polyline is defined by a header line and a series of coordinate pairs The header line only contains the number of the coordinate pairs Refer to Section 6 2 4 for the format of the Line Map files gt To import a DXF map or a Line map 1 Select the Vector Graphics tab 2 Right Click on any of the DXF File or Line Map File fields and then select a file from a Map Files dialog box 3 If necessary use a scale factor to enlarge or reduce the appearance size of the map Then use the values in X and Y to shift the scaled map to the desired position For details see the section Scaling a vector graphic below 4 Click the colored button in the front of the edit field and select a color for the DXF map from a Color dialog box The color will be assigned to a DXF graphics entity if the entity s color is not defined in the DXF file A line map will always use the selected color 5 Check the box at the front of the edit field The map will be displayed only when the box is checked gt Scaling a vector graphic X and Y should be 0 and Scale should be 1 if a DXF file is generated by P
311. f MODFLOW was released in 2005 called MODFLOW 2005 57 This version however does not support parameter estimation process at the time of this writing As a result users are encouraged to take advantage of external parameter estimation programs such as PEST PEST 33 37 38 The purpose of PEST is to assist in data interpretation and in parameter estima tion If there are field or laboratory measurements PEST an adjust model param eters and or excitation data in order that the discrepancies between the pertinent model generated numbers and the corresponding measurements are reduced to a minimum PEST does this by taking control of the model MODFLOW and running it as many times as is necessary in order to determine this optimal set of parameters and or excitations PEST includes many cutting edge parameter estimation techniques According to Doherty 37 the most profound advance is the SVD assist scheme This method combines two important regularization methodologies truncated singular value decomposition and Tikhonov regu larization MODPATH 93 93 94 MODPATH is a particle tracking code written in FORTRAN To run a particle tracking simulation with MODPATH the users need to key in parameters in a text screen and have the options to save the input values in a separate file for later use A graphical post processor such as MODPATH PLOT 95 3D Ground water Explorer 21 or 3D Master 23 is required for displaying
312. f a porous medium and b the finite difference approach 000 00000 0 3 3 Schematic illustration of the spurious intersection of two pathlines in a two dimensional cell 0 0 0 eee eee eee 3 4 The PMPATH modeling environment 04 3 5 The Add New Particles dialog box 000 020000 3 6 The Environment Options dialog box of PMPATH 3 7 The Cross Sections tab of the Environment Options dialog box of PMPATH reesei 2 sna Snipes th abe hale sees ache bustle ctus Dba tibia bog post eat 216 3 8 The Contours tab of the Environment Options dialog box of PMPATH 217 3 9 The Color Spectrum dialog box 0 0 0 eee ee eee 3 10 The Contour Labels dialog box 0 0 0 eee eee ee 3 11 The Label Format dialog box 0 0 eee eee eee 3 12 The Particle Tracking Time dialog box 3 13 The Pathline Colors tab of the Particle Tracking Time dialog box 218 220 222 3 14 The RCH EVT Options tab of the Particle Tracking Time dialog box 222 3 15 The Maps Options dialog box 0 0 0 eee eee eee ee 3 16 The Save Plot As dialog box 0 eee eee eee 4 1 Configuration of the hypothetical model 4 2 The spatial discretization scheme and cell indices of MODFLOW 4 3 The Model Dimension dialog box 0 000002 eee 44 The generated model grid 0 cee 4 5 The
313. f the current layer will be copied another layer if you move to the other model layer while layer copy is on Move to the second layer and the third layer by pressing PgDn twice Set fixed head boundaries BOUND 1 in layer 3 at the west and east bound aries where the river enters and leaves the model area Copy the fixed head boundaries from layer 3 to layer 1 by clicking the Current Layer edit field in the tool bar typing in the layer number 1 and pressing the Enter key remember that layer copy is still on We do not need to specify fixed head cells in the second layer because the horizontal flow component in the silty layer is considered to be negligible The model grid in layers 1 and 3 should look like Fig 4 51 The model grid in layer 2 should look like Fig 4 52 Select File Leave Editor or click the leave editor button w The top of each aquifer slopes gradually from west to east To save you entering this data the top elevation of each aquifer has been saved in ASCH Matrix file gt To specify the top elevation of each aquifer 1 Select Grid Top of Layers TOP PM will ask if you want to use the layer bottom elevations as the layer top elevations Click No 2 Click the l button if the display mode is not Grid View 3 Select Value Matrix Load to import examples tutorials tutorial3 aq1top dat as the elevation of the top of aquifer 1 4 Move to Layer 2 S Granite Hills
314. ference transport models MT3DMS or MOC3D to simulate transport processes As shown in Fig 4 1 an aquifer system with two stratigraphic units is bounded by no flow boundaries on the North and South sides The West and East sides are bounded by rivers which are in full hydraulic contact with the aquifer and can be considered as fixed head boundaries The hydraulic heads on the west and east boundaries are 9 m and 8 m above reference level respectively 228 4 Tutorials The aquifer system is unconfined and isotropic The horizontal hydraulic conduc tivities of the first and second stratigraphic units are 0 0001 m s and 0 0005 m s respectively Vertical hydraulic conductivity of both units is assumed to be 10 per cent of the horizontal hydraulic conductivity The effective porosity is 25 percent The elevation of the ground surface top of the first stratigraphic unit is 10m The thickness of the first and the second units is 4 m and 6 m respectively A constant recharge rate of 8x 10 m s is applied to the aquifer A contaminated area lies in the first unit next to the west boundary The task is to isolate the contaminated area using a fully penetrating pumping well located next to the eastern boundary A numerical model has to be developed for this site to calculate the required pumping rate of the well The pumping rate must be high enough so that the con taminated area lies within the capture zone of the pumping well We will use PM to cons
315. ff and Hill and others 63 p 83ff for more details about the use of the prior information 140 2 Modeling Environment PRCH1 22 36500 x RCH_1_1 STAT 5 0 1 4 PHK1 10 HK_1 STAT 0 5 11 5 PS1 amp 2 0 02 20 x SS_1 30 SS_2 STAT 0 5 11 5 The Control Data Tab The control data are used to control the regression calculations The control data are written in the input file PES DAT for the Parameter Estimation Process Following Hill and others 63 the items of the control data are described below MAX ITER is the maximum number of parameter estimation iterations If MAX ITER 0 the program calculates the variance covariance matrix on parameters and related statistics the parameter correlation coefficients generally are of most interest using the starting parameter values and parameter estimation stops after one iteration Note that the starting parameter values are obtained by multiplying PARVAL with the cell values of the parameter see Parameters Tab MAX CHANGE is the maximum fractional change for parameter values in one iteration step MAX CHANGE commonly equals to 2 0 or less if parameter val ues are unstable during parameter estimation iterations TOL is the parameter estimation closure criterion as a fractional change in pa rameter values TOL commonly equals 0 01 Larger values often are used during preliminary calibration processes value as small as 0 001 may be used for theo retical works SOSC is the second
316. fied data will be used by MT3DMS or SEAWAT to replace the effective molecular dif fusion coefficient in the Dispersion package The specified data are used only if the Dispersion package is activated 2 6 2 6 MT3DMS SEAWAT Chemical Reaction The Chemical Reaction package can be used to simulate sorption and chemical reac tions The type of reaction is selected in the Simulation Settings MT3DMS SEAWAT dialog box Fig 2 44 The type of sorption and the parameters for sorption and chemical reactions are defined in the the Chemical Reaction MT3DMS dialog box Fig 2 51 of the Data Editor The required parameters for the selected sorption and reaction types are summarized below Chemical Reaction MT3DMS Type of Sorption Dual domain mass transfer with sorption Distribution Coefficient Kd L 3 M Mass transfer rate between mobile and immobile domains 1 T Porosity of the immobile domain 0 Current Position Layer Row Column 1 7 8 Cancel Help Fig 2 51 The Chemical Reaction MT3DMS dialog box e Type of Sorption Sorption is implemented in MT3DMS through use of the retar dation factor R 98 2 Modeling Environment No sorption Sorption is not simulated Linear isotherm equilibrium assumes that the sorbed concentration Ci j is directly proportional to the dissolved concentration Cy equation 2 42 The retardation factor is therefore independent of the concentration values and is ca
317. fied to couple MODFLOW 2000 56 and a later version of MT3DMS 123 Flexible equations were added to the fourth version of the program i e SEAWAT_V4 77 to al low fluid density to be calculated as a function of one or more MT3DMS species Fluid density may also be calculated as a function of fluid pressure The effect of fluid viscosity variations on groundwater flow was included as an option This option is however not supported by PM Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport temperature can be simulated as one of the species by entering appropriate transport coefficients For example the process of heat conduction is mathematically analogous to Fickian diffusion Heat conduction can be represented in SEAWAT by assigning a thermal diffusiv ity for the temperature species instead of a molecular diffusion coefficient for a solute species Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption See Langevin and others 77 for details about heat transport Water Budget Calculator 18 This code calculates the groundwater budget of user specified subregions and the exchange of flows between subregions 1 2 Compatibility Issues 5 1 2 Compatibility Issues For many good reasons MODFLOW and most of its related groundwater simulation programs such as MT3DMS are written in FORTRAN and save simulation results in binary f
318. file types ASCII Ma trix Warp form ASCII Matrix SURFER files and SURFER files real world An ASCII Matrix file may be loaded into the model by the Data Editor at a later time The format of the ASCII matrix file is described in Section 6 2 1 A lt gt Results Extractor q x MODFLOW mocap mTaD mT3Dms ATaD Result Type Hydraulic Head Stress Period i Time Step zz Orientation Plan View 7 Layer 1 Columnwidth fia 7 96 328 92 38017 88 26356 84 06091 96 3084 92 33601 88 18815 83 92777 100 96 27117 92 25205 88 04498 83 67083 100 96 22002 92 1367 87 84912 83 30923 100 96 16011 92 00169 87 62212 82 87221 96 09744 91 86084 87 38972 82 39841 96 03806 91 72806 87 17769 81 93382 95 9873 91 61536 87 00618 81 52367 95 94917 91 53153 86 88625 81 20448 95 92638 91 48232 86 8224 80 99949 95 92039 91 47204 86 82876 80 91421 95 93092 91 50393 87 01642 1E 30 Fia Save Help Close Fig 2 93 The Results Extractor dialog box 2 7 The Tools Menu 187 SURFER file has three columns containing the x y coordinates and the value of each cell If the file type is SURFER files the origin of the coordinate system for saving the file is set at the lower left corner of the model grid If the file type is SURFER files real world the coordinates system as defined in the Environment Options dialog box Fig 2 105 is used 2 7 7 Water Budget There are situations in which
319. files anyway I Generate input files only don t start MODFLOW Cancel Help Fig 4 7 The Run Modflow dialog box 4 1 2 4 Step 4 Check Simulation Results During a flow simulation MODFLOW writes a detailed run record to path OUT PUT DAT where path is the folder in which the model data are saved When a flow simulation is completed successfully MODFLOW saves the simulation results in various unformatted binary files as listed in Table 4 1 Prior to running MOD FLOW the user may control the output of these unformatted binary files by choos ing Models MODFLOW Output Control The output file path INTERBED DAT will only be generated if the Interbed Storage Package is activated see Chapter 2 for details about the Interbed Storage Package The system of equations of the finite difference model MODFLOW actually con sists of a flow continuity statement for each model cell Since MODFLOW uses it erative equation solvers the accuracy of the simulation results need to be checked after each simulation run Continuity should exist for the total flows into and out of the entire model or any sub region of the model This means that the difference be tween total inflow and total outflow should theoretically equal to 0 for a steady state flow simulation or equal to the total change in storage for a transient flow simula tion To verify the accuracy of the results MODFLOW calculates a volumetric water budget for the entire model a
320. files are overwritten during sub sequent forward model runs and thus only the listing file unique to final parameter values is available for inspection with the Text Viewer see Section 2 3 4 Parameter estimation processes are often terminated unexpectedly because MOD FLOW fails to complete a flow calculation due to an unsuitable parameter combina tion used by an estimation iteration In that case MODFLOW writes error messages to the listing file OUTPUT DAT and terminates the simulation It is therefore rec ommended to check this file when PEST fails to complete the parameter estimation iterations 2 6 The Models Menu 175 PEST Parameter Estimation View Estimated Parameter Values At the end of each optimization iteration PEST writes the best parameter set achieved so far i e the set for which the objective function is lowest to a file named PESTCTL PAR Select this menu item to use the Text Viewer see Section 2 3 4 to display this file The first line of the PESTCTL PAR file contains the values for the character variables PRECIS and DPOINT which were used in the PEST con trol file Then follows a line for each parameter each line containing a parameter name its current value and the values of the SCALE and OFFSET variables for that parameter Refer to Doherty 34 for details about PRECIS DPOINT SCALE and OFFSET Using values from intermediate parameter estimation iterations that are likely to be closer to the optimal param
321. flow Geological Survey of Hamburg Germany Chiang WH Kinzelbach W and Rausch R 1998 Aquifer Simulation Model for Win dows Groundwater flow and transport modeling an integrated program Gebrder Born traeger Berlin Stuttgart ISBN 3 443 01039 3 Chiang WH Bekker M and Kinzelbach W 2001 User guide for three dimensional visualization for MODFLOW related groundwater flow and transport models Institute for Groundwater Studies University of the Free State South Africa Chiang WH and Kinzelbach W 2001 3D Groundwater Modeling with PMWIN First Edition Springer Berlin Heidelberg New York ISBN 3 540 67744 5 346 pp Chiang WH Chen J and Lin J 2002 3D Master A computer program for 3D visual ization and real time animation of enviromental data Excel Info Tech Inc 146 pp Chiang WH 2005 3D Groundwater Modeling with PMWIN Second Edition Springer Berlin Heidelberg New York Clement TP 1997 RT3D A modular computer code for simulating reactive multi species transport in 3 dimensional groundwater systems Battelle Pacific Northwest Na tional Laboratory Richland Washington 99352 Clement TP 2000 RT3D Version 2 0 A modular computer code for simulating reac tive multispecies transport in 3 dimensional groundwater systems Clement TP 2002 RT3D Version 2 5 A modular computer code for simulating reac tive multispecies transport in 3 dimensional groundwater systems Cooper Jr HH and Rorabaugh MJ 1963 Ground water m
322. flow boundary X EA a a cut off wall fixed head boundary h fixed head boundary h no flow boundary 2 1785 m Fig 5 23 Plan view of the model T observation borehole Fig 5 24 Location of the cutoff wall and pumping wells 5 3 Parameter Estimation and Pumping Test 327 To calculate the required time to reach the steady state condition the estimated pumping rate of 7 9 x 1075 m s is specified to each well A transient simulation with one stress period subdivided into 25 equal time steps is carried out The total simulation time is set at 1 x 10 seconds The calculated head time curve Fig 5 25 shows that the steady state is reached at t 4 x 107 s eee ee ee ee ee ee ee i Hydraulic Head Creare eee ae eee eee ae ee 2 0E 07 4 0E 07 6 0E 07 80E 07 1 0E 08 Time Fig 5 25 Time series curve of the calculated hydraulic head at the center of the contaminated area 328 5 Examples and Applications 5 3 3 The Theis Solution Transient Flow to a Well in a Confined Aquifer Folder pmdir examples calibration calibration3 Overview of the Problem This example gives an approximation of the Theis solution with a numerical model Given the aquifer properties transmissivity and confined storage coefficient the Theis solution predicts drawdow
323. for Ground Water Research Rice Uni versity Rifai HS Newell CJ Gonzales JR Dendrou S Kennedy L and Wilson J 1997 BIO PLUME III Natural attenuation decision support system version 1 User s Manual Air Force Center for Environmental Excellence Brooks AFB San Antonio Texas Robinson RA and Stokes RH 1965 Electrolyte Solutions 2nd ed Butterworth London Saad Y 1985 Practical use of polynomial preconditionings for the conjugate gradient method SIAM Journal of Scientific and Statistical Computing 6 4 865 881 Scandrett C 1989 Comparison of several iterative techniques in the solution of sym metric banded equations on a two pipe Cyber 205 Appl Math Comput 34 2 95 112 Seber GAF and Wild CJ 1989 Nonlinear Regression John Wiley amp Sons NY 768 pp Shepard D 1968 A two dimensional interpolation function for irregularly spaced data Proceedings 23rd ACM126 National Conference 517 524 Spitz K and Moreno J 1996 A practical guide to groundwater and solute transport modeling 461 pp John Wiley amp Sons New York ISBN 0 471 13687 5 Sun NZ 1995 Mathematical modeling of groundwater pollution 377 pp Springer Berlin Heidelberg New York Theil H 1963 On the use of incomplete prior information in regression analysis Amer ican Statistical Association Journal 58 302 401 414 Trescott PC and Larson SP 1977 Comparison of iterative methods of solving two dimensional groundwater flow equations Water Resour Res 1
324. for some reason the user wishes the increment to be reduced if three point derivatives calculation is employed DERINCMUL should be less than 1 0 Experience shows that a value between 1 0 and 2 0 is usually satisfactory e DERMTHD defines the variant of the central i e three point method used for derivatives calculation and is used only when FORCEN is Always_3 or Switch PEST provides three variants Parabolic Best_fit or Outside_pts Refer to the manual of PEST for details about these methods The Prior Information Tab It often happens that we have some information concerning the parameters that we wish to optimize and that we obtained this information independently of the current experiment This information may be in the form of other unrelated estimates of some or all of the parameters or of relationships between parameters It is often useful to include this information in the parameter estimation process because it may lend stability to the process To define prior information first check the Active box in the Prior Information tab and then enter the prior information equation in the Prior Information column The syntax of a prior information equation is Pilbl Pifac Parnme Pifac x log Parnme Pival Weight Obgnme 2 60 The variables of the prior information equations are defined as follows All variables and symbols must be separated from by at least one space e Pilbl Each prior information article must begin with a cas
325. g the Drain package D in Fig 5 31 Parameter values 1 0 m d 0 01 m d 1 x 1074 m d 1 x 107 m d 4 1 3 1 x 1074 m d 4 x 1074 m d 1 0 m d 1 0 m d Starting PARVAL 1 5 0 5 1 2 2 0 0 25 10 0 1 42 0 75 0 5 2 0 Estimated PARVAL 0 999990 0 999989 0 999987 1 000330 1 000010 1 000040 0 999988 0 999968 0 999988 0 999990 340 5 Examples and Applications 5 4 Geotechnical Problems 5 4 1 Inflow of Water into an Excavation Pit Folder pmdir examples geotechniques geo1 Overview of the Problem This example is adapted from Kinzelbach and Rausch 72 Fig 5 32 shows the plan view and a cross section through a shallow aquifer situated in a valley In the north the aquifer is bounded by the outcrop of the sediments in the valley while the south boundary is a river which is in contact with the aquifer The aquifer extends several kilometers to the west and east it is unconfined homogeneous and isotropic The top and bottom elevations of the aquifer are 7 m and 0 m respectively The average horizontal hydraulic conductivity of the sandy sediments is 0 001 m s the effective porosity is 0 15 The groundwater recharge from precipitation is 6 x 107 m s m The water stage in the river is 5 m above the flat aquifer bottom which is the ref erence level for the simulation At a distance of 200 m from the river there is an excavation pit The length of the pit is 200 m the width 100 m
326. g box By defining transmissivity and storage coefficient as esti mated parameters the parameter estimation program PEST can estimate the param eters automatically Select Models PEST Parameter Estimation Run to see how fixed head boundary observation borehole fixed head boundary a ic 3 fa a 3 o D T 3 D x fixed head boundary Fig 5 26 Plan view of the model 330 5 Examples and Applications the parameter estimation programs work Since the analytical drawdown values were used as the observations the results from the parameter estimation programs must be transmissivity 0 0023 m s and storage coefficient 0 00075 0 8 Drawdown m 2 gt o o o Oo D M en gt on nm J gt b 0 20000 40000 60000 80000 Time second Fig 5 27 Time series curves of the calculated and observed drawdown values 5 3 Parameter Estimation and Pumping Test 331 5 3 4 The Hantush and Jacob Solution Transient Flow to a Well ina Leaky Confined Aquifer Folder pmdir examples calibration calibration4 Overview of the Problem This example demonstrates how to approach leaky confined aquifers A leaky con fined aquifer is overlaid and or underlaid by geologic formations which are not com pletely impermeable and can transmit water at a sufficient rate Fig 5 28 Hantush and Jacob 52 give an analy
327. g box Fig 2 56 will be displayed in place of the Run MT3DMS dialog box 106 2 Modeling Environment E Output Control MT3D MT3DMS Output Terms Output Times Mise Output Frequency 11 Method 1 gt Click on the column header Output Time gt Specify Min Max output times and interval Basic Transport Package simcorespmwin8 examples transport transport8 mtrr Advection Package c simcore pmwin8 examples transport transport8 mtrr Dispersion Package c simcore pmwin8 examples transport transport8 mtrr Generalized Conjugate Gradient Solver F c simcoreSpmwin8 examples transport transport8 mtrr Sink and Source Mixing Package c simcore pmwin8 examples transport transport8 mtrr r Options I Regenerate all input files I Use legacy Name File format e 9 MT3D99 Generate input files only don t start MT3DMS Cancel Help Fig 2 55 The Run MT3DMS dialog box Run MT3DMS dialog box The available settings of the Run MT3DMS dialog box are described below e The File Table has three columns Generate Prior to running a transport simulation PM uses the user specified data to generate input files for MT3DMS An input file will be generated if it does not exist or if the corresponding Generate box is checked Normally 2 6 The Models Menu 107 we do not need to worry about these boxes since PM will take care of the settings Descrip
328. g box Fig 2 53 to set the out put options of MT3D The options in this dialog box are grouped under three tabs described below e Output Terms The MT3DMS transport model always generates a listing file OUTPUT MTM which documents the details of each simulation step Option ally you can save other output terms by checking the corresponding output terms in this tab All output terms denoted by ASCII are also saved in the listing file The calculated dissolved phase concentration values are saved in the unformat ted binary files MT3Dnnn UCN where nnn is the species number The calculated sorbed phase or immobile liquid phase concentration values are saved in the un formatted binary files MT3DnnnS UCN All output files are located in the same folder as your model You can use the Result Extractor to read the unformatted binary files e Output Times The value of the output frequency NPRS indicates whether the output is produced in terms of total elapsed simulation time or the transport step 2 6 The Models Menu 105 E Output Control M1 3D MT3DMS Output Terms Output Times Misc M Concentration unformatted I Cell by Cell mass unformatted only MT3D96 MT3D99 I Concentration ASCII I Number of particles ASCII Ratardation factor ASCII I Dispersion coefficient ASCII Cancel Help Fig 2 53 The Output Control MT3D MT3DMS dialog box number If NPRS 0 simulation results will only be saved at the end of simu
329. g rate of the well Because of the symmetry of the system we could use one half of the model area only To show the whole catchment area we decided to use the entire model area The aquifer is simulated using a grid of one layer 50 rows and 51 columns A reg ular grid space of 50 m is used for each column and row The layer type is 1 uncon fined Fig 5 2 shows the contours the catchment area and the 365 days isochrones of the pumping well using a 2D approach where the groundwater recharge is treated as a distributed source within the model cells and 50 particles are initially placed around the pumping well in the middle of the aquifer If the groundwater recharge is applied on the groundwater surface refer to RCH EVT Tab page 222 particles will be tracked back to the ground water surface Fig 5 3 We can easily imagine that the size and form of the calculated catchment area depend on the boundary con dition recharge rate and the vertical position of the well screen if the well is only partially penetrating A discussion about the determination of catchment areas in two and three spatial dimensions can be found in Kinzelbach and others 71 5 1 Basic Flow Problems 299 aaant vv Fig 5 2 Catchment area and 365 days isochrones of the pumping well 2D approach ground water recharge is treated as distributed source within the model cells Fig 5 3
330. g the Polyline input method right click on a vertex to specify its prop erties in the River Parameters dialog box Fig 2 26 If the properties are assigned to one vertex only the properties of all vertices of the polyline are assumed to be the same The settings of the dialog box are described below W Stream Parameters Parameters Stream Structure IV Calculate stream stages in reaches Options apply to the selected polyline Layer Option Assign layer number manually d Segment Number 1 Inflow to this Segment L 3 T 50000 Parameters apply to the selected vertex M Active Hydraulic Conductivity of Streambed L T Stream Stage L Elevation of the Streambed Top L Elevation of the Streambed Bottom L Width of the Stream Channel L Slope of the Stream Channel Manning s Roughness coefficient n C Parameter Number Layer Number Cancel Help Fig 2 26 The Stream Parameters dialog box Calculate stream stages in reaches If this option is selected the stream water depth dstr in each reach is calculated from Manning s equation under the assumption of a rectangular stream channel See equation 2 25 below Options apply to the selected polyline Layer Option and Layer Number Layer Option controls how the layer number of a stream reach is determined x 2 6 The Models Menu 55 If Layer Option is Assign layer number manually the value of Layer Number defines
331. ge a noted South African mining geologist and statistician PM assumes that the measurement data are stationary and isotropic The Kriging method estimates the value at a model cell from a user specified number of adjacent data values while considering the interdependence expressed in the variogram A variogram is a plot of semivariance p versus vector distance h The vari ogram is used to define the relationship of the measurement values or to estimate the distance over which measurement values are interdependent When Kriging is selected as the gridding method a Variogram button appears Click this button to display the Variogram dialog box Fig 2 87 The user needs to select a vari ogram model from the drop down box and specify the parameters for the selected variogram model PM does not provide a procedure for fitting the selected vari ogram curve to the measurement data This is a task for geostatistical software e g VarioWin 92 or GEO EAS 42 and beyond the objective of this software Consider other interpolation methods if the variogram type is unknown The meaning of necessary parameters and the equations for the variogram models are listed below Power and linear model Yn a A co a gt Oand0 lt w lt 2 2 66 Logarithmic model Vn 3 a log h co a gt 0 2 67 2 7 The Tools Menu 181 Spherical model 3 hl IAP h lt Yn C G aaa Co h lt a Yn C 0 h gt a 2 68 Gaussian mod
332. gen are assumed to react instantaneously the stoichiometric ratio for the reaction is approximately 3 0 i e one mass unit of hydrocarbon reacts with three mass unit of oxygen The other model parameters used in the simulation are given below Cell width along columns I direction 10m Cell width along rows J direction 10m Layer thickness K direction 10m Groundwater seepage velocity 0 3333 m day Effective Porosity 0 3 Longitudinal dispersivity 10m Ratio of transverse to longitudinal dispersivity 0 3 Volumetric injection rate 1 m day Simulation time 730 days The concentration distributions of hydrocarbon and oxygen after a simulation period of 730 days 2 years need to be calculated Modeling Approach and Simulation Results The model grid is aligned with the flow direction along the x axis and consists of 1 layer 31 rows and 46 columns The flow model is surrounded by constant head boundaries on the east and west borders and no flow boundaries on the north and south borders To establish the required uniform hydraulic gradient the head values 11 m and 10 m are assigned to the first and last columns respectively The point source is simulated using an injection well located at column 11 and row 16 The injection rate is sufficiently small so that the flow field remains approx imately uniform The background oxygen concentration is modeled by setting the initial concentration of species 2 to 9 ppm in all model cells and by assig
333. geometrischen Datenverarbeitung B G Teubner Stuttgart Germany Hsieh PA 1986 A new formula for the analytical solution of the radial dispersion problem Water Resour Res 22 11 1597 1605 Hsieh PA and Freckleton JR 1993 Documentation of a computer program to simulate horizontal flow barriers using the U S Geological Survey s modular three dimensional finite difference ground water flow model U S Geological Survey Open File Report 92 477 Hunt BW 1978 Dispersive sources in uniform groundwater flow ASCE Journal of the Hydraulics Division 104 HY1 p 75 85 Javandel I Doughty C and Tsang CF 1984 Groundwater transport Handbook of math ematical models 228 pp American Geophysical Union Kinzelbach W 1986 Groundwater Modelling An introduction with sample programs in BASIC Elsevier ISBN 0 444 42582 9 Kinzelbach W Ackerer P Kauffmann C Kohane B and Mller B 1990 FINEM Nu merische Modellierung des zweidimensionalen Strmungs und Transportproblems mit Hilfe der Methode der finiten Elemente Programmdokumentation Nr 89 23 HG 111 Institut fr Wasserbau Universitt Stuttgart Kinzelbach W Marburger M and Chiang WH 1992 Determination of catchment areas in two and three spatial dimensions J Hydrol 134 221 246 Kinzelbach W and Rausch R 1995 Grundwassermodellierung Einfhrung mit bungen Gebrder Borntraeger Berlin Stuttgart ISBN 3 443 01032 6 Konikow LF and Bredehoeft JD 1978 Computer model of two dime
334. ghest active cell is used so that recharge will penetrate through inactive cells down to the water table The specific recharge rate of 0 05 foot per day 0 0152 m d simulates leakage of 3 125 cubic feet per day 88 5 m3 d through one quarter of the pond bottom a simulated area of 62 500 square feet 580677 Reasonable solutions to the ground water mounding problem can be obtained in two steady state simulations by using the PCG2 solver In the first simulation dry 306 5 Examples and Applications Cross Section infiltration pond 70 pond leakage ayer 60 4 2 HEHE i 3 50L UNTI 4 Groundwater mound ae L 5 6 L i A 8 w Oo m Water table _ 10 11 N ratio of horizontal to vertical 10 hydraulic conductivity is 20 to 1 n 14 Elevation in feet above arbitrary datum EN Fixed head cells h 25 feet column 1 2 3 recharge cells Plan View 40 infiltration pond modeled quarter Fig 5 9 Hydrogeology and model grid configuration cells are converted to wet by comparison of the wetting threshold THRESH to heads in underlying cells only which is indicated by a negative value of THRESH The wetting iteration interval is 1 and THRESH is 0 5 foot which means that the wetting threshold is
335. ght click on any of the DXF File or Line Map File edit fields and select a file from a Map Files dialog box 2 If necessary use a scale factor to enlarge or reduce the appearance size of the map Then use the values in X and Y to shift the scaled map to the desired position For details see Scaling a vector graphic in Section 2 102 x DXF File Filename Ye Factor Ill gt program fles wt360 pmainiex rrp mrj W bp R moj b bp h mrt fo R w po p p Line Map Filename lie Factor ep i mof o o fo fo h meg o aooo ie the right mouse button on the DXF or LINE MAP file fields to open files Fig 3 15 The Maps Options dialog box 224 3 The Advective Transport Model PMPATH 3 Click the colored button in the front of the edit field and select a color for the DXF map from a Color dialog box The color will be assigned to a DXF graphics entity if the entity s color is not defined in the DXF file A line map will always use the selected color 4 Check the check box next to the edit field The map will be displayed only when the box is checked 3 4 PMPATH Output Files 3 4 1 Plots gt To create plot files 1 Select File Save Plot As to display the Save Plot As dialog box Fig 3 16 2 Select a format from the Format drop down box The following five formats are available Drawing Interchange Format DXF Hewlett Packard Graphics Language HP GL MODPATH PMPATH and Windows Bitmap BMP If the MO
336. given in this table The Name should be unique for each observation A borehole is active if the Active flag is checked To input a new borehole scroll down to the end of the table and simply type the name and coordinates to the last blank row To delete a borehole the user selects the row to be deleted by clicking on its record selector CJ before the first column of the table then pressing the Del key After a simulation the user may select View Head Scatter Diagram from the Modflow or PEST menus to compare the calculated and observed values The user can also select View Head Time Curves of these menus to display time series curves of both the calculated and observed values The Observation Data group contains two tables Layer Proportion and Head Observation s These tables contain the data of the selected borehole which is marked by on the Observation Borehole table The Layer Proportions table PM supports multi layer observations by using this table If an observation borehole is screened over more than one model layer and the observed hydraulic head is affected by all screened layers then the associated simulated value is a weighted average of the calculated hy draulic heads of the screened layers The simulated head value h is calculated by 72 2 Modeling Environment nlay XO H x PR h 2 33 nlay 5 PR i 1 Where nlay is the number of model layers H and PR are the calculated head va
337. grid After specifying these data and clicking the OK button the Grid Editor shows the model grid Fig 2 3 A summary of the tool bar buttons of the Grid Editor is given in Table 2 3 Using the Environment Options dialog box see Section 2 9 2 the user can adjust the coordinate system the extent of the Viewing Window and the position of the model grid to fit the study site By default the origin of the coordinate system is set at the lower left corner of the model grid and the extent of the Viewing Window is set to twice that of the model grid The first time the Grid Editor is used the user 10 2 Modeling Environment iigiiModel Grid and Coordinate System Model Grid Coordinate System r Layer K Dimension Number of Layers 3 Model Thickness 10 Model Top Elevation 0 r Row I Dimension Number of Rows 30 Model Extent 600 r Column J Dimension Number of Columns 30 Model Extent 600 r Cross Sectional Display Vertical Exaggeration 10 Load Help Cancel P Fig 2 2 The Model Dimension dialog box can insert or delete columns or rows see below After leaving the Grid Editor and saving the grid the existing model grid can be subsequently refined by calling the Grid Editor again In each case the width of any column or row can be modified If the grid is refined depending on the nature of the model parameters they are either kept the same or scaled by the cell si
338. hange of solutes between the mobile and immobile domains can be defined through equation 2 50 TE E On C 2 50 Rim C 2 50 where nim is the secondary porosity i e the portion of total porosity filled with immobile water Cm M L is the concentration in the mobile 100 2 Modeling Environment domain Cim ML is the concentration in the immobile domain and T is the first order mass transfer rate between the mobile and immobile domains As the mass transfer rate increases the dual domain model functions more and more like the single domain model with a porosity approaching the total porosity of the porous medium For a very small value of the right hand side of equation 2 50 approaches zero i e there is no change of the concen tration in the immobile domain and the model functions like a single porosity model with the primary effective porosity One of the advantages of this approach is that the fracture structure does not need to be known However a problem may arise when one tries to estimate the mass transfer rate by measuring the concentrations Cm and Cim When the concentration is measured at a certain point only one value is obtained which cannot be distinguished between mobile and immobile concentration It is therefore more likely that must be estimated through a model calibra tion using Cm values only e Type of Reaction No kinetic reaction is simulated reaction is n
339. he contaminated area Repeat previous step for the case that the cutoff wall reaches the depth 10m 4 Use a pumping well located in the cell row column 12 6 to capture the contaminants Calculate the required pumping rate and penetration depth W Modeling Approach and Simulation Results The aquifer is simulated using a grid of 5 layers 23 rows and 23 columns All layers have the same layer type 3 confined unconfined Transmissivity varies The cutoff wall is modeled by using the Horizontal Flow Barriers package An impervious cover can be easily simulated by reducing the recharge rate Figures 5 43 and 5 44 show the flowlines by performing forward and backward particle tracking with PMPATH The particles are initially placed in the center of each cell which is located in the first model layer and within the cutoff wall It is obvious that the contaminants will be washed out even if the cutoff wall is going deeper The contaminated area can be captured by using a pumping well located in the cell row column 12 6 penetrating in the first model layer with a pumping rate of 0 0025 m s This low pumping rate is possible because of the low groundwater flow velocity within the zone around the contaminated area 5 4 Geotechnical Problems Plan View Cutoff Wall 0 4m 0 5 m tte fixed head
340. he fluid density and the flow field MT3DMS simulations are carried out on the basis of flow fields computed beforehand by MODFLOW Variable Density Flow and Transport with SEAWAT If this option is selected SEAWAT will be used to simulate coupled variable density flow and solute transport With this option fluid density is calculated by using an equation of state and the simulated solute concentration values of involved species The Simulation Settings MT3DMS SEAWAT Simulation Mode Variable Density Flow and Transport with SEAWAT Type of Reaction No kinectic reaction is simulated Species MT3099 SEAWAT Description DRHODC __ CRHOREF a Saltwater Temperature JOAAAAAAAAAAAAAAAAAAAAAARI s s KK Fig 2 44 The Simulation Settings MT3DMS SEAWAT dialog box 86 2 Modeling Environment density effect of a particular species may be turned on or off in the Species tab see below The flow and transport processes are computed by MODFLOW and MT3DMS that are incorporated in SEAWAT e Type of Reaction Select a type of reaction that you want to simulate from this dropdown box MT3DMS includes the type of First order irreversible reaction only The last three reaction types are supported by the proprietary MT3D99 code 122 If you do not have access to MT3D99 or need to simulate more complex reaction scenarios conside
341. he maximum number of optimization itera tions see NOPTMAX lt in the Control Data tab will be set to 0 PEST will run in the Parameter Estimation mode but will not calculate the Jacobian ma trix Instead it will terminate execution after just one model run This setting can thus be used when you wish to calculate the objective function corre sponding to a particular parameter set and or to inspect observation residuals corresponding to that parameter set Regularization Within each optimization iteration PEST s task when work ing in regularization mode is identical to its task when working in parameter estimation mode i e it must minimize an objective function using a lin earized version of the model encapsulated in a Jacobian matrix However just before calculating the parameter upgrade vector PEST calculates the ap propriate regularization weight factor to use for that iteration This is the factor by which all of the weights pertaining to regularization information are multiplied in accordance with equation 2 33 of the PEST manual 37 prior to formulating the overall objective function whose task it is for PEST to minimize on that iteration As parameters shift and the Jacobian matrix changes an outcome of the nonlinear nature of most models the regular ization weight factor also changes Hence it needs to be re calculated during every optimization iteration 152 2 Modeling Environment Use of PEST in regularization
342. he parameter plays only a limited role in the estimation process However the parameter to which the tied parameter is linked this parent parameter must be neither fixed nor tied itself takes an active part in the parameter estimation process the tied parameter simply piggy backs on the parent parameter the value of the tied parameter maintaining at all times the same ratio to the parent parameter as the ratio of their initial values If a parameter is neither fixed nor tied and is not log transformed the parameter transformation variable PARTRANS must be supplied as None PARCHGLIM is used to designate whether an adjustable parameter is relative limited or factor limited See the discussion on RELPARMAX and FACPAR MAX page 169 For tied or fixed parameters PARCHGLIM has no significance PARGP is the number of the group to which a parameter belongs Parameter groups are discussed in Group Definitions below PARTIED is the name of the parent parameter to which the parameter is tied You can select a name from a drop down list SCALE and OFFSET Just before a parameter value is written to an input file of MODFLOW it is multiplied by the real variable SCALE after which the real variable OFFSET is added The use of these two variables allows you to redefine the domain of a parameter Because they operate on the parameter value at the last moment before it is sent they take no part in the estimation process
343. he selected simulation time are displayed Axes Bounds The bounds of the axes are defined by Upper Bound and Lower Bound which are determined automatically if the Fix Bounds box is not 2 6 The Models Menu 81 checked or if the Reset Bounds button is pressed When editing the upper and lower bounds the scatter diagram will be updated accordantly if Fix Bounds is not checked Check it to fix the bounds at specified values Variance is the mean squared error between observed and calculated value of Plot marked observations which are displayed on the scatter diagram Copy to Clipboard Press this button to place a copy of the scatter diagram on the clipboard The user can recall this copy by pressing Ctrl v in almost all word or graphics processing software This button is enabled only when the Chart tab is chosen Save Plot As Press this button to save the scatter diagram in Windows bitmap or Metafile formats This button is enabled only when the Chart tab is chosen MODFLOW View Drawdown Scatter Diagram This menu item is available only if Drawdown Observations have been defined see Section 2 6 1 15 Select this menu item to open a Scatter Diagram Drawdown dia log box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 except the drawdown values replace the head values Note that drawdown is defined by ho h where ho is the user specified initial hydraulic head and A is the calculat
344. he settings 4 1 Your First Groundwater Model with PM 261 E output Control MOC3D x Concentration Velocity Particle locations Disp Coeff Misc I Save data in a separate binary file These data will be printed or saved at the end of every stress period id These data will be printed or saved every Nth particle moves N 20 Fig 4 31 The Output Control MOC3D dialog box x Generate Description Deestination Fie _ __ v Basic Package c program files wt360 pmwinexamples sample bas Vv Block Centered Flow c program files wt360 pmwin examples sample bef c Vv Output Control c program files wt360 pmwin examples sample oc d Vv Well c program files wt360 pmwinexamples samplel wel c Vv Recharge c program files wt360 pmwin examples sample rch c Vv Solver PCG2 c program files wt360 pmwin examples sample pegz Vv MOC3D Main Package c program files wt360 pmwinexamples sample mocr Vv MOCS3D concentration in recharge c program files wt360 pmwin examples sample mocc Options J7 Check model data I Regenerate all input files JT Generate input files only don t start MOC3D coe Fig 4 32 The Run Moc3d dialog box gt Check simulation results and produce output During a transport simulation MOC3D writes a detailed run record to the file path MOC3D LST where path is the folder in which your model data are saved MOC
345. hes sete GAR ee tae 27 24 3 CelbsStats lt re coe ve as PESEE E eh waar dhe eee eee a 31 2 4 3 1 IBOUND MODFLOW 31 2 4 3 2 ICBUND MT3D MT3DMS 32 2 4 4 Top of Layers TOP 0 0 0 cee eee eee 32 2 4 5 Bottom of Layers BOT 0 0 eee eee eee eee 32 2 5 The Parameters Menu wa enr oriana iig a wees Geese whence eens ooh 33 25 Me TAM igs secs eid gett oars E S855 Ss Sepia ute eas sw egy area E 33 2 5 2 Initial amp Prescribed Hydraulic Heads 36 2 5 3 Horizontal Hydraulic Conductivity and Transmissivity 36 VI 2 6 Contents 2 5 4 Horizontal Anisotropy 0 0 36 2 5 5 Vertical Leakance and Vertical Hydraulic Conductivity 37 2 5 6 Vertical Anisotropy and Vertical Hydraulic Conductivity 37 2 5 7 Effective Porosity varpai neee s eee ee eee 37 2 5 8 Specific Storage Storage Coefficient and Specific Yield 38 25 9 Bulk Density a Ses Se Ra eS ee BE ep BURA AES 38 25 9 Layersby Layers csacss ood stew oe eta ks 38 25 92 Cell by Celli correer ei ieee ee ees wees ok 38 The Models Menu 0 0 cece eee eee 39 26 1 MODFLOW 3 06 52 45 88 895 sob ie A a peste eta ES 39 2 6 1 1 MODFLOW Flow Packages Drain 39 2 6 1 2 MODFLOW Flow Packages Evapotranspiration 41 2 6 1 3 MODFLOW Flow Packages General Head Boundary ei Geer al E Mae es 42 2 6 1 4 MODFLOW Flow Packages Hori
346. hydraulic heads or drawdowns PM provides an animation technique to display a sequence of the saved images in rapid succes sion Although the animation process requires relatively large amount of computer resources to read process and display the data the effect of a motion picture is often very helpful The 2D Visualization tool is used to create animation sequences The following steps show how to use the Environment Options and Animation dialog boxes to cre ate an animation sequence for displaying the motion of the concentration plume in the third layer gt To create an animation sequence 1 Select Tools 2D Visualization 2 Select the MT3DMS tab in the Result Selection dialog box 3 Click OK to accept the default result type Solute Concentration and species 1 PM displays the model grid sets the Simulation Time on the toolbar to the beginning of the simulation and automatically loads the results pertained to the Simulation Time 4 Click the Simulation Time drop down list and set the simulation time to 9 467E 07 the end of the simulation By default PM sets 10 contour levels ranging from the minimum to the maximum concentration values of the selected simulation time Fig 4 25 One can customize the contour levels and the appearance of the contours by using the Environment Options dialog box Click the button if the display mode is not Grid View Move to the third layer Select Options Environment Click the
347. i multaneous use of the MT3DMS chemical reaction package RCT and PHREEQC 2 as reaction simulator s is possible However this should be done with appropriate care i e control of potential operator splitting errors 2 6 3 1 PHT3D Simulation Settings The simulation settings of PHT3D are completed in two dialog boxes The Chemical Reaction Module PHT3D dialog box Fig 2 57 will appear first allowing the user to select a pre defined chemical reaction module For simpler problems such as those that only include equilibrium reactions all of the aqueous species components and minerals are already included in the original PHREEQC 2 Standard database In addition PM includes more than 10 reaction modules from PHT3D examples See Section 5 6 for a complete list of PHT3D examples In some cases a problem specific reaction module needs to be prepared and added to PM before using PHT3D See Section 6 5 for the steps of defining a customized reaction module Once a reaction module is selected and the Chemical Reaction Module PHT3D di alog box is closed the Simulation Settings PHT3D dialog box Fig 2 58 appears The tabs of the dialog box are described below e Component equilibrium This tab contains a table and each row of the table defines an aqueous component that are assumed to be in chemical equilibrium The columns of the table are defined as follows Active Check the box to include the respective component in the simulatio
348. ial transformation and are given below Cell width along columns I direction lom Cell width along rows J direction 0 5 cm Layer thickness K direction lem Longitudinal dispersivity 1 8 cm Groundwater seepage velocity 0 1 em hr First order reaction rate for PCE species 1 0 05 hrt First order reaction rate for TCE species 2 0 03 hrt First order reaction rate for DCE species 3 0 02 hrt First order reaction rate for VC species 4 0 01 hrat Retardation factor for PCE species 1 2 Yield coefficient between PCE and TCE Y1 2 0 792 Yield coefficient between TCE and DCE Y2 3 0 738 Yield coefficient between DCE and VC Y3 4 0 644 Simulation time 200 hours Modeling Approach and Simulation Results The model grid consists of 1 layer 1 row and 101 columns In the flow model the first and last columns are constant head boundaries To establish the required uniform hydraulic gradient the head values 0 5 cm and 0 cm are assigned to the first and last columns respectively In the transport model the first column is a constant concentration boundary for all species with the concentration values equal to 1 0 mg liter for PCE species 1 and zero for other species The last column is sufficiently far away from the source to approximate a semi infinite one dimensional flow domain The initial concentration values for all species are assumed to be zero The retardation factor of 2 is simulated by assigning ne 0 1 bulk density pp 1000kg
349. ialog box Fig 2 43 will appear and the following options are available e Select a species and click the Edit button to specify the initial concentration for that species e Click the Close button to close the dialog box and to stop editing data e The Data box has three types of status as given below Once the data is specified you may click on the Data box to check or clear it B Data has been specified and will be used for simulation Initial Concentration Select a species and click Edit to specify its associated data No Description 1iHydrocarbon 2 Oxygen Edit Close Help Fig 2 43 The Initial Concentration dialog box 2 6 The Models Menu 85 Data has been specified but will not be used the default value of zero will be used Data is not available the box is dimmed and deactivated the default value of zero will be used 2 6 2 1 MT3DMS SEAWAT Simulation Settings The Simulation Settings dialog box Fig 2 44 controls the type of reaction and the species involved in the simulation It also controls whether variable density flow and or transport should be simulated The available settings are described as follows e Simulation Mode Constant Density Transport with MT3DMS If this option is selected the con stant density flow solution of MODFLOW will be used by MT3DMS to sim ulate solute transport processes It is assumed that the solution concentration does not affect t
350. ical reactions of contaminants in groundwater systems Documentation and Users Guide Contract Report SERDP 99 1 U S Army Engineer Research and Development Center Vicksburg MS Zheng C 1999 MT3D99 A modular 3D multispecies transport simulator S S Pa padopulos and Associates Inc Bethesda Maryland Zheng C 2006 MT3DMS 5 2 Supplemental Users Guide The University of Alabama Alabama Zheng C and Wang PP 2002 MGO A Modular Groundwater Optimizer The Univer sity of Alabama Alabama Index 2D Visualization 27 184 3D Visualization 25 184 adjustable parameter define 135 149 advection MOC3D 119 MT3D 126 MT3DMS SEAWAT 89 RT3D 114 advective transport 176 advective transport model 203 aerobic biodegradation 361 animation 27 anisotropy 36 horizontal 29 vertical 29 artificial oscillation 91 127 ASCII Matrix File 376 average pore velocity 205 213 biodegradation 131 bivariate interpolation 179 Block Centered Flow 24 BMP 26 224 bottom of layers 32 BTEX 113 bulk density 38 catchment area 297 Cell Status 31 cell by cell data modify 16 cell by cell flow terms 75 Cell by Cell Input Method 16 chain reactions 363 chemical reaction MT3D 130 MT3DMS SEAWAT 97 columns delete 10 insert 10 compaction 351 compaction observations 73 compaction scatter diagram MODFLOW 81 Compatibility Issues 5 concentration observation MOC3D 124 MT3D 131 MT3DMS SEAWAT 104 RT3D 116
351. ich means that some terms in A depend on simulated head Example of head de pendent terms in A are transmissivity for water table layers which is based 2 6 The Models Menu 65 on the saturated thickness flow terms for rivers drains and evapotranspira tion convert between head dependent flow and constant flow and the change in storage coefficient when a cell converts between confined and unconfined When a non linear flow equation is being solved external iteration is nor mally required in order to accurately approximate the non linearities Note that when non linearities caused by water table calculations are part of a sim ulation there are not necessarily any obvious signs in the output from a sim ulation that does not use external iteration to indicate that iteration is needed In particular the budget error may be acceptably small without iteration even though there is significant error in head because of non linearity To under stand this consider the water table correction for transmissivity For each iteration a new transmissivity value is calculated based on the previous head Then the flow equations are solved and a budget is computed using the new head with the same transmissivities No budget discrepancy results because heads are correct for the transmissivity being used at this point however the new heads may cause a significant change in transmissivity The new trans missivity will not be calculated unless there is another
352. ient Set the Storage Coefficient flag to User Specified if you want to specify the confined storage coefficient manually For an unconfined layer the storage values are equal to specific yield The setting of the Storage Coefficient flag has no influence on the specific yield e Interbed Storage PM supports the Interbed Storage package for calculating stor age changes from both elastic and inelastic compaction of each model layer Check the Interbed Storage setting of a specific layer to calculate its storage changes and compaction by using the Interbed Storage package Refer to Sec tion 2 6 1 5 for details about this package 2 4 3 Cell Status 2 4 3 1 IBOUND MODFLOW The flow model MODFLOW requires an IBOUND array which contains a code for each model cell A positive value in the IBOUND array defines an active cell the hydraulic head is computed a negative value defines a constant head or fixed head cell the hydraulic head is kept constant at a given value throughout the flow simu lation and the value 0 defines an inactive cell no flow takes place within the cell It is suggested to use 1 for active cells O for inactive cells and 1 for constant head cells Any outer boundary cell which is not a constant head cell is automatically a zero flux boundary cell Flux boundaries with non zero fluxes are simulated by as signing appropriate infiltration or pumping wells in the corresponding cell via the well package For constant
353. ific equation For ex ample the Groundwater Flow Process GWF deals with the groundwater flow equation and replaces the original MODFLOW The parameter estimation capa bility of MODFLOW 2000 is implemented by Hill and others 63 using three processes in addition to the GWF process The Observation Process OBS cal culates simulated values that are to be compared to measurements calculates the sum of squared weighted differences between model values and observa tions and calculates sensitivities related to the observations The Sensitivity Pro cess SEN solves the sensitivity equation for hydraulic heads throughout the 1 Introduction grid and the Parameter Estimation PES Process solves the modified Gauss Newton equation to minimize an objective function to find optimal parameter values Although the OBS SEN and PES processes allow MODFLOW 2000 to perform a model calibration without the need for any external parameter es timation software there will still be many situations in which it is preferable to calibrate a MODFLOW model using external parameter estimation software rather than using built in MODFLOW 2000 parameter estimation functionality 36 To combine the strengths of PEST ASP and MODFLOW 2000 a modi fied version of MODFLOW 2000 called MODFLOW ASP 35 allows a cou pled PEST ASP MODFLOW 2000 approach using MODFLOW ASP to calcu late derivatives and using PEST ASP to estimate parameter values The latest major version o
354. ile v c simcore pm8 modfiw96ykmt2 modfiow2i exe PMPATH M C Simcore PM8 pmpath exe TEXT VIEWER M c windows notepad exe MODFLOW 2000 Parameter Estimat PEST Parameter Estimation C Simcore PMS mF2k mf2k exe C Simcore PMB pest pest exe MT3D C Simcore PMB mt3d mt3di exe MOC3D MT3DMS C Simcore PM8 moc3d moc3di exe imcore PM8 mt3dms nt3dms5b exe 3D VISUALIZATION ojects pm2006 programs pmwin32 seer3d exe imcore PM8 RT3 RT325 exe E C Simcore PM8 pht3d pht3dv2 exe C Simcore PMB seawat swt_v4 exe alalalalalalalalalalala Fig 2 13 The Preferences dialog box Modflow Version Several variants of MODFLOW are supported and included in PM Each variant is associated with an executable program The full paths and file names of all executable programs of MODFLOW are given in Table 2 5 The default Modflow Version is gt MODFLOW 96 This version works with all supported transport models Of particular note is that when using MODFLOW 2000 for parameter estimation Modflow Version must be set to gt MODFLOW 2000 MODFLOW 2005 otherwise it is not possible to switch the Flow Pack age see below to the LPF package which are required for estimating aquifer parameters within MODFLOW 2000 24 2 Modeling Environment e Flow Package This dropdown box is enabled when Modflow Version is set to MODFLOW 2000 MODFLOW 2005 which includes the Laye
355. iles This includes groundwater models distributed by the U S Geologi cal Survey and most popular graphical user interfaces such as Processing Modflow ModIME 119 Groundwater Modeling System known as GMS Groundwater Vis tas Argus ONE and Visual MODFLOW PM is capable of reading binary files cre ated by the above mentioned codes Binary files are often saved in the unformatted sequential or transparent for mat An unformatted sequential file contains record markers before and after each record whereas a transparent file contains only a stream of bytes and does not contain any record markers Of particular importance is that different FORTRAN compilers often use different and incompatible formats for saving unformatted sequential files Thus when compiling your own codes the following rules should be followed so that PM can read the model generated binary files e When Lahey Fortran compiler is used Create a transparent file by specifying FORM UNFORMATTED and AC CESS TRANSPARENT in the OPEN statement e When Intel Visual Fortran is used Create a transparent file if it is opened using FORM BINARY and AC CESS SEQUENTIAL e If you are using other compilers please consult the user manual for the settings of creating transparent binary files 2 Modeling Environment This chapter is a complete reference of the user interface of PM With the exception of PHT3D PM
356. imal separator where N is the value specified in Decimal digits Exponential This option displays numbers in scientific format and E is in serted between the number and its exponent i Color Spectrum x Minimum Color Maximum Color OK Cancel Help Fig 3 9 The Color Spectrum dialog box xi First labeled contour line fi Labeled line frequency fi OK Cancel Fig 3 10 The Contour Labels dialog box Label Format x 3 3 PMPATH Options Menu 219 Exponential Decimal digits 200 Prefix Sufie Cancel Fig 3 11 The Label Format dialog box Decimal digits The value of Decimal digits determines the number of digits to the right of the decimal separator For example if Decimal digits 2 the value 1241 2 will be displayed as 1241 20 for the fixed option or 1 24E 03 for the exponential option Prefix is a text string that appears before each label Suffix is a text string that appears after each label Restore Defaults Clicking on this button PMPATH sets the number of contour lines to 11 and uses the maximum and minimum values found in the current layer as the minimum and maximum contour levels The label height and spacing will also be set to their default values Load and Save The contents of the contour level table can be loaded from or saved to separate Contour files Refer to Section 6 2 2 for the format 3 3 2 Particle Tracking Time The available settings of
357. ime series curves of a borehole will be displayed only when its Plot box is checked Color This column defines the plot color for each borehole Click the J button to change the color Simulation Time Displays the times at the end of each stress period or time step to which the calculated values and observed values pertain Calculated value Displays simulated head values at observation boreholes If a borehole lies in an inactive or dry cell the default value for dry cells defined in Models MODFLOW Output Control is displayed Refer to MODFLOW View Head Scatter Diagram page 78 for details of interpo lating simulated heads to the observation boreholes Observed Value The user specified observed values in the Head Observa tions dialog box Fig 2 35 are linearly interpolated to the simulation times and displayed in this column Save Table Press this button to save the data of OBSNAM Simulation Time Calculated Value Observed Value in an ASCII file This button is enabled only when the Data tab is chosen e The Chart Tab The Chart tab Fig 2 42 displays time series curves using the calculated and observed values The available settings are summarized below Chart The Chart has a lot of built in features Time Series Curves Hydraulic Head x OBSNAM Plot Color OBSNAM Simulation Time Calculated Value Observed Value 1 100 2252 0 ojojo D D a m2 si lt I z oe Ti 126 945
358. imited degradation of BTEX using multiple electron acceptors Sim ulates kinetic limited biodegradation of BTEX via five different degradation pathways aerobic respiration O2 denitrification NO iron reduction Fe sulfate reduction S077 and methanogenesis C H4 Rate limited sorption reactions Simulates first order reversible kinetic sorp tion This option is equivalent to First order kinetic sorption in the chemical reaction package of the MT3DMS Models MT3DMS SEAWAT Chemical Reaction Double Monod model Simulates the reaction between an electron donor and an electron acceptor mediated by actively growing bacteria cells living in both aqueous and soil phases Sequential decay reactions Simulates reactive transport coupled by a series of sequential degradation reactions up to four components under anaerobic conditions Anaerobic and aerobic biodegradation of PCE TCE DCE VC Simulates se quential degradation of perchloroethene PCE trichloroethene TCE dichloroethene DCE vinyl chloride VC via both aerobic and anaerobic paths e Sorption Parameter Defines whether the sorption parameters are going to be specified layer by layer Use Layer by Layer mode or cell by cell Use Cell by Cell mode The latter can only be used by RT3D version 2 0 or later The sorption parameters are specified using Models RT3D Sorption Parameters e Convergence Criteria for iterative solver The ta
359. imum number of estimated parameters 500 Maximum number of species 60 There is no limit to the polylines and number of wells general head boundary cells rivers drains and horizontal flow barrier cells 6 1 2 Boreholes and Observations No limit to the maximum number of boreholes Maximum number of observations for each borehole 4000 6 1 3 Digitizer Maximum number of digitized points 50000 376 6 Supplementary Information 6 1 4 Field Interpolator Maximum number of cells in a layer 1 000 000 Maximum number of cells along rows or columns 5000 Maximum number of input data points 5000 6 1 5 Field Generator Maximum number of cells in a layer 250000 Maximum number of cells along rows or columns 500 6 1 6 Water Budget Calculator Maximum number of subregions 50 6 2 File Formats 6 2 1 ASCII Matrix File An ASCII Matrix file can be saved or loaded by the Browse Matrix dialog box see Section 2 8 1 of the Data Editor The Results Extractor Field Interpolator and Field Generator save their generated data in this format File Format 1 Data NCOL NROW 2 Data MATRIX NCOL NROW Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NCOL is the number of model columns NROW is the number of model rows MATRIX is a two dimensional data matrix saved row by row Matrix can be saved in free format If the wrap from is used to save the
360. in Parameters Layer Option apply to the selected polyline Assign layer number manually Parameters apply to the selected vertex Active Equivalent Hydraulic Conductivity L T Elevation of the Drain L 124 Layer Number 1 Parameter Number 0 SEAWAT Drain Bottom Elevation L 122 Cancel Fig 2 18 The Drain Parameters dialog box 40 2 Modeling Environment Tf Layer Option is Assign layer number automatically the drain is as signed to a layer where the drain elevation d see below is located be tween the top and bottom of the layer The layer number is set to 1 if d is higher than the top of the first layer The layer number is set to the last layer if d is lower than the bottom of the last layer Active Check this box to activate a vertex Clear the Active box to deactivate a vertex The properties of an active vertex will be used in the simulation The properties of an inactive vertex are ignored Equivalent Hydraulic Conductivity K LT and Elevation of the Drain d L The value K describes all of the head loss between the drain and the aquifer It depends on the material and characteristics of the drain itself and the immediate environment Since the Drain package requires the input of drain hydraulic conductance Cz and drain elevation d to each cell of a drain the input values K and d at active vertices are linearly interpolated or extrapolated to each cell
361. in fact 2 6 The Models Menu 155 they can conceal from PEST the true value of a parameter as seen by the model PEST optimizing instead the parameter bp where bp bm of f set scale 2 59 Here b is the parameter optimized by PEST bm is the parameter seen by the model while scale and of f set are the scale and offset values for that parameter respectively If you wish to leave a parameter unaffected by scale and offset enter the SCALE as 1 0 and the OFFSET as 0 0 The Parameter Groups Tab In PEST the input variables that define how derivatives are calculated pertain to pa rameter groups rather than to individual parameters These input variables are speci fied in the Parameter Groups tab of the Simulation Settings PEST dialog box Fig 2 80 Thus derivative data do not need to be entered individually for each parameter however if you wish you can define a group for every parameter and set the deriva tive variables for each parameter separately In many cases parameters fall neatly into separate groups which can be treated similarly in terms of calculating derivatives Simulation Settings PEST Operation Mode Parameter Estimation i Prior Information Regularization SVD SVD Assist Control Data 1 Relative 7 Always_2 Parabolic Relative 7 Always 2 1 Parabolic Relative T Always_2 Parabolic Relative Always_2 Parabolic Relative y JAlways_2 Parabolic Relative Always_2 Parabolic Relative y Always
362. in spite of the fact that it uses a number of different values for the Marquardt lambda in attempting to do so If it cannot lower the measurement objective function to an acceptable level it simply ac cepts the upgraded parameters proceeds to the next optimization iteration and tries again However if it does succeed in lowering the measurement objective function to an acceptable level or if it has succeeded in doing this on previous iterations then PEST slightly alters its philosophy of choosing new Marquardt lambdas in that it now attempts to lower the regularization component of the ob jective function while maintaining the measurement component of the objective function below this acceptable level This acceptable level is PHIMACCEPT it should be set slightly higher than PHIMLIM in order to give PEST some room to move 2 6 The Models Menu 161 FRACPHIM Optional PEST ignores the value supplied for FRACPHIM unless it is greater than zero A value of between zero and 1 0 but normally less than about 0 3 can be supplied for this variable if you are unsure what value to use for PHIMLIM See Section 7 3 4 of the PEST manual 37 for a full discussion of this variable Initial regularization weight factor WFINIT This is the initial regularization weight factor During every optimization iteration PEST calculates a suitable regularization weight factor to use during that optimization iteration using an iterative numerical solution
363. in the file CHECK LIS located in the same folder as the model data Generate input files only don t start MOC3D Check this option if the user does not want to run MOC3D The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file MOC3D BAT e OK Click OK to generate MODFLOW and MOC3D input files In addition to the input files PM creates a batch file MOC3D BAT in the model folder When all files are generated PM runs MOC3D BAT in a Command Prompt window DOS box During a simulation MOC3D writes a detailed run record to the file MOC3D LST saved in the model folder MOC3D saves the simulation results in various unformatted binary files only if a transport simulation has been suc cessfully completed See the previous section for details about the output terms and the corresponding result files from MOC3D 2 6 5 11 MOC3D View MOCS3D View Run Listing File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run list file MOC3D LST which contains a detailed run record saved by MOC3D MOCS3D View Concentration Scatter Diagram This menu item is available only if Concentration Observations have been defined see Section 2 6 5 9 Select this menu item to open a Scatter Diagram Concentra tion dialog box which is identical to the Scatter Diagram Hydraulic Head dialog box Fig 2 38 except the concentration values replace the head
364. in which case equation 27 of Hill and others 63 is used to convert Statp which equals o of equation 27 to of p and Weight 1 Cin b 2 Stat flag 1 Statp is the standard deviation associated with Prm and is re lated to the native prior value Weight 1 Statp unless the parameter is defined as log transformed in which case equation 27 of Hill and others 63 is used to convert Statp which equals o of equation 27 to oF p and Weight 1 07 p 3 Stat flag 2 Statp is the coefficient of variation associated with Prm and is related to the native prior value Weight 1 Statp x Prm unless the parameter is defined as log transformed in which case equation 27 of Hill and others 63 is used to convert Statp which equals o b of equation 27 to of p and Weight 1 07 p 4 Stat flag 10 Statp is the variance associated with the log base 10 trans form of Prm Weight 1 Statp x 2 30267 5 Stat flag 11 Statp is the standard deviation associated with the log base 10 transform of Prm Weight 1 Statp x 2 30267 6 Stat flag 12 Statp is the coefficient of variation associated with the log base 10 transform of Prm Weight 1 Statp x logy PRM x 2 30267 e Plot Symbol is an integer that will be written to output files intended for graphical analysis to allow control of the symbols used when plotting data related to the prior information The following lines show some examples refer to Hill 62 p 43
365. ined and at least for more complex cases it is strongly recom mended to first test and debug reaction definitions in batch mode i e by setting up a PHREEQC 2 batch type simulation To add a user defined PHT3D reaction module for PM you need to complete the following three steps 1 Create a database file analogous to the original PHREEQC 2 database files You can find a number of examples such as pht3d_datab ex1 pht3d_datab ex2 etc in the pmdir pht3d Database folder where pmdir is the installation folder of PM 2 Create a module file that contains information about the number names and types of chemical and reaction rate constants that are used in the correspond ing database file created in the first step You can find a number of examples and templates in the pht3d Database For example pmwin_pht3dv2 standard contains information corresponding to the standard PHREEQC 2 database file pht3d_datab standard 3 Add module definition to the pmdir pht3d Database pht3d_module definition txt file To add a module definition you need to modify the number of modules in the pht3d_module_definition txt file and then add the four lines containing the following information to the end of the pht3d module definition txt file e Name of the module e Description of the module e Name of the PHREEQC database file created in step 1 e Name of the module file created in step 2 References 10 11 12 13 14 15 Akima H
366. ing method 5 8 Miscellaneous Topics 371 Fig 5 60 Contours produced by Renka s triangulation algorithm 372 5 Examples and Applications 5 8 2 An Example of Stochastic Modeling Folder pmdir examples misc misc2 Overview of the Problem Aquifer remedial measures are often designed by means of groundwater models Model results are usually uncertain due to the imperfect knowledge of aquifer param eters We are uncertain about whether the calibrated values of parameters represent the real aquifer system We never know the actual small scale distribution of some parameters e g hydraulic conductivity or recharge Thus all groundwater models involve uncertainty Stochastic models are often employed to take into account un certainty In the stochastic modeling approach the model parameters appear in the form of probability distributions of values rather than as deterministic sets We use the aquifer described in Section 4 1 to illustrate the concept of stochas tic modeling Using a two dimensional approach to model the aquifer we may use the Field Generator to create log normal correlated distributions of the horizontal hydraulic conductivity The mean horizontal hydraulic conductivity of the aquifer is equal to 4 x 0 0001 6 x 0 0005 10 3 4 x 1074 m s The standard deviation is assumed to be o 0 5 A correlation length of 60 m is used In Section 4 1 the pumping rate of the well was determin
367. ings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start SEAWAT Check this option if the user does not want to run SEAWAT The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file SEAWAT BAT e OK Click OK to generate SEAWAT input files In addition to the input files PM creates a batch file SEAWAT BAT in the model folder When all input files are generated PM automatically runs SEAWAT BAT in a Command Prompt window DOS box During a simulation SEAWAT writes a detailed run record to the file OUTPUT SWT saved in the model folder See Section 2 6 2 12 on page 104 for details about the output terms 2 6 2 14 MT3DMS SEAWAT View MT3DMS SEAWAT View Run Listing File Select this menu item to use the Text Viewer see Section 2 3 4 to display the run list file OUTPUT MTM of MT3DMS or OUTPUT SWT of SEAWAT which contains a detailed run record saved by MT3DMS or SEAWAT respectively MT3DMS SEAWAT View Concentration Scatter Diagram This menu item is available only if Concentration Observations hav
368. ion a constant concentration cell once defined remains a constant concentration cell during the simulation but its concentration value can be specified to vary in different stress period To change the concentration value in a particular stress period simply set a non zero value to Flag and assign the desired concentration value to Specified Concentration In a multispecies simulation the Flag is applied to all species 2 6 The Models Menu 117 e Specified Concentration ML This value is the concentration in the cell from the beginning of a stress period If the constant concentration condition does not apply to a particular species assign a negative concentration value for that species The negative value is used by RT3D to skip assigning the constant concentration for the designated species 2 6 4 10 RT3D Concentration Observations Select this menu item from the RT3D menu or from MOC3D MT3DMS or MT3D to specify the locations of the concentration observation boreholes and their associ ated observed measurement data in a Concentration Observations dialog box Its use is identical to the Head Observation dialog box see Section 2 6 1 14 The only difference is that the head observations are replaced by concentration observations 2 6 4 11 RT3D Output Control The output control of RT3D is the same as that of MT3DMS SEAWAT See Section 2 6 2 12 on page 104 for details 2 6 4 12 RT3D Run The available settings of the
369. ion may involve up to seven unknown values of head and because the set of unknown head values changes from one equation to the next through the grid the equations for the entire grid must be solved simultaneously at each time 62 2 Modeling Environment step The system of simultaneous finite difference linear equations can be expressed in matrix notation as A z b 2 32 where A is a coefficient matrix assembled by MODFLOW using user specified model data b is a vector of defined flows terms associated with head dependent boundary conditions and storage terms at each cell x is a vector of hydraulic heads at each cell One value of the hydraulic head for each cell is computed at the end of each time step PM supports four packages solvers for solving systems of simulta neous linear equations Direct Solution DE45 package Preconditioned Conjugate Gradient 2 PCG2 package Strongly Implicit Procedure SIP package Slice Successive Over Relaxation SSOR package and Geometric Multigrid Solver GMG package Input parameters of these solution methods are discussed below See McDonald and Harbaugh 85 59 Harbaugh 53 and Wilson and Naff 115 for detailed mathematical background and numerical implementation of these solvers Various comparisons between the solution methods can be found in Trescott 112 Kuiper 75 Behie and Forsyth 14 Scandrett 106 and Hill 60 Hill 60 indicates that the greatest differences in solver
370. ions Determination of the wetting threshold THRESH see Modflow Wetting Capa bility often requires considerable effort The user may have to make multiple test runs trying different values in different areas of the model In many cases positive THRESH values may lead to numerical instability and therefore the user should try negative THRESH values first 5 1 Basic Flow Problems 305 5 1 4 Water Table Mount resulting from Local Recharge Folder pmdir examples basic basic4 Overview of the Problem This example is adapted from the the first test problem of the BCF2 package Mc Donald and others 86 Localized recharge to a water table aquifer results in for mation of a ground water mound For example a ground water mound may form in response to recharge from infiltration ponds commonly used to artificially replen ish aquifers or to remove contamination by filtration through a soil column If the aquifer has low vertical hydraulic conductivity or contains interspersed zones of low hydraulic conductivity it may be necessary to simulate the aquifer using multiple model layers in which the mound crosses more than one layer The conceptual model consists of a rectangular unconfined aquifer overlain by a thick unsaturated zone Fig 5 9 The horizontal hydraulic conductivity is 5 feet per day and vertical hydraulic conductivity is 0 25 feet per day 0 0762 m d A leaking pond recharges the aquifer resulting in the formation of a ground
371. ions are available e Run Mode Perform Parameter Estimation is the default run mode which instructs MOD FLOW 2000 to estimate values of active parameters listed in the Pa rameters tab Perform Sensitivity Analysis directs MODFLOW 2000 to evaluate sensi tivities using the initial PARVAL and parameter values Using this option MODFLOW 2000 calculates one percent sensitivities for hydraulic heads for the entire grid The one percent sensitivities can be contoured just like hy draulic heads can be countered The one percent scaled sensitivity map can be used to identify where additional observations of hydraulic head would be most important to the estimation of different parameters and to compare the sensitivity of hydraulic heads throughout the model to different parameters Perform Forward Model Run using PARVAL values given in the Parameters tab This option directs MODFLOW 2000 to replace the model parameters by the product of PARVAL values and the cell values of parameters and then perform a forward model run e Max Change This option determines whether MAX CHANGE specified in the Control Data tab is applied to the native parameter value or to the log transform of the parameter value This option only applies to log transformed parameters 2 6 7 2 MODFLOW 2000 Parameter Estimation Head Observations Select Head Observations from the MODFLOW 2000 Parameter Estimation menu or MODFLOW or PEST menus to specify the loca
372. ipitation dissolution EX03 Migration of precipitation dissolution fronts EX04 Cation exchange flushing of a sodium potassium nitrate solution with calcium chloride EX05 Cation exchange during artificial recharge EX06 Cation exchange and precipitation dissolution during tenside injection EX07 Kinetic sequential parallel degradation of multiple species EX08 Kinetic sequential degradation of chlorinated hydrocarbons EX09 Kinetic degradation of BTEX using multiple electron acceptors EX10 Dissolution degradation and geochemical response EX11 Transport and surface complexation of uranium EX12 Modelling of an oxidation experiment with pyrite calcite exchangers organic matter containing sand 368 5 Examples and Applications 5 7 SEAWAT Examples Folder pmdir examples SEAWAT Overview of the Problem The examples presented here are based on the example problem described in the user s guide of SEAWAT_V4 77 The example problem consists of a two dimen sional cross section of a confined coastal aquifer initially saturated with relatively cold seawater at a temperature of 5 C Warmer freshwater with a temperature of 25 C is injected into the coastal aquifer along the left boundary to represent flow from inland areas The warmer freshwater flows to the right where it discharges into a vertical ocean boundary The ocean boundary is represented with hydrostatic con ditions based on a fluid density calculated from seawater salinities at 5 C
373. is the calculated stream discharge n is Manning s roughness coefficient Wstr L is the width of the channel and C is a conversion factor which depends on the length and time units of the model 1 3 1 3 C 1 86400 day 1 3 1 3 1 486 128383 E s day 2 26 Although n and C appear separately in equation 2 25 only the values of n C or C n are used in the computer code The user needs therefore only to specify the value of n C Some of the experimental values of the Manning s roughness coefficient can be found in the documentation of the STR package 98 Parameter Number Since Cstr is usually unknown it needs to be es timated Parameter Number is used to group cells where the C str values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps The value of Parameter Number is assigned to all model cells downstream from a vertex until the next vertex redefines the parameter number The ALL button Click the ALL button of a property to copy the property value to all other active vertices Stream Structure describes the configuration of a stream system Each row in the table Fig 2 27 represents a stream segment in the model Each segment can have up to 10 tributary segments The numbers of the tributary segments are specified in the columns 1 to 10 The column Iupseg
374. is the previous minimum head value in the aquifer For model cells in which the specified preconsolidation head is greater than the corresponding value of the starting head the preconsolidation head will be set to the starting head Subsidence compaction and preconsolidation head are saved in the unformatted binary file INTERBED DAT Interface file to MT3D is an unformatted binary file containing the com puted heads fluxes across cell interfaces in all directions and locations and flow rates of the various sinks sources The interface file is created for the transport models MT3D MT3DMS RT3D and PHT3D e Output Frequency The simulation results are saved whenever the time steps and stress periods are an even multiple of the output frequency and the results for the first and last stress periods and time steps are always saved Use 0 zero for the output frequency if only the result of the last stress period or the last time step should be saved e Predefined Head Values The predefined heads for no flow cells HNOFLO and dry cells HDRY are given in the Predefined Head Values group 2 6 1 19 MODFLOW Run Select this menu item to open the Run Modflow dialog box Fig 2 37 to run the flow simulation with MODFLOW or to check the model data The available settings of the dialog box are described below e The File Table has three columns 76 2 Modeling Environment Generate Prior to running a flow simulation PM uses the u
375. istribution and the form of the seepage surface The seepage rate is about 4 8 x 1075 m s m and the total seepage rate through the dam length 100 m is 4 8 x 107 3 m3 s 5 4 Geotechnical Problems 345 The analytical solution of the seepage rate after the Dupuit assumption is hi es hi th hy h gora Me _ x i 2 B 2 5 2 where B is the length of the dam L is the thickness of the dam K is the hydraulic conductivity h and h are the heads at the upstream and downstream sides of the dam respectively The modified form of the analytical solution is Darcy s Law with a mean transmissivity of K hl h2 2 For this example with h 10 m hg 2m L 10m B 100 m and K 1 x 107 m s the seepage rate Q is exactly equal to 4 8 x 1078 m3 s Note that in a 3D model such as MODFLOW this problem should be solved as a vertical cross section by using the wetting capability Section 2 6 1 12 with a discretization of 20 layers 1 row and 21 columns It is however instructive to try out the iteration by hand to better appreciate the wetting procedure The attentive reader will notice that using the 2D horizontal model for a vertical cross section is not quite correct The transmissivity of a cell is not changed with the water table location This corresponds to choosing the layer type 2 confined unconfined Transmissivity const in a multi layer MODFLOW model However the wetting capability cannot be used for layers of type 2 b
376. it If the con centration of a source or sink is not specified the default value for the concentration is zero Using the menu item Time Variant Specified Concentration the user may define constant concentration cells anywhere in the model grid and different concentration values may be specified for different stress periods A time varying specified concen tration cell is defined by setting the following data in the Data Editor e Flag A non zero value indicates that a cell is specified as a constant concen tration cell In a multiple stress period simulation a constant concentration cell once defined remains a constant concentration cell during the simulation but its concentration value can be specified to vary in different stress period To change the concentration value in a particular stress period simply set a non zero value to Flag and assign the desired concentration value to Specified Concentration In a multispecies simulation the Flag is applied to all species e Specified Concentration M L This value is the concentration in the cell from the beginning of a stress period If the constant concentration condition does not apply to a particular species assign a negative concentration value for that species The negative value is used by MT3DMS to skip assigning the constant concentration for the designated species 2 6 The Models Menu 103 2 6 2 9 MT3DMS SEAWAT Mass Loading Rate Instead of specifying a source co
377. ity unit 2 15b semiconfining unit by lumping the vertical hydraulic conductivity and thickness of the confining unit into a vertical leakance term between two adjacent layers These kinds of models are often called quasi three dimensional models because semi confining units are not explicitly included in a simulation In this case the user must manually calculate the VCONT values using equation 2 2 and enter them into the Data Editor 2 VCONT Mit Ae An 2 2 KaJu K o K L where Kz u K c and K 7 are the vertical hydraulic conductivity val ues of the upper layer semi confining unit and lower layer respectively a a b Geohydrologic Unit A Upper layer ce O en A et j___ AV ilik jj k semiconfining unit k J hit Geohydrologic AZ J Unit B v Lower layer AZ T e Jj ci ae Ta Med 7 bb Az 7 T ae Fig 2 15 Grid configuration used for the calculation of VCONT Storage Coefficient For transient flow simulations MODFLOW BCF package requires dimensionless storage terms to be specified for each model layer For a confined layer these storage terms are given by the confined storage coefficient specific storage L71 x layer thickness L If the Storage Coefficient setting 2 4 The Grid Menu 31 is set to Calculated PM uses user specified specific storage and the elevations of the top and bottom of each layer to calculate the confined storage coeffic
378. ix or press Ctrl R A Reset Matrix dialog box appears Enter 10 in the dialog box then click OK The elevation of the top of the first layer is set to 10 Move to the second layer by pressing PgDn Repeat steps 3 and 4 to set the top elevation of the second layer to 6 and the top elevation of the third layer to 3 Select File Leave Editor or click the leave editor button eel 234 4 Tutorials Z SAMPLEPMS EIT Processing Modflow Pro ITTE Fie Value Options Heip Layer elel Row ele Column elel fr j olala n ole Bla ap prm pmen Grid cursor e Position of the Grid cursor ndsflow boundary 8 m contaminated ti ar oe EHA canstant head boundary A 3 m constant head boundary h no flow boundary 614 9738 877 3273 1 666667 1 2 30 Time independent Boundary Condition BOUND FT i Fig 4 6 The Data Editor displaying the plan view of the model grid gt To specify the elevation of the bottom of model layers 1 Select Grid Bottom of Layers BOT 2 Repeat the same procedure as described above to set the bottom elevation of the first second and third layers to 6 3 and 0 respectively 3 Select File Leave Editor or click the leave editor button ee We are going to specify the temporal and spatial parameters of the model The spa tial parameters for sample problem include the initial hydraulic head horizontal
379. kage MT3D MT3DMS RT3D dialog box gt To assign the chemical reaction parameters 1 2 Select Models MT3DMS Chemical Reaction A Chemical Reaction Data MT3DMS dialog box appears In the Chemical Reaction Data MT3DMS dialog box select the first species which is only one species in this example and click Edit to start the Data Editor Select Value Reset Matrix or press Ctrl R A Reset Matrix dialog box appears Fig 4 22 Set the Type of Sorption to Lin ear equilibrium isotherm and type 0 000125 for the distribution coefficient then Click OK to assign the value to the first layer Turn on layer copy by clicking the layer copy button EJ Move to the second layer and the third layer by pressing PgDn twice The cell values of the first layer are copied to the second and third layers Select File Leave Editor or click the leave editor button ee The Chemical Reaction Data MT3DMS dialog box appears again Click Close to close this dialog box The last step before running the transport model is to specify the output times at which the calculated concentration should be saved gt To specify the output times 1 Select Models MT3DMS Output Control The Output Control MT3D Family dialog box appears Fig 4 23 The options in this dialog box are grouped under three tabs Output Terms Output Times and Misc Click the Output Times tab then click the header Output Time of the
380. kage dialog box Fig 2 32 The parameters are described below e MXITER is the maximum number of iterations in one time step in an attempt to solve the system of finite difference equations e JPRSIP is the printout interval for this package A positive integer is required The maximum head change positive or negative is saved in the run record file OUTPUT DAT for each iteration of a time step whenever the time step is an even multiple of IPRSIP This printout also occurs at the end of each stress period regardless of the value of IPRSIP e NPARM is the number of iteration parameters to be used Five parameters are generally sufficient e ACCLis the acceleration parameter It must be greater than zero and is generally equal to one e Head Change L is the head change criterion for convergence When the maxi mum absolute value of head change from all cells during an iteration is less than or equal to Head Change iteration stops MODFLOW Solvers SSOR The required parameters for SSOR package are specified in the Slice Successive Overrelaxation Package dialog box Fig 2 33 The parameters are described below e MXITER is the maximum number of iterations in one time step in an attempt to solve the system of finite difference equations 68 2 Modeling Environment Slice Successive Overrelaxation Pa Allowed Iteration Number MXITER 200 2 CO Printout From the Solver _ Cancel Interval IPRSOR 1 Help A
381. kage for MODFLOW the U S Geological Survey 404 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 References finite difference groundwater flow model U S Geological Survey Open file report 94 464 Prommer H 2002 PHT3D A multicomponent transport model for three dimensional reactive transport in saturated porous media Personal communication Prommer H and Vincent P 2010 PHT3D Version 2 A Reactive Multicomponent Trans port Model for Saturated Porous Media WWW PHT3D ORG 183 p Prudic DE 1988 Documentation of a computer program to simulate stream aquifer relations using a modular finite difference ground water flow model U S Geological Survey Open File Report 88 729 Carson City Nevada Rausch R 1998 Computer program for the calculation of 1 D and 2 D concentration distribution Personal communication Renka RJ 1984a Interpolation of the data on the surface of a sphere ACM Transac tions on Mathematical Software 10 417 436 Renka RJ 1984b Algorithm 624 Triangulation and interpolation at arbitrarily dis tributed points in the plane ACM Transactions on Mathematical Software 10 440 442 Rifai HS Bedient PB Borden RC and Haasbeek JF 1987 BIOPLUME II Computer model of two dimensional contaminant transport under the influence of oxygen limited biodegradation in ground water National Center
382. l The first step in running a flow simulation is to create a new model gt To create a new model il Select File New Model A New Model dialog box appears Select a folder for saving the model data such as C Models tutorial3 and type the file name TU TORIAL3 as the model name A model must always have the file extension PM5 All file names valid under MS Windows with up to 120 characters can be used It is a good idea to save every model in a separate folder where the model and its output data will be kept This will also allow PM to run several models simultaneously multitasking Click OK PM takes a few seconds to create the new model The name of the new model name is shown in the title bar 4 3 1 2 Step 2 Generate the Model Grid gt To generate the model grid 1 2 3 Select Grid Mesh Size A Model Grid and Coordinate System dialog box appears Enter the values as shown in Fig 4 49 to the dialog box The values for the Model Thickness and Model Top Elevation are not relevant at this stage since we are going to import the elevations from disk files We will generate a model grid of 3 layers The unconfined aquifer is the layer 1 in the model The silty layer and the confined aquifer are represented by layer 2 and layer 3 respectively Click OK to close the dialog box 286 4 Tutorials ligModel Grid and Coordinate System x Model Grid Coordinate System r Layer K Dimension Num
383. l grid where the columns and rows are regularly spaced see Section 2 8 1 for how to load an ASCII matrix file The simulation of the hydraulic conductivity distribution produced in this way is not constrained to match the measurement values In a constrained sim ulation existing measurements are used which reduce the space of possible realiza tions A constrained simulation of a single realization proceeds in five steps 184 2 Modeling Environment 1 The parameter value for each model cell is interpolated from the measurements using the Kriging method The correlation length is determined from the mea surements 2 An unconstrained generation is performed using the Field Generator with the same correlation length correlation scale 3 The unconstrained generated values at the measurement locations are used to interpolate values for each model cell by using the Kriging method again 4 The distribution from step 3 is subtracted from the distribution from step 2 yield ing kriging residuals 5 The Kriging residuals are added to the distribution from step 1 yielding a real ization which has the same correlation length and passes through the measured values at the measurement points 2 7 4 2D Visualization The 2D Visualization tool is based on the Data Editor and displays the contours of a selected model result type on the model grid Fig 2 91 The simulation result type is selected by using the Result Selection dialog box Fig 2 92
384. l procedure in MT3D MXSTRN is the maximum number of transport steps TTSMULT is the multiplier for the length of successive transport steps within a flow time step if the Generalized Conjugate Gradient GCG solver is used and the solution option for the advection term is the upstream finite difference method TRANS is used by MODFLOW 2000 only A stress period is simulated in tran sient state is TRANS 1 otherwise a steady state solution will be calculated for the stress period Reserved Reserved for future use Enter 0 in the file 6 2 6 Head Drawdown Concentration Observation Files The Head or Drawdown or Concentration Observation dialog box uses the fol lowing four formats for saving and loading data The formats are described in the following sections e Observation Boreholes obs_borehole contains names and coordinates of ob servation boreholes e Layer Proportions layer_prop contains the proportion values of each layer Using the Head Observation dialog box a Layer Proportions file can be loaded to an observation borehole at a time e Observations observation contains observation times observed values and weights Using the Head Observation dialog box an Observations file can be loaded to an observation borehole at a time e Complete Information complete_obs contains all information mentioned above for all boreholes 6 2 File Formats 381 6 2 6 1 Observation Boreholes File
385. l the window covers the pumping well 6 Release the left mouse button An Add New Particles dialog box appears Assign the numbers of particles to the edit fields in the dialog box as shown in Fig 4 13 Click the Properties tab and click the colored button to select an appropriate color for the new particles When finished click OK 246 4 Tutorials 7 To set particles around the pumping well in the second and third layer press PgDn to move down a layer and repeat steps 4 through 6 Use other colors for the new particles in the second and third layers 8 Click Ito start the backward particle tracking PMPATH calculates and shows the projections of the pathlines as well as the capture zone of the pumping well Fig 4 14 To see the projection of the path lines on the cross section windows in greater details open an Environment Options dialog box by selecting Options Environment and setting a larger exaggeration value for the vertical scale in the Cross Sections tab Fig 4 15 shows the same path lines by setting the vertical exaggeration value to 10 Note that some path lines end up at the groundwater surface where recharge occurs This is one of the major differences between a three dimensional and a two dimensional model In two dimensional simulation models such as ASM for Win dows 20 FINEM 70 or MOC 73 a vertical velocity term does not exist or always equals to zero This leads to the result that path lines can nev
386. lator see Sec tion 2 7 2 if the model grid is irregularly spaced Li x Parameter Column Width Initial Hydraulic Heads x fia 7 Fig 2 95 The Browse Matrix dialog box xi File c eagle dav_xyz_data eS Start Position Options Column Ji Row 1 Replace i 1 C Add Cancel Mari C Subtract aximum Numbers y Layer 3 Row 18 Column 18 C Multiply Help C Divide Fig 2 96 The Load Matrix dialog box 2 8 The Value Menu 191 Starting position finite difference grid Fig 2 97 The starting position of a loaded ASCII matrix f Reset Matrix xj Horizontal Hydr Conductivity L T 0004 Parameter Number i Apply to the entire model OK Cancel Hel Apply to the current layer Cercel Hep Fig 2 98 The Reset Matrix dialog box 2 8 2 Reset Matrix Select this menu to open the Reset Matrix dialog box Fig 2 98 which is used to assign uniform values to the current model layer or to the entire model The options Apply to the entire model and Apply to the current layer are available when edit ing Cell Status arrays IBOUND or ICBUND aquifer parameters or concentration values 1 Apply to the entire model the specified value s in the Reset Matrix dialog box will be applied to all cells of the entire model 2 Apply to the current layer is the default option which assigns the specified value s to all cells of the c
387. lculated only once for each cell at the beginning of the simulation by equation 2 43 Crig Ka Cri 2 42 Reig 1 Ka 2 43 ij where nx i is the porosity of the porous medium in the cell k i j Ka L M is the distribution coefficient that depends on the solute species nature of the porous medium and other conditions of the system and pp ML is the bulk density of the porous medium The bulk density is the ratio of the mass of dried soil to total volume of the soil Freundlich isotherm nonlinear equilibrium is expressed by equation 2 44 The retardation factor at the beginning of each transport step is calculated by equation 2 45 Crag Kf Chi 2 44 Rigg 1t Goa Ofig Ky 2 45 BJ where Ck i j is the solute concentration in the cell in the cell k i j at the beginning of each transport step a is the Freundlich exponent and K L3 M71 is the Freundlich constant Langmuir isotherm nonlinear equilibrium is defined by equation 2 46 The retardation factor at the beginning of each transport step is calculated by equation 2 47 a Ky S Chi Okij et 2 46 kij 1 Kr COkij K S Pei t L 2 47 Nkig L Kr Cki where Kz L3 MT is the Langmuir constant and S MMT is the maxi mum amount of the solute that can be adsorbed by the soil matrix First order kinetic sorption nonequilibrium When the local equilibrium assumption is not valid MT3DMS assumes tha
388. ld The model parameters used in the simulation are given below Cell width along columns I direction 1m Cell width along rows J direction 10m Layer thickness K direction lm Longitudinal dispersivity 10m Groundwater seepage velocity 0 24 m day Effective Porosity 0 25 Simulation time length 2000 days Three simulations using different parameters for the Monod kinetics as given below need to be carried out Note that these reaction parameters are intended for demonstration purposes only and have no particular physical relevance Casel Mt Umas 2 mg liter day Ks 1000 mg liter Case 2 Mi Umar 2 X 1078 mg liter day Ks 1 mg liter Case 3 Mi Umar 2 X 1078 mg liter day Ks 0 001 mg liter Modeling Approach and Simulation Results The model grid consists of 1 layer 1 row and 101 columns In the flow model the first and last columns are constant head boundaries To establish the required uniform hydraulic gradient the initial hydraulic head values of 70 m and 10 m are assigned to the first and last columns respectively In the transport model the first column is a constant concentration boundary with a concentration value of 1 0 mg liter The last column is sufficiently far away from the source to approximate a semi infinite one dimensional flow domain Fig 5 52 shows the simulation results For Case 1 the Monod kinetics should approach a first order reaction since Ks is three orders greater than the maximum concentration
389. le Use the Label Format button to specify an appropriate format 4 Click OK to close the Environment Options dialog box Contours should now appear and if everything has gone well they will look similar to Fig 4 46 Note The display of the model grid is deactivated by using the Appearance tab of the Environment Options dialog box 280 4 Tutorials oss oss os si opg 00 91 aoa ager osa osai o er orci ooz Well 1 Well 2 Well 3 oszt T og z n OS ti oake T 00 Well 4 Sheng BE m m FE o sim osei m OS 006 0 4 Well 7 Well B Well 9 a a a Fig 4 46 Steady state head distribution 5 To save or print the graphics select File Save Plot As or File Print Plot 6 You may save the calculated head values in ASCII Matrix files by selecting Value Matrix to open a Browse Matrix dialog box and then clicking the Save button 7 Select File Leave Editor or click the leave editor button ee 4 2 3 Transient Flow Simulation It is now time to perform the transient simulations with the wet season recharge 120 days and dry season pumping 240 days The hydraulic heads resulting from the steady state simulation are used as the starting heads for the transient analysis gt To set the steady state heads as the starting values for the simulation 1 Select Parameters Initial amp Prescribed Hydraulic Heads to start the Data Edi tor 2 Select Value Import Results to open an Import Resul
390. leave editor button ee Repeat the above process to set the elevation of the base of the aquifer to 0 m Al though the default value in this model is zero we still have to enter the editor to let the model know that the parameter has been specified gt To specify the horizontal hydraulic conductivity 1 Select Parameters Horizontal Hydraulic Conductivity 2 Since the horizontal hydraulic conductivity is uniform throughout the model it is possible to set a single value to the entire grid by selecting Value Reset Matrix 3 Enter 160 in the Reset Matrix dialog box and click OK to exit 4 Select File Leave Editor or click the leave editor button w MODFLOW requires initial hydraulic head conditions to enable it to perform the flow simulation The hydraulic head values of the constant head cells are important as these do not change throughout the simulation The values in the other cells serve as initial guesses for the iterative solvers In a transient simulation the hydraulic heads at the start of the simulation are the basis for determining the resulting head Well 1 Well 2 Well 3 i E E Well 4 Well 5 Well amp m E m Well 7 Well B Well 9 a a Fig 4 45 Model Boundaries 278 4 Tutorials distribution after the aquifer is subject to some time dependent stresses It is usual to perform a steady state flow simulation first and use the resulting head distribution as the basis for the transient simulations which is wha
391. lic conductivity value at the location of the well to 1 in all layers 4 1 2 3 Step 3 Perform the Flow Simulation Before starting the computation a solver has to be chosen This example uses the de fault solver PCG2 with its default settings For details about the solvers see Section 2 6 1 13 gt To perform the flow simulation 1 Select Models MODFLOW Run The Run Modflow dialog box appears Fig 4 7 2 Click OK to start the flow simulation Prior to running MODFLOW PM will use the user specified data to generate input files for MODFLOW and optionally MODPATH as listed in the table of the Run Modflow dialog box An input file will be generated only if its generate flag is set to M Normally the flags do not need to be changed since PM will take care of the settings automatically If necessary click on the check box to toggle the generate flag between M and D 238 4 Tutorials x Modflow Version MODFLOW96 INTERFACE TO MT3D96 AND LATER Generate Description Destination File Basic Package c models bas dat Vv Block Centered Flow BCF1 2 c models bef dat Vv Output Control c models oc dat Vv Well c models wel dat Vv Recharge c models rch dat M Solver PCG2 c models pcg2 dat Vv Modpath Vers 1 x c models main dat MW Modpath Vers 3 x _ e models main30 dat_ gt Options I Check model data J Regenerate all input files IV Don t generate MODPATH
392. linearly interpolated or extrapolated to each cell along the trace of the polyline and the value C is obtained by CO K L 2 9 where L is the length of the general head boundary within a cell Flow through a GHB cell Q L T is calculated by Qo Ca hy h 2 10 where h is the hydraulic head in the aquifer By default MODFLOW saves the calculated flow rates in the BUDGET DAT Since the GHB package does not limit the value of flow in either direction a GHB cell is equivalent to a constant head cell if a very large Cy is used Therefore care must be used in utilizing the GHB package to insure that unrealistic flows into or out of the groundwater system do not develop during the course of simulation Parameter Number Since Cy is usually unknown it must be estimated Parameter Number is used to group cells where the C values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps The value of Parameter Number is assigned to all model cells downstream from a vertex until the next vertex redefines the parameter number GHB Elevation L This the elevation of the general head boundary from which the equivalent reference head is calculated This value is required by SEAWAT to accurately calculate the flow of variable density groundwater to the general head boundary Density of GHB Fluid M L This value
393. ling uncertainty due to unknown spatial variability of the model parameters is addressed directly by assuming that the parameters are random vari ables Hydraulic conductivity or transmissivity is commonly assumed to be lognor mally distributed We denote the hydraulic conductivity by X and define a variable Y log X When Y is normally distributed with a mean value jz and standard deviation g then X has a log normal distribution The Field Generator runs independently from PM To start the program select Tools Field Generator from PM or select Field Generator from the Start menu of Windows The program displays one dialog box Fig 2 90 and is fairly easy to use It uses the correlation scales in both I row and J column directions and the mean value u and standard deviation o of log transformed measurement values to generate a quantitative description a realization of the hydraulic conductivity or transmissivity field The size of the field number of cells and the number of desired realizations are specified in the dialog box Realizations are saved in the ASCII Matrix format see Section 6 2 1 using the file names filename nnn where filename is the output file name specified in the dialog and nnn is the realization number Note that filename must not be the same as the name of the model The generated field is log normally to base 10 distributed Using the Data Ed itor the user can load the generated field into an area of the mode
394. listed below Activate SVD Assist Check this box to enable SVD assisted parameter estimation With SVD Assist activated PM will create two PEST control files namely pre svda pst and base svda pst prior to running PEST The former is used for the purpose of derivatives calculation by a pre SVD assist PEST run The latter is used by the utility pro gram SVDAPREP which is a part of PEST to create a third PEST control file used for the estimation of super parameters PM will also create a batch file called pest bat which encapsulates the individual steps of an SVD assisted PEST run as follows 1 Commence a pre SVD assist PEST Run Copy presvda pst to svda pst and then run PEST with svda pst This step will create a file called svda jco storing the Jacobian matrix 2 Execute SVDAPREP Copy basesvda pst to svda pst and then run SVDAPREP EXE to generate the third PEST control file pestctl pst based on svda pst and a new batch file svdabatch bat The required input data to SVDAPREP EXE are entered in the present interface and are stored in the svdaprep dat file prior to running PEST The svdabatch bat file encapsulates necessary steps for running the model 3 Run PEST PEST is executed to use the pestctl pst file generated in the previous step This PEST run will create two files namely pestctl par and svda bpa The former stores the estimated values of super parameters the latter contains the estimated values of the base parameters 4 Rename
395. lity or overfitting of model outputs to measurements occurs resulting in unrealistic parameter values Alternatively set MAXSING very high for example equal to the number of estimable param eters and let EIGTHRESH determine the number of singular values employed in the parameter estimation process Eigenvalue ratio threshold for truncation EIGTHRESH EIGTHRESH is the ratio of lowest to highest eigenvalue at which truncation is implemented this then determines the number of singular values that are used in the inversion process for only those singular values are used whose ratio to the maximum singular value is above this threshold Limited experience to date indicates that 10 or 1077 is a good setting for EIGTHRESH set it higher e g 1075 if numerical instability or over fitting occurs SVD Assist SVD Assist is a hybrid method which combines the strengths of the Tikhonov and SVD regularization methods while accomplishing enormous gains in efficiency is described in this section Although truncated SVD can be used with Tikhonov regu larization this process is not expected to be as efficient as the SVD assist methodol ogy It is fairly easy to setup a SVD Assisted run with the help of PM The user is encouraged to consult Sec 8 5 of the PEST manual 37 for detailed explanation of 2 6 The Models Menu 165 the mechanism of SVD assisted parameter estimation The available settings of the SVD Assist group of Fig 2 82 are
396. ll is shown at the bottom of the status bar The default value of the IBOUND array is 1 The grid cursor can be moved by using the arrow keys by clicking the mouse on the desired position or by using buttons in the tool bar To jump to another layer click the Layer edit box in the tool bar type the new layer number and then press enter Note A DXF map is loaded by using the Maps Options dialog box See Section 2 9 1 for details Layer Property x Flow Package Block Centered Flow BCF Horizontal Vertical Ap 1 1 VK 1 Unconfined Calculated Caleu 3 Confined Unconfined j1 Calculated Calet Transmissivity varies 3 3 Confined Unconfined zh i Calculated Caleu Transmissivity varies Fig 4 5 The Layer Options dialog box and the layer type drop down list fon 10 4 1 Your First Groundwater Model with PM 233 Move the grid cursor to the cell 1 1 1 and press the Enter key or the right mouse button to display a Cell Value dialog box Type 1 in the dialog box then click OK The upper left cell of the model has been specified to be a constant head cell Now turn on duplication by clicking the duplication button Pl Duplication is on if the duplication button is depressed The current cell value will be duplicated to all cells passed by the grid cursor if it is moved while duplication is on Duplication is turned off by clicking the duplication button again Move
397. lls having no particles exceeds FZERO the program will automatically regen erate an initial particle distribution before continuing the simulation typically 0 01 lt FZERO lt 0 05 Initial number of particles per cell NPTPND Valid options for default geom etry of particle placement include 1 2 3 or 4 for one dimensional transport simulation 1 4 9 or 16 for two dimensional transport simulation and 1 8 or 27 for three dimensional transport simulation The user can also customize initial placement of particles by specifying a negative number to NPTPND pressing the Tab key and entering local particle coordinates into table in the lower part of the dialog box shown in Fig 2 64 where PNEWL PNEWR and PNEWC are rela tive positions for the initial placement of particles in the layer row and column direction respectively The local coordinate system range is from 0 5 to 0 5 and represents the relative distance within the cell about the node location at the center of the cell so that the node is located at 0 0 in each direction 2 6 5 4 MOC3D Dispersion amp Chemical Reaction The types of reactions incorporated into MOC3D are restricted to those that can be represented by a first order rate reaction such as radioactive decay or by a retarda tion factor such as instantaneous reversible sorption desorption reactions governed by a linear isotherm and constant distribution coefficient Ka Use the Dispersion Chemical Reac
398. lock 93 94 is used to calculate the groundwater paths and travel times Through the interactive graphical modeling environment of PMPATH the user can place particles and perform particle tracking with just a few mouse clicks While most available particle tracking models need post processors for visualization of computed paths and times data PMPATH cal culates and animates the pathlines simultaneously Fig 3 1 Moreover PMPATH provides various on screen graphical options including head contours drawdown contours and velocity vectors for any selected model layer and time step Both forward and backward particle tracking are allowed for steady state and transient flow simulations For transient flow simulations particles can start from the beginning of any time step During the simulation the particle tracking algorithm will check the current time of every particle If a particle reaches the end forward tracking or the beginning backward tracking of a time step PMPATH forces the particle to wait until the flow field of the next time step has been read The particle tracking simulation proceeds until all particles have left the model via sinks or until the user specified time limit is reached The time length of a single particle tracking step and the maximum number of tracking steps can be specified Each particle can have its own color and retardation factor With these features PMPATH can be used to simulate advective transport in grou
399. loped by Shepard 108 Akima 1 2 and Renka 100 101 The programs interpolate or extrapolate the measurement data to each model cell The model grid can be irregularly spaced Interpolation results are saved in the ASCII Matrix format see Section 6 2 1 which can be imported by the Data Editor into the model grid Depending on the interpolation method and the interpolation parameters the results may be different Using the Data Editor the user may create contour maps of the interpolation results and visually choose a best one 178 2 Modeling Environment Theory is not emphasized in this description since it is introduced in extensive literature For example Watson 113 presents a guide to the analysis and display of spatial data including several interpolation methods Franke 45 provides a brief re view and classification of 32 algorithms Hoschek and Lasser 64 give a comprehen sive discussion of theories in geometrical data processing and extensive references in the area of data interpolation and computer graphics techniques Akin and Siemes 3 and Davis 30 provide fundamental mathematical background on the statistics and data analysis in geology 2 7 2 2 Using the Field Interpolator The Field Interpolator runs independently from PM To start the program select Tools Field Interpolator from PM or select Field Interpolator from the Start menu of Windows The settings of the Field Interpolator Fig 2 85 are grouped under
400. ls which lie in the Set Particle window These numbers NK NI and NJ can range from 0 to 999 In the case shown in Fig 3 5 8 2 x 2 x 2 particles will be placed within each cell 3 3 x 1 particles will be placed on each cell face and 15 particles will be placed around each cell at a distance of 20 The particles will get the color and the retardation factor given in the Properties tab of this dialog box gt To place a single particle 1 Click the Set particle button E 2 Change the local vertical coordinate and the particle color for the definition of the local vertical coordinate see equation 3 7 3 Place a particle by right clicking the desired position This particle will have the retardation factor see below specified in the Properties tab of the Add New Particles dialog box Once particles are placed their color and retardation factor cannot be changed any more The retardation factor R is defined by Po Ne R 1 Ka 3 8 where p is the bulk density of the porous medium ne is the effective porosity and K4 is the distribution coefficient A detailed description of these parameters can be found in the literature e g Freeze and Cherry 46 The retardation factor was first applied to groundwater problems by Higgins 58 and Baetsle 11 Baetsle indicated that it may be used to determine the retardation of the center of mass of a contaminant moving from a point source while undergoing adsorption PMPATH
401. ls on this boundary are modeled as drain cells with a high drain hydraulic conductance L T value The elevation of the drain is set the same as the bottom elevation of each cell for example the 2 0 m for the cell 1 16 21 and 2 5 m for the cell 1 15 21 The drain cells are activated only if water table is higher than the level of the drain The selected model grid and the boundary conditions are shown in Fig 5 39 Except the four fixed head cells at the right hand side of the dam the initial hydraulic head for all cells are 10 m The first step in solving this problem is to carry out a steady state flow simulation with these data Fig 5 40 shows the calculated hydraulic heads By comparing the calculated heads with the elevation of the cell bottom we can easily find that the hydraulic heads of some of the cells at the upper right corner of the model are lower than the cell bottom This means that these cells went dry In the second step these dry cells will be defined as inactive cells by setting IBOUND 0 and a steady state flow simulation will be carried out again Now it is possible that some of the calculated heads are higher than the top elevation of the highest active cell In this case these cells will be defined as active and a steady state flow simulation will be performed again This iterative solution will be repeated until the water table remains unchanged between two iteration steps Fig 5 41 shows the calculated head d
402. lu tion for transport simulations e PMWIN 4 x tab This tab is used to convert groundwater models created by PMWIN 4 x to PM To convert click the open file button and select a PMWIN 4 x model from an Open dialog box then click the Convert button to start the conversion Groundwater models created by PMWIN 5 x or later are compatible with PM and do not need to be converted e MODFLOW 88 96 tab This tab is used to import models stored in MODFLOW 88 or MODFLOW 96 formats to PM To import click the open file button and select a MODFLOW Name File from an Open dialog box then click the Convert button to start the conversion Refer to Section 6 3 1 for the definition of the name file A MODFLOW 88 96 name file usually has lines with the file type i e Ftype BAS or BCF e MODFLOW 2000 2005 tab This tab is used to import models stored in MODFLOW 2000 2005 formats to PM To import click the open file button and select a MODFLOW Name File from an Open dialog box then click the Convert button to start the conversion Refer to Section 6 3 1 for the definition of the name file A MODFLOW 2000 2005 name file usually has lines with the file type i e Ftype BASO6 BCF6 or LPF e Telescoping Flow Model Fig 2 12 This tab creates local scale sub models from a regional scale model To create a sub model select an existing PM model and specify the sub region Then click the Convert button Prior to converting the flow sim
403. ludes three versions of RT3D rt3d1v exe version 1 rt3d2v exe version 2 and rt3d25v exe version 2 5 They can be found in the folder pmhome rt3d where pmhome is the installation directory of PM The associated program is used when selecting the menu item RT3D Run PHT3D PHT3D 97 couples MT3DMS 123 for the simulation of three dimensional advective dispersive multi component transport and the geo chemical model PHREEQC 2 91 for the quantification of reactive pro cesses The associated program is used when selecting the menu item PHT3D Run 26 2 Modeling Environment SEAWAT SEAWAT is designed to simulate three dimensional variable density saturated groundwater flow and transport The associated program is used when selecting the menu item MT3DMS SEAWAT Run e Active Check or clear the active flag to activate or deactivate a model module Please note that the first three modules MODFLOW PMPATH and TEXT VIEWER are required and cannot be deactivated When a module is deactivated its associated menu item under the Models menu is removed This feature is use ful when several modules are not used and the Models menu should be kept as short as possible Deactivating or activating of a module does not affect the model data in any way e Paths to Simulation Program File If the user intends to use an executable pro gram located in another position click the corresponding button and select the desired program fro
404. lue and the proportion value of the ith layer respectively The propor tion values generally are assigned using the thickness screened within each layer and the local hydraulic properties A more realistic representation of this problem would be produced by calculating proportions that are based on the flow system and hydraulic properties 63 For a single layer borehole simply specify a non zero proportion value to the layer where the borehole is screened and assign a proportion value of zero to all other layers If the proportion values of all layers are zero the observation borehole is considered as inactive and thus no graphical display can be generated for this borehole The Head Observation s table When specifying head observations for MOD FLOW 2000 the third column of this table is Statistic otherwise it is Weight Inserting or deleting an observation row is identical to the table for Observation Borehole described above Time The observation time to which the measurement pertains is mea sured from the beginning of the model simulation You may specify the observation times in any order By clicking on the column header or the OK button the observation times and the associated values will be sorted in ascending order When calibrating a steady state flow model with one stress period the observation time should be the length of the period Of particular note is that when calibrating a transient flow model with PE
405. lues upper and lower bounds for each parameter gt To define the region of horizontal hydraulic conductivity Select Parameters Horizontal Hydraulic Conductivity Click the J button if the display mode is not Grid View Move to the third layer Select Value Reset Matrix or press Ctrl R A Reset Matrix dialog box appears pO Be Table 4 5 Measured hydraulic head values for parameter estimation Borehole X Coordinate Y Coordinate Layer Observation Time Hydraulic Head hl 130 200 3 9 46728E 07 8 85 h2 200 400 3 9 46728E 07 8 74 h3 480 250 3 9 46728E 07 8 18 h4 460 450 3 9 46728E 07 8 26 4 1 Your First Groundwater Model with PM 265 Head Observation x Observations Options r Observation Borehole m Observation Data Proportion Layer po Head Observation s _ Time JHOBS Weight 3 46720E 07 _ 8 85 Load OK Cancel Help Fig 4 36 The Head Observation dialog box 5 Enter 1 to the Parameter Number edit box then click OK The horizontal hy draulic conductivity of the third layer is set to the parameter 1 6 Select File Leave Editor or click the leave editor button w gt To specify the coordinates of the observation boreholes and measured values 1 Select Head Observations from the MODFLOW MODFLOW 2000 Parameter Estimation or PEST Parameter Estimation menu The Head Observation dialog box appears Fig 4 36 2 Enter the
406. lver of MODFLOW see page 65 within the inner loop all coefficients in the transport matrix A and the right hand side vector b remain unchanged during inner iterations The inner loop continues until ITER1 iterations are executed or the convergence criterion is met If some of the coef ficients in A are dependent on the concentration being solved as in the case of nonlinear sorption they must be updated in outer iterations So MXITER should be set to an integer greater than one only when a nonlinear sorption isotherm is included in the simulation For ITER1 a value between 30 and 50 should be adequate for most problems Generalized Conjugate Gradient GCG Preconditioning Method Jacobi Max Number of Outer Iterations MxITER Max Number of Inner Iterations ITER 1 Relaxation Factor Concentration Closure Criterion Concentration Change Printout Interval I Include full dispersion tensor memory intensive Cancel Help Fig 2 52 The Generalized Conjugate Gradient GCG dialog box 104 2 Modeling Environment e Relaxation Factor is only used for the SSOR option a value of 1 0 is generally adequate e Concentration Closure Criterion is the convergence criterion a value between 1076 and 1074 is generally adequate Before solving the system of transport equations it is normalized by dividing the concentration terms by the maximum concentration of all cells When the change of the normalized concentration
407. ly In the Layer Property dialog box the Interbed storage flag for the second layer is checked The pit is modeled as fixed head boundary with the hydraulic head h 40 m The compaction and thus the land surface subsidence of the confining bed is modeled using the Interbed Storage package A transient flow simulation with one stress period and 30 time steps has been carried out The length of the stress period is one year 3 1536 x 10 seconds The required withdrawal rate changes with time and can be calculated by using the water budget calculator by assigning the subregion number to the pit For the first time step the required withdrawal rate is 0 0134 m s 48 2 m3 h For the last time step it is reduced to 0 0066m s 23 76m h The distribution of the subsidence caused by this withdrawal rate can be obtained by using the Results Extractor tool Fig 5 46 shows the contours of the land surface subsidence for the last time step The maximum subsidence is about 0 11 m 352 5 Examples and Applications For detailed description of the Interbed Storage package and the calculation of compaction and subsidence refer to Leake and Prudic 78 which includes two test cases We have rebuilt the test cases and saved them in pmdir examples geotechniques geo5a and pmdir examples geotechniques geoSb 45m ae oa 25m Cross Sec
408. m 175 head time curves 176 Output Options 171 parameter estimation 149 Parameter Groups 155 Parameters 152 Prior Information 157 Regularization 159 run 172 SVD 162 SVD Assist 162 PHIRATSUF 168 PHIREDSTP 170 PHIREDSWH 170 PHT3D 4 25 109 395 Define Reaction Module 397 Examples 367 PMPATH 2 25 176 203 polygon assign value 18 delete 18 modify 19 polygon file format 385 Polygon Input Method 17 polygons 191 polyline assign value 20 delete 19 modify 20 Polyline Input Method 19 polylines 10 preconditioning method 103 preconsolidation head 75 Preferences 23 Prescribed Fluid Density SEAWAT 102 Print Plot 26 Prior Information MODFLOW 2000 138 radioactive decay 121 131 raster graphic 195 import 195 reaction 412 Index among species 86 reaction parameters RT3D 115 recharge 271 Recharge package 47 refine 12 refinement 22 RELPARMAX 169 RELPARSTP 171 Reservoir package 48 Results extractor 184 retardation 122 retardation factor 96 121 212 river 284 River package 51 RLAMBDAI 167 RLAMFAC 168 RMAR 140 RMAR M 140 rows delete 10 insert 10 RT3D 3 25 113 395 advection 114 concentration observation 116 concentration scatter diagram 118 concentration time curves 118 dispersion 114 output control 117 run 117 Simulation Settings 113 sink source concentration 116 run MOC3D 125 MODFLOW 75 MODFLOW 2000 144 MT3D 133 MT3DMS SEAWAT 105 PE
409. m a dialog box Note The following programs must be located in the same directory as the PEST PEST ASP program mf2kasp exe mf2pest exe modbore exe par2sen exe and pestchek exe 2 3 5 Save Plot As Use Save Plot As to save the contents of the worksheet in graphics files Three graph ics formats are available Drawing Interchange File DXF Hewlett Packard Graph ics Language HP GL and Windows Bitmap BMP DXF is a fairly standard format developed by Autodesk for exchanging data between CAD systems HP GL is a two letter mnemonic graphics language developed by Hewlett Packard Most graphics or word processing software and graphics devices can process these graphics formats To save a plot use the Format drop down box to select a graphic format Then en ter a filename into the File edit field or click and select a file from a dialog box When finished click OK Note that in the Map View display mode only the BMP format may be used 2 3 6 Print Plot This menu item is only activated in the Data Editor After selecting this item a Print Plot dialog box is displayed with a preview window The options are described below e Use full page The plot is scaled to fit the paper the original aspect ratio will not be changed e Center on page The plot is placed on the center of the page e Image Size millimeters Specify the width and height of the printed image in millimeters e Margins millimeters Specify the left and top
410. m weighting is preferred as the central in space weighting scheme can lead to excessive artificial oscillation Particle Tracking Algorithm is used in combination with the method of charac teristics Using the first order Euler algorithm numerical errors tend to be large unless small transport steps are used The allowed transport step t of a particle is determined by MT3D using equation 2 35 Ax Ay Az ee oem 2 35 At lt ye R MIN Ur Vy v where Ax Ay and Az are the cell widths along the row column and layer directions respectively c is the Courant number The particle velocities vz Vy and v at the position x y z are obtained by linear interpolation from the specific discharges at the cell faces The minimum At of all particles is used in a transport step The basic idea of the fourth order Runge Kutta method is to calculate the particle velocity four times for each tracking step one at the initial point 92 2 Modeling Environment twice at two trial midpoints and once at a trial end point A weighted velocity based on values evaluated at these four points is used to move the particle to a new position The fourth order Runge Kutta method permits the use of larger tracking steps However its computational effort is considerably larger than the first order Euler method For this reason a mixed option combining both methods is introduced in MT3DMS The mixed option is implemented by automatic selecti
411. margins of the image in millime ters e Printer A Printer dialog box allows the user to select an installed printer and specify the print quality the paper size source and orientation and other printing parameters 2 4 The Grid Menu 27 e Print Print the contents shown on the preview window e Close Close the Print Plot dialog box without printing 2 3 7 Animation This menu item is only activated when the 2D Visualization Tools 2D Visualiza tion tool is selected Before creating an animation sequence the user should use the Environment Option and Maps Option dialog boxes refer to Section 2 9 for details to make sure that the model grid maps and contours are set properly gt To create an animation sequence 1 Select File Animation to display an Animation dialog box 2 In the Animation dialog box click the open file button to display a Save File dialog box Select an existing frame file or specify a new base file name for the frame files in the dialog box then click Open Like a movie an animation sequence is based on a series of of frames Each frame is saved by using the filename basename nnn where basename is the base file name and nnn is the serial number of the frame files Note To protect the model data the frame files must not be saved in the same folder as the model data 3 Check or clear Create New Frames Check Create New Frames if a new animation sequence should be created Clear the Create New Fra
412. me box if a saved sequence should be played back 4 Set Delay s Delay is the number of seconds between frames 5 In the Animation dialog box click OK to start the animation PM will create a frame image for each time point at which the simulation results have been saved When all frames are created PM will repeat the animation indefinitely until the Esc key is pressed 2 4 The Grid Menu 2 4 1 Mesh Size Allows the user to generate or modify a model grid using the Grid Editor See Section 2 1 for how to use the Grid Editor 2 4 2 Layer Property The layer properties are defined in the Layer Property dialog box Fig 2 14 Many settings of this dialog box depend on the selection between the Block Centered Flow BCF and Layer Property Flow LPF packages Refer to Section 2 3 4 for details about the BCF and LPF package When the LPF Package is used the columns 28 2 Modeling Environment Transmissivity Leakance and Storage Coefficient are dimmed to indicate that their settings are ignored because the LPF package only uses HK VK Ss and Sy When the BCF package is used the column Vertical Anisotropy is dimmed since it is not supported by the BCF package The settings of this dialog box are described below e Type The numerical formulations which are used by the BCF or LPF package to describe groundwater flow depend on the type of each model layer The available layer types are Za Layer Prop Flow Package Type 0
413. mechanism will exclude dissolved chemicals which results in an increase in concen tration at the location of the sink Items of this menu are dimmed if the corresponding package in the Models MODFLOW Flow Packages menu are not used checked The specified concentra tion will be used by MOC3D if a corresponding menu item is checked If a checked 124 2 Modeling Environment E output Control MOC3D x Concentration Velocity Particle locations Disp Coeff Mise J Save data in a separate binary file These data will be printed or saved at the end of every stress period id c These data will be printed or saved every Nth particle moves N 0 Cancel Help Fig 2 67 The Output Control MOC3D dialog box item is no longer necessary for a transport simulation simply select the item again and deactivate it 2 6 5 8 MOC3D Output Control The main output file of MOC3D is the listing file MOC3D LST MOC3D includes output options to create separate ASCII or binary files for concentration velocity and the location of particles Optionally the dispersion equation coefficients on cell faces can be written to the listing file The dispersion equation coefficient is a combination of dispersion coefficient D porosity ne thickness b and an appropriate grid dimen sion factor For example the dispersion equation coefficient for the interface between cells k j i and k j 1 i in the column directi
414. meter type e g HK or Ss and may be any integer ranging between 1 and 500 Set the parameter number to zero if the specified parameter value should not be estimated Please note the following rules when assigning parameter values and parameter numbers e During a parameter estimation process the parameter values for an estimation iteration are calculated as the product of the parameter s initial cell values and a parameter multiplier PARVAL The latter is to be estimated by MODFLOW 2000 It is to note that if the parameter s initial cell values are heterogeneously distributed then the result is also a distribution scaled by the estimated parameter multiplier In contrast if the value of 1 is used as the parameter s initial cell value then the estimated parameter multiplier repre sents the physical parameter value e To estimate the conductance values of head dependent cells e g drain gen eral head boundary river or stream cells or pumping rates of wells a non zero conductance value or pumping rate must be assigned to those cells Con ductance values or pumping rate will not be adjusted if the user specified values are equal to zero e na transient flow model when a parameter is varying with time parameter numbers should not be repeated in different stress periods That is different parameter numbers should be used for different stress periods 3 Select MODFLOW 2000 Parameter Estimation Parameter List to open a List
415. mples and Applications 5 3 5 Parameter Estimation with MODFLOW 2000 Test Case 1 Folder pmdir examples calibration calibration5 Overview of the Problem This example model is adapted from Hill and others 63 The physical system for this example is shown in Fig 5 30 The synthetic system consists of two confined aquifers separated by a confining unit Each aquifer is 50 m thick and the confining unit is 10 m thick The river is hydraulically connected to aquifer 1 Groundwater flow from the hillside adjoining the system is connected to aquifers 1 and 2 at the boundary farthest from the river The parameters that define aquifer properties are shown in Fig 5 30 and listed in Table 5 5 The observations of head and river flow gain used in the parameter estimation were generated by running the model with the given parameter values and the parameter multiplier PARVAL 1 for all parameters the actual parameter values used in the simulation are calculated as the product of the parameter values and the parameter multiplier PARVAL Different starting values are used for PARVAL and the estimated PARVAL values are expected to be close to 1 The hydraulic conductivity of the second aquifer is known to increase with dis tance from the river The variation is defined by a step function with the value 1 0 x HK_3 in columns 1 and 2 2 0 x HK_3 in columns 3 and 4 and so on to the value 9 0 x HK_3 in columns 17 and 18 aquifers 1and2 7 d UO m
416. mples mf2k ex1 oc dat Vv General Head Boundary c program files eit pmwin examples mf2k ex1 ghb6 c Vv River c program files eit pmwin examples mf2k ex1 riv6 da Vv Well c program files eit pmwin examples mf2k ex1 wel6 d Vv Recharge c program files eit pmwin examples mf2k ex1 rch6 d vO Solver LMG e program files eit pmwin examples mf2k ex1 lmg da Vv Hydraulic Head Observation c program files eit pmwin examples mf2k ex1 Shob de Vv River Flow Observation c program files eit pmwin examples mf2k ex1 rvob d Vv Sensitivity Process c program files eit pmwin examples mf2k ex1 sen da Vv Parameter Estimation Process c program files eit pmwin examples mf2k ex1 pes da Vv Link MT3DMS Package LMT6 c program files eit pmwin examples mf2k ex1 imt6 de i Options I Check model data I Regenerate all input files r Generate input files only don t start MODFLOW 2000 Cancel Help Fig 2 77 The Run MODFLOW 2000 Sensitivity Analysis Parameter Estimation dialog box 2 6 The Models Menu 145 Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start MODFLOW 2000 Check this option if the user does not want to run MODFLOW 2000 The simulation can be started at a later time or can be started at th
417. mples samplel bas Vv Block Centered Flow BCF1 2 c program files wt360 pmwin examples sample1 bef Vv Output Control c program files wt360 pmwinexamplessamplel oc c Vv Well c program files wt360 pmwin examples sample1 wel Vv Recharge c program files wt360 pmwin examplessamplel rch Vv Solver PCG2 c program files wt360 pmwinsexamples samplel Speg Options I Check model data Regenerate all input files J Perform PESTCHEK prior to running PEST I Generate input files only don t start PEST Cancel Help Fig 4 38 The Run PEST dialog box gt To operate on the estimated parameters 1 2 4 3 Select Models PEST Parameter List to open the List of Parameters PEST dialog box Click the Update button to retrieve the estimated parameter values into the pa rameter list Click the Options tab and set the Run Mode to Perform Forward Model Run using PARVAL values given in the Parameters tab Click OK to close the List of Parameters PEST dialog box Select Models PEST Run to run PEST in the forward model run mode Alternatively you can create a new model with the estimated parameters by using the Convert Models dialog box see Section 2 3 3 for details You can create a scatter diagram to present the parameter estimation result The observed head values are plotted on one axis against the corresponding calculated values on the other If there is an exact agre
418. mulate two dimensional trans port having a permanent point source in a steady state radial flow field numerical results were compared with the analytical solution given by Hsieh 65 This model is described in the section MODEL TESTING AND EVALUATION Point Initial Condition in Uniform Flow of the user s guide of MOC3D A numerical model consisting of 26 lay ers 26 rows and 26 columns is used to simulate three dimensional transport having an initial point source in a parallel steady state flow at 45 degrees to the x direction numerical results were com pared with the analytical solution given by 114 The point source was simulated at layer 12 row 4 column 4 5 6 PHT3D Examples 367 5 6 PHT3D Examples Folder pmdir examples PHT3D Overview of the Problem Twelve documented examples complete with problem statements input data sets and discussion of results are presented in the user s guide of PHT3D 97 Those examples are designed to use as benchmark problems as well as to demonstrate the application of PHT3D A complete list of the examples is given in Table 5 7 Modeling Approach and Simulation Results Most of the models described in the user s guide of PHT3D were created or re created by using the present version of PM You can find the models in sub folders under path examples PHT3D Table 5 7 PHT3D Examples Example Description EX01 Single Species Transport with Monod Kinetics EX02 Transport and mineral prec
419. n A transport simulation will be carried out for each of the included aqueous components except for pH and pe As pH and pe are included in all simula tion they cannot be deactivated Component Name of the component 110 2 Modeling Environment Chemical Reaction Module PHT3D Standard database provided by PHREEGC v 2 0 Fig 2 57 The Chemical Reaction Module PHT3D dialog box i Simulation Settings PHT 3D Reaction Module PHREEGC 2 Standard database Components equilibrium Components kinetic Minerals equilibrium Minerals kinetic Exchange Species Surfaces Options Mobile Equilibrium Active ent Options v M C C C m r C m r C m r C D C r m r Fig 2 58 The Simulation Settings PHT3D dialog box 2 6 The Models Menu 111 Options This is an optional argument that is passed to the PHREEQC 2 in put file to take advantage of the numerous options in PHREEQC to define concentration values For example the charge option can be invoked or the option to calculate the input concentration of an element from equilibrium with a pure phase See the PHREEQC 2 manual 91 for more details Component kinetic This tab contains two tables that define mobile kinetic re actants and immobile kinetic reactants respectively For each reactant a rate expression is defined in the database file of the selected reaction module
420. n all points lie on a 45 line The narrower the area of scatter around this line the better is the match The available settings are sum marized below Scatter Diagram The Scatter Diagram has a lot of built in features Right click on the scatter diagram to open a 2D Chart Control Properties dialog box which allows the user to change the titles and axes settings Most options of this dialog box are self explanatory however the user can click the Help button for detailed descriptions of all options To zoom an area of the scatter diagram Press the Shift or the Ctrl key and hold down left mouse button Drag mouse to select zoom area and release the mouse button Performing a zoom with the Ctrl key enlarges the selected area of a chart while not necessarily showing the axes To remove the zooming effect press the r key Label Check the boxes to display the name of the observation boreholes or the observation times on the scatter diagram Observation Select Use results of all observations if all Plot marked obser vations listed in the Data table should be used If the option Use results of the following OBSNAM is chosen only the results of the selected observa tion borehole OBSNAM are displayed Simulation Time Select Use results of all simulation time s if all results listed in the Data table should be used If the option Use results of the fol lowing simulation time is chosen only the results of t
421. n Flow Type PM allows to perform steady state or transient flow simu lations by selecting an option from the Simulation Flow Type group It is possible to run a steady state simulation over several stress periods In this case a steady state solution is calculated for each stress period 36 2 Modeling Environment e Save As and Load Using these buttons the user can save or load the contents of the table in or from a time parameter file or a ASCII time parameter file The format of the ASCII time parameter file is given in Section 6 2 5 2 5 2 Initial amp Prescribed Hydraulic Heads MODFLOW requires initial hydraulic heads at the beginning of a flow simulation Initial hydraulic heads at constant head cells are used as specified head values of those cells and remain constant throughout the flow simulation For transient flow simulations the initial heads must be the actual values since they are used to account for the storage terms For steady state flow simulations the initial heads are used as starting values for the iterative equation solvers The initial heads at the constant head cells must be the actual values while all other values can be set at an arbitrary level For an unconfined or convertible layer layer type 1 or 3 the initial hydraulic head of a constant head cell should be higher than the elevation of the cell bottom because MODFLOW does not convert a dry fixed head cell to an inactive cell If any constant head cell becom
422. n and Pumping Test 329 Modeling Approach and Simulation Results To meet the requirement of an infinite areal extent the modeled domain is chosen fairly large The boundary could alternatively be moved even further from the pump ing well by using the General Head Boundary see Section 5 1 2 A single layer model simulates the aquifer An increasing grid spacing expansion is used to ex tend the model boundaries Fig 5 26 The layer type is 0 confined In the Layer Property dialog box the flags of Transmissivity and Storage Coefficient are set to User specified The top and bottom elevations of the model layer are not required in this example since the geometrical information is included in Transmissivity and Storage Coefficient The analytical drawdown values at the borehole are specified in the Drawdown Observation dialog box Models Modflow Drawdown Observation Both the ana lytical and calculated drawdown curves are shown in Fig 5 27 An exact comparison is not attained because of the approximations made in the numerical model These include 1 use of a discrete rather than continuous spatial domain 2 use of a discrete rather than continuous time domain 3 use of an iterative solution with a convergence tolerance 4 artificial placement of boundaries In practice we can use this model to estimate transmissivity and confined stor age coefficient by specifying the real observation time and data in the Drawdown Observation dialo
423. n in a confined aquifer at any distance from a well at any time since the start of pumping The assumptions inherent in the Theis solution include The aquifer is homogeneous isotropic and of uniform thickness The aquifer is confined between impermeable formations on top and bottom and of infinite areal extent The initial piezometric surface is horizontal and uniform The pumping rate of the well is constant with time The well penetrates the entire aquifer and the well diameter is small Water is removed from storage instantaneously with decline in head D AnA A numerical model can represent all of these assumptions with the exception of infinite areal extent In this example a fully penetrating well is located at the center of the model domain and withdraws water at a constant rate The drawdown of the hydraulic head is monitored with time at a borehole 55 m from the pumping well The task is to construct a numerical model calculate the drawdown curve at the borehole and compare it with the analytical Theis solution The model parameters are given below Initial hydraulic head 0 0m Transmissivity 0 0023 m s Storage coefficient 0 00075 Pumping rate 4 x 1078 m3 s Total simulation time 86400 s Number of time steps 20 Time step multiplier 1 3 Number of SIP iteration parameters 5 Convergence criterion of head change 0 0001 m Maximum number of iterations 50 5 3 Parameter Estimatio
424. n linear problems ACCL should always be 1 for linear prob lems When Maximum Iterations 1 ACCL is changed to regardless of the input value Printout From the Solver If the option All available information is selected the maximum head change and residual positive or negative are saved in the run listing file OUTPUT DAT for each iteration of a time step whenever the time step is an even multiple of Printout Interval If the option The number of iterations only is checked the printout of maximum head change and residual is suppressed Select the option None to suppress all printout from the solver A positive integer is required by Printout Interval Problem Type The choice of problem type affects the efficiency of solution sig nificant work can be avoided if it is known that A remains constant all or part of the time Linear indicates that the flow equations are linear To meet the linearity re quirement all model layers must be confined and there must be no formu lations that change based upon head such as seepage from a river changing from head dependent flow to a constant flow when head drops below the bot tom of the riverbed Examples of non linearity are cases with riverbed con ductance drain conductance maximum evapotranspiration rate evapotran spiration extinction depth general head boundary conductance and reservoir bed conductance Nonlinear indicates that a non linear flow equation is being solved wh
425. n the Layer Indicator array IRCH which defines the layer where recharge is applied 3 Recharge is applied to the highest active cell in each vertical column The user does not have to predetermine the layer to which recharge should be applied The appropriate layer is automatically selected by the Recharge package If the highest active cell is a constant head cell recharge will be intercepted and cannot go deeper Refer to the description of the Recharge package in McDonald and Harbaugh 85 for an example of using these options 48 2 Modeling Environment Recharge Package Recharge Flux L T 6 9E 08 Parameter Number 0 Recharge Options applied to entire model Recharge is only applied to the top grid layer Vertical distribution of recharge is specified in IRCH Recharge is applied to the highest active cell Current Position Layer Row Column 1 12 23 The recharge option is applied to the entire matrix IACH is only required if the second recharge option is selected Cancel Help Fig 2 22 The Recharge Package dialog box 2 6 1 7 MODFLOW Flow Packages Reservoir The Reservoir package 43 is designed for cases where reservoirs are much greater in area than the area represented by individual model cells More than one reservoir can be simulated using this package The area subject to inundation by each reservoir is specified by assigning the reservoir number to selected cells For rese
426. n two model layers MODFLOW uses VCONT to formulate the flow rate equation between two vertically adjacent cells PM provides two options for each model layer to facilitate the data input Set the Leakance setting of a layer to User Specified The user specified vertical leakance values are used in the simulation In the Data Editor the vertical leakance between the layers i and i 1 is given as the data of the i th layer The leakance data are not required for the bottom layer since MODFLOW assumes that the bottom layer is underlain by imperme able material Set the Leakance setting of a layer to Calculated PM calculates vertical leakance by using the rules explained below The cal culated vertical leakance values are used in the simulation 30 2 Modeling Environment As illustrated in Fig 2 15a when each model layer represents a different hydrostratigraphic unit or when two or more layers represent a single hydro stratigraphic unit PM uses equation 2 1 to calculate the vertical leakance VCONT VCONT 5z as 2 1 Kz kaij Ke k iij where Kz xij and Kz k 1 j are the vertical hydraulic conductivity val ues of layers k and k 1 respectively The ratio of horizontal to vertical hy draulic conductivity ranging from 1 1 to 1000 1 is common in model applica tion 8 A summary of hydraulic conductivity values can be found in 109 It is not uncommon to represent resistance to flow in a low hydraulic con ductiv
427. ncentration associated with a fluid source the mass loading rate MTT into the groundwater system can directly be specified by using this menu item This is of interest for example for the case where dissolution of an oil spill occurs and the groundwater flowing through the residually saturated oil body picks up hydrocarbons 2 6 2 10 MT3DMS SEAWAT Solver GCG MT3DMS includes a general purpose iterative solver based on the generalized con jugate gradient method for solving the system of the transport equations The solver is implemented in the Generalized Conjugate Gradient package A detailed descrip tion of the method can be found in Zheng and Wang 121 This solver must always be activated Using this solver dispersion sink source and reaction terms are solved implicitly without any stability constraints on the trans port step size The required settings and parameters for this package are specified in the Generalized Conjugate Gradient GCG dialog box Fig 2 52 e Preconditioning Method The GCG package has three preconditioning options Jacobi Symmetric Successive Overrelaxation SSOR and the Modified Incom plete Cholesky MIC The MIC preconditioner usually takes less iterations than the other methods but it requires significantly more memory e Max Number of Outer Iterations MXITER and Max Number of Inner Itera tions ITER1 The GCG solver has two iteration loops an inner loop and an outer loop Like the PCG2 so
428. ncy in nonuniform or diverging converging flow fields NPLANE gt 0 the fixed pattern is selected for initial placement The value of NPLANE serves as the number of planes on which initial particles are placed within each cell Fig 2 48a on page 93 This fixed pattern may work better than the random pattern only in relatively uniform flow fields For two dimensional simulations in plan view set NPLANE 1 For cross sectional or three dimensional simulations NPLANE 2 is normally adequate Increase NPLANE if more resolution in the vertical direction is desired No of particles per cell in case of DCCELL lt DCEPS NPL is the number of initial particles per cell to be placed at cells where the relative cell concentration gradient DCCELL is less than or equal to DCEPS Generally NPL can be set to zero since advection is considered insignificant under the condition DCCELL lt DCEPS Setting NPL equal to NPH causes a uniform number of particles to be placed in every cell over the entire grid i e the uniform approach No of particles per cell in case of DCCELL gt DCEPS NPH is the number of initial particles per cell to be placed at cells where the relative cell concentration gradient DCCELL is greater than DCEPS The selection of NPH depends on the nature of the flow field and also the computer memory limitation Generally use a smaller number in relatively uniform flow fields and a larger number in relatively nonuniform flow field
429. nd each time step length is 1 2 times the length of the previous time step length Ground water flow into the system from the adjoining hillside is represented us ing the General Head Boundary Package Thirty six general head boundary cells are specified in column 18 of layers 1 and 3 each having an external head of 350 m and a hydraulic conductance of 1 x 1077 m s The river is treated as a head dependent boundary which is simulated using the River Package to designate 18 river cells in column of layer 1 the head in the river is 100 m The parameter RIV_1 specifies the conductance of the riverbed for each cell Recharge in zone 1 RCH_1 applies to cells in columns 1 through 9 recharge in zone 2 RCH_2 applies to cells in columns 10 through 18 The pumpage is simulated using the Well Package Wells are located at the center of the cells at row 9 column 10 there is one well is in each of layer 1 and 3 Both wells have the same pumping rate The parameter WEL_1 specifies the pumping rate for each of the wells As shown in Table 5 5 the estimated values of PARVAL are as expected close to 1 The final parameter values are obtained by multiplying the estimated PARVAL with the parameter s initial cell values 336 5 Examples and Applications Table 5 5 Parameters defined for MODFLOW 2000 test case 1 parameter values starting and estimated PARVAL PARNAM Description Parameter values Starting Estimated PARVAL PARVAL HK
430. nd its attributes in an active row of the table A row is active when the Active flag is checked The search range is given by the minimum lower limit and the maximum upper limit The color in the Color column will be assigned to the finite difference cells that have a value located within the search range Regularly spaced search ranges can be assigned to each active row by clicking on one of the headers Minimum or Maximum and then enter a minimum and a maximum value to a Search Level dialog box The colors can be automatically assigned to get a gradational change from one color to another To do this click the header Color of the table and assign a minimum color and a maximum color to a Color Spectrum dialog box To change the color individually click on the colored cell a ZJ button appears then click on the l button and select a color from a Color dialog box Cell values are modified according to the user specified value in the Value col umn and the operation option in the Options column The available operations are listed below Display Only No operation takes place Replace The cell values are replaced by the user specified value Add The user specified value is added to the cell values 2 8 The Value Menu 193 4a Import Results x MODFLOW mocan mTaD mT3DMs AT30 Result Type Sete Stress Period 1 Time Step 1 Fig 2 100 The Import Results dialog box Multiply The cell valu
431. nd the local equilibrium assumption is assumed to be invalid The columns of the table are defined as follows Active Check the box to include the respective mineral in the simulation Mineral Name of the mineral Stoichiometry Stoichiometry is expressed in the form of reactant mole_rl reactant2 mole_r2 product mole_p1 product2 mole_p2 and is pre defined in the database file of the selected reaction module Parm l to 8 Parameters used to define the reaction rate The parameters are pre defined in the database file of the selected reaction module Exchange Species Each row of the table contains an exchange species involved in cation exchanging reactions with an exchanger The columns of the table are defined as follows Active Check the box to include the respective species in the simulation Exchange Species Name of the exchange species 112 2 Modeling Environment Surfaces The dropdown box Surface Complexation Model contains the information on which type of SCM calculation will be executed by PHREEQC Each row of the table contains a Surface Master Species defined in the database file of the selected reaction module Active Check the box to include the respective surface master species in the simulation Surface Master Species The name of surface master species Surface Area defines the specific surface area of a surface either in m g when the number of sites and mass of a surf
432. nd then click on the button or choose Options Input Method Polyline The use of this input method is straightforward First you draw a polyline along a drain river or stream and then assign parameter values to vertices of the polyline Within a polyline parameter values needed for constructing MODFLOW input files are assigned to at least one vertex Properties needed for cells along traces of polylines are obtained using the parameter values of vertices These property values are used in addition to the cell by cell values to generate MODFLOW input files prior to running MODFLOW gt To draw a polyline 1 If the display mode is not Grid View or Map View click the I button or the button to switch to the Grid View or Map View 2 Click the assign value button M and click the lea button 3 Click the mouse pointer on a desired position to anchor one end of a line 4 Move the mouse pointer to another position then press the left mouse button again 5 Repeat steps 3 and 4 until the desired polyline is drawn click on the latest vertex again to complete the polyline or press the right mouse button to abort drawing gt To delete a polyline 1 If the display mode is not Grid View or Map View click the I button or the button to switch to the Grid View or Map View 2 Click the assign value button 3 Move the mouse pointer over a polyline The polyline will be highlighted 4 Press the Delete key 20 2 Modeling Enviro
433. nductivity L T 0025 Head on the External Source L 213 Parameter Number 0 Layer Number 1 SEAWAT GHB Elevation L 201 Density of GHB Fluid L 1000 OK Cancel Help Fig 2 19 The General Head Boundary Parameters dialog box 2 6 The Models Menu 43 Tf Layer Option is Assign layer number manually the value of Layer Number defines the model layer number for all model cells downstream from a vertex until the next vertex redefines the layer number Tf Layer Option is Assign layer number automatically the boundary is assigned to a layer where Head on Boundary hy see below is located between the top and bottom of the layer The layer number is set to 1 if hy is higher than the top of the first layer The layer number is set to the last layer if hy is lower than the bottom of the last layer Active Check this box to activate a vertex Clear the Active box to deactivate a vertex The properties of an active vertex will be used in the simulation The properties of an inactive vertex are ignored Equivalent Hydraulic Conductivity K LT and Head on the External Source hy L The value K depends on the material and characteristics of the medium between the external source and the model Since the GHB package requires the input of GHB hydraulic conductance C and head on the external source hy to each cell of a general head boundary the input values K and h at active vertices are
434. ndwater to delineate contaminant capture zones injection zones and wellhead protection areas or to find the point of origin of water in specified zones PMPATH creates several output files including hydraulic heads distribution velocity field the x y z coordinates and travel times of particles Furthermore the coordinates along the path of each particle can be saved and used by 3D Master 23 for advanced 3D Visualization 204 3 The Advective Transport Model PMPATH is PMPATH miro_gro pm5 File Run Options Help ejfe x 9 8 lt lt gt gt ofr GeO C O Fig 3 1 PMPATH in action 3 1 The Semi analytical Particle Tracking Method Assume that the density of groundwater is constant Consider an infinitesimal volume of a porous medium as shown in Fig 3 2a and the law of conservation of mass The three dimensional form of the partial differential equation for transient groundwater flow in saturated porous media at constant density can be expressed as a b Q22 Q2 Ga Y222 Qa Qx2 z 451521 y Qa 4 Qa x Fig 3 2 a Flow through an infinitesimal volume of a porous medium and b the finite difference approach 3 1 The Semi analytical Particle Tracking Method 205 Use OUsy OVsz Oh s i wl Ox i Oy i az 8 Ot ey where Uses Vays and Vaz LT are values of the specific discharge or Darcy velocity through the unit volume along the x y and z coordinate axes w T7 is a volumet
435. ned by Minimum Elevation and Maximum Elevation By de fault the maximum elevation is set to the highest elevation of the model grid or the largest hydraulic head The minimum elevation is set to the lowest elevation of the model grid or the smallest hydraulic head The Velocity Vectors Tab Velocity vectors describe the direction of water movement at any instant of a given time step of the simulation see Section 3 3 2 for the definition of time step Check ing the Visible check box the projection of velocity vectors of each active model cell will be displayed on the Viewing Window and cross section windows Click the color 3 3 PMPATH Options Menu 217 button next to the Visible check box to change the appearance color of the velocity vectors The appearance size of the largest velocity vector is defined by the Vector size in pixels which defaults to 25 and can be ranged from 1 to 32767 The Contours Tab PMPATH displays contours based on the calculated hydraulic head or drawdown values The Contours tab Fig 3 8 controls the display of the contour levels labels and colors The options of this tab are listed below e Visible Contours are visible if this box is checked e Orient label uphill If this box is checked the contours labels are displayed so that they are always oriented uphill i e oriented towards places with higher cell values e Head or Drawdown Use the options Head or Drawdown to decide which kind of contou
436. nfined aquifer the IBS package uses the following equation in anal ogy to equation 2 11 to calculate the approximate inelastic compaction Abx L Ab Ah Sfo Ah Sskv bo 2 13 where Ssky LT is the skeletal component of inelastic specific storage Foran unconfined aquifer the inelastic compaction of sediments can be ex pressed as Abs Ah Sty Ah 1 n nw Sskv bo 2 14 where n is porosity and n is moisture content above water table as a fraction of total volume of porous medium e Starting Compaction L Compaction values computed by the IBS package are added to the starting compaction so that stored values of compaction and land subsidence may include previous components The starting compaction does not affect the calculation of storage changes or resulting compaction 2 6 The Models Menu 47 e Parameter Number Parameter Number is used to group cells where the s fy values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps 2 6 1 6 MODFLOW Flow Packages Recharge The Recharge package is designed to simulate distributed recharge to the ground water system Recharge is defined by assigning the following data to each vertical column of cells The input parameters are assumed to be constant during a given stress period For transient flow simula
437. ng PM These models are saved in the sub folders under path examples trans port listed below All these models are ready to run It is recommended that the users try these test problems first to become familiarized with the various options before applying MT3D MT3DMS or MOC3D to solve their own problems Folder Description transport6 This model is described in Section 7 5 of the manual of MT3DMS A numerical model consisting of 1 layer 31 rows and 31 columns is used to simulate the two dimensional transport in a radial flow field numerical results were compared with the analytical solution of Moench and Ogata 88 transport7 This model is described in Section 7 6 of the manual of MT3DMS A numerical model consisting of 1 layer 31 rows and 31 columns is used to simulate the concentration change at the injection abstraction well numerical results were compared with the approximate analyt ical solution of Gelhar and Collins 48 transport8 This model is described in Section 7 7 of the manual of MT3DMS A numerical model consisting of 8 layers 15 rows and 21 columns is used to solve three dimensional transport in a uniform flow field The point source was simulated at layer 7 row 8 and column 3 Nu merical results were compared with the analytical solution of Hunt 67 transport9 This model is described in Section 7 9 of the manual of MT3DMS This example illustrates the application of MODFLOW and MT3D MT3DMS to a problem i
438. ng species Required stoichiometric ratios be tween the species are to be specified in the Stoichiometry tab Fig 2 45 of the Simulation Settings MT3DMS SEAWAT dialog box in Section 2 6 2 1 Use the initial concentration for nonequilibrium sorbed or immobile liquid phase This check box is only used with if the type of sorption is First order ki netic sorption nonequilibrium Dual domain mass transfer without sorption or Dual domain mass transfer with sorption For First order kinetic sorption nonequilibrium If this box is checked the initial concentration of all species for the sorbed phase need to be entered in this dialog box see below If this box is cleared the sorbed phase is assumed to be in equilibrium with the dissolved phase For Dual domain mass transfer If this box is checked the initial concentra tion of all species for the immobile liquid phase need to be entered in this dialog box see below If this box is cleared the concentration of immobile liquid phase is assumed to be zero 102 2 Modeling Environment 2 6 2 7 MT3DMS SEAWAT Prescribed Fluid Density The prescribed fluid density is used by SEAWAT if the simulation mode is set as Variable Density Flow and Transport with SEAWAT and the density effect of all the simulated species is turned off Refer to the Species tab of Section 2 6 2 1 for details 2 6 2 8 MT3DMS SEAWAT Sink Source Concentration This menu is used for specifying the concentration a
439. ning 9 ppm to the species 2 concentration of the inflow from the constant head boundary The concentrations for hydrocarbon and oxygen at the end of the two year simu lation period are calculated by RT3D and shown in Figures 5 53 and 5 54 The max imum concentration of hydrocarbon is approximately 50 ppm at the injection point 362 5 Examples and Applications Fig 5 53 The oxygen plume is depleted where the concentration of hydrocarbon is above zero Fig 5 54 For this example the TVD scheme is chosen for solving the advection term while all other terms are solved by the explicit finite difference option The mass balance discrepancies for both species are less than 1074 The calculated hydrocarbon and oxygen plumes are nearly identical to those calculated using MT3D99 122 Point source Constant Head h 11m Constant Head h 10 m Fig 5 53 Calculated concentration values of hydrocarbon Constant Head h 11 m Constant Head h 10 m Fig 5 54 Calculated concentration values of oxygen 5 5 Solute Transport 363 5 5 5 First Order Parent Daughter Chain Reactions Folder pmdir examples transport transport5 Overview of the Problem The example problem is adapted from Zheng 122 It involves one dimensional transport of three species in a uniform flow field undergoing first order sequential transformation The model parameters used in this example are identical to those used in Clement 25 for the PCE TCE DCE VC sequent
440. nment Follow the steps below to assign parameter values to polylines Refer to the explana tion of the River Drain General head boundary and Streamflow routing packages for details about the required parameters of each package gt To assign value s to polylines 1 If the display mode is not Grid View or Map View click the J button or the button to switch to the Grid View or Map View Click the assign value button LH and click the button Move the mouse pointer over a vertex and right click The Data Editor displays a dialog box which allows the user to assign parameter value s to the vertex In the dialog box type new parameter value s Once the parameter values are specified the display color of the vertex is changed to indicate that its parameter values are specified gt To modify a polyline 1 2 3 The user may drag vertices of a polyline by pointing the mouse pointer at a vertex node pressing down the left mouse button and moving the mouse Use Shift left click on a segment of the polyline to insert a new vertex Use ctrl left click on a vertex to delete it 2 2 4 Specifying Data for Transient Simulations If a model has more than one stress period the button appears in the Tool bar Clicking on this button opens the Temporal Data dialog box Fig 2 10 which is used to manage model data for transient simulations The following describes the use of the dialog box The table displays
441. nsional solute transport and dispersion in ground water U S Geological Survey Water Resources Investigation Book 7 Chapter C2 90 pp Konikow LF Goode DJ and Homberger GZ 1996 A three dimensional method of characteristics solute transport model U S Geological Survey Water Resources Inves tigations report 96 4267 Kuiper LK 1981 A comparison of the incomplete Cholesky conjugate gradient method with the strongly implicit method as applied to the solution of two dimensional ground water flow equations Water Resour Res 17 4 1082 1086 Langevin CD Shoemaker WB and Guo W 2003 MODFLOW 2000 the U S Geolog ical Survey modular ground water modelDocumentation of the SEAWAT 2000 Version with the variable density flow process VDF and the integrated MT3DMS transport process IMT U S Geological Survey Open File Report 03 426 43 p TI 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 References 403 Langevin CD Thorne Jr DT Dausman AM Sukop MC and Guo W 2008 SEAWAT Version 4 A Computer Program for Simulation of Multi Species Solute and Heat Trans port Techniques and Methods Book 6 Chapter A22 U S Geological Survey Leake SA and Prudic DE 1991 Documentation of a computer program to simu late aquifer system compaction using the modular finite difference ground water flow model U S Geological Survey Leonard BP 1979 A stable and accura
442. nu item to open a Time Series Curves Concentration dialog box which is identical to the Time Series Curves Hydraulic Head dialog box Fig 2 41 on page 82 except the concentration values replace the head values 2 6 7 MODFLOW 2000 Parameter Estimation This section describes the interface for the built in parameter estimation capability of MODFLOW 2000 The parameters and or excitations which can be estimated by MODFLOW 2000 are listed in Table 2 8 Since the BCF package does not sup port parameterization of aquifer parameters it cannot be used with the parameter estimation procedures of MODFLOW 2000 In other words if the user plans to use MODFLOW 2000 to estimate aquifer parameters then one has to use the LPF pack age with adjustable aquifer parameters HK VK HANI VANI Ss and Sy See Sec tion 2 3 4 for how to switch between the BCF and LPF packages During a parameter estimation process MODFLOW 2000 searches optimum pa rameter values for which the sum of squared deviations between model calculated and observed hydraulic heads at the observation boreholes is reduced to a minimum The coordinates of the observation boreholes and observed head values are given in MODFLOW 2000 Parameter Estimation Head Observations It is to note that MODFLOW 2000 does not accept drawdown observations rather it has an option of using the temporal changes in hydraulic heads as observations see Section 2 6 1 14 for details Of particular note is
443. nvolving transport of contaminants in a two dimensional heterogeneous aquifer 366 5 Examples and Applications Folder transport10 transport1 1 transport12 transport13 transport14 Description This model is described in Section 7 10 of the manual of MT3DMS This example illustrates the application of MT3D MT3DMS to an actual field problem involving the evaluation of the effectiveness of proposed groundwater remediation schemes This model is described in the section MODEL TESTING AND EVALUATION One Dimensional Steady Flow of the user s guide of MOC3D A numerical model consisting of 1 layer 1 row and 122 columns is used to simulate one dimensional transport having a third type source boundary condition in a steady state flow field nu merical results were compared with the analytical solution of Wexler 114 This model is described in the section MODEL TESTING AND EVALUATION Three Dimensional Steady Flow of the user s guide of MOC3D A numerical model consisting of 40 layers 32 rows and 12 columns is used to simulate three dimensional trans port having a permanent point source in a steady state flow field nu merical results were compared with the analytical solution of Wexler 114 This model is described in the section MODEL TESTING AND EVALUATION Two Dimensional Radial Flow and Dispersion of the user s guide of MOC3D A numerical model consisting of 1 layer 30 rows and 30 columns is used to si
444. o OUT to the lower adjacent layer For example the flow rate from the first layer to the second layer 2 6107365E 03 m3 s is saved in EXCHANGE LOWER of REGION 1 and LAYER 1 W Nn The percent discrepancy in Table 4 3 is calculated by 100 IN OUT IN OUT 2 4 2 hs Water Budget x Specify the stress period and time step for which the water budget should be calculated Click the Subregions button to define subregions When finished click OK to start the calculation Time Stress Period 1 Time Step 1 Subregions __ox_ Cancel Help Fig 4 8 The Water Budget dialog box 4 1 Your First Groundwater Model with PM 241 Table 4 3 Output from the Water Budget Calculator WATER BUDGET OF SUBREGIONS WITHIN EACH INDIVIDUAL LAYER REGION 1 IN LAYER 1 FLOW TERM IN OUT IN OUT STORAGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 CONSTANT HEAD 1 8595711E 04 2 4354266E 04 5 7585552E 05 HORIZ EXCHANGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 EXCHANGE UPPER 0 0000000E 00 0 0000000E 00 0 0000000E 00 EXCHANGE LOWER 0 0000000E 00 2 6107365E 03 2 6107365E 03 WELLS 0 0000000E 00 1 0000000E 10 1 0000000E 10 DRAINS 0 0000000E 00 0 0000000E 00 0 0000000E 00 RECHARGE 2 6880163E 03 0 0000000E 00 2 6880163E 03 SUM OF THE LAYER 2 8739735E 03 2 8542792E 03 1 9694213E 05 DISCREPANCY 0 69 REGION 2 IN LAYER 2 FLOW TERM IN OUT IN OUT STORAGE 0 0000000E 00 0 0000000E 00 0 0000000
445. o assign the parameters for dispersion and chemical reaction 1 2 gt 1 Select Models MOC3D Chemical Reaction to display a Dispersion Chemical Reaction MOC3D dialog box Check Simulate Dispersion and enter the values as shown in Fig 4 30 The retardation factor R 2 is calculated as follows 2000 R 1 Kyi 0 000125 2 4 3 n 0 25 e Note that the parameters for dispersion and chemical reaction are the same for each layer Click OK to close the dialog box To set Strong Weak Flag Select Models MOC3D Strong Weak Flag 2 Move the grid cursor to the cell 1 15 25 Parameters for Advective Transport MOC3D x Interpolation scheme for particle velocity Bilinear X Y directions Maximum number of particles NPMAX 500 Courant number CELDIS 5 Fraction limit for regenerating initial particles FZERO o Initial number of particles per cell NPTPND 8 Cancel Help Fig 4 29 The Parameters for Advective Transport MOC3D dialog box 260 4 Tutorials Dispersion Chemical Reaction MOC3D xj IV Simulate Dispersion First order decay rate 1 T 0 Effective molecular diffusion coefficient L 2 T 0 scam tersen dispersivity L 1 1 1 H 10 2 10 Fig 3 4 5 4 30 The Dispersion Chemical Reaction MOC3D dialog box Press the right mouse button once to open a Cell Value dialog box type 1 into the dialog box th
446. obian matrix contained in the nominated base Jacobian matrix file SVD on XtQx This option sets SVDA_EXTSUPER to 3 in the PEST control file which directs PEST to formulate super parameters through singular value decom position of XtQX LSQR without orthogenalization This option sets SVDA EXTSUPER to 2 in the PEST control file which directs PEST to calculate super parameters using the first m v vectors com puted by the LSQR algorithm where m is the number of super parameters see below LSQR with orthogonalization Same as above however the vectors are orthogonalized before being em ployed for definition of super parameters This option sets SVDA_EXT SUPER to 2 in the PEST control file Number of super parameters to estimate Enter an appropriate number It is sometimes wise to enter a number here which is somewhat above the expected dimensionality of estimable parameter space to ac commodate shortcomings in the linearity assumption involved in determination of super parameters from base parameters Inclusion of Tikhonov regularization in the inversion process or use of singular value decomposition will guaran tee numerical stability of the SVD assisted process In either case this number should be less often significantly less than the number of base estimable param eters parameter reduction factors of up to 10 are not uncommon Where parame ters are outnumbered by observations the number of super parameters sh
447. odel grid used to simulate flow Within the subgrid the row and column 258 4 Tutorials spacing must be uniform but the thickness can vary from cell to cell and layer to layer However the range in thickness values or product of thickness and effective porosity should be as small as possible The initial concentration must be specified throughout the subgrid within which solute transport occurs MOC3D assumes that the concentration outside of the sub grid is the same within each layer so only one value is specified for each layer within and adjacent to the subgrid The use of constant concentration boundary condition has not been implemented in MOC3D gt To set the initial concentration 1 Select Models MOC3D Initial Concentration For the current example we accept the default value 0 for all cells 2 Select File Leave Editor or click the leave editor button w gt To define the transport subgrid and the concentration outside of the subgrid 1 Select Models MOC3D Subgrid The Subgrid for Transport MOC3D dialog box appears Fig 4 28 The op tions in the dialog box are grouped under two tabs Subgrid and C Outside of Subgrid The default size of the subgrid is the same as the model grid used to simulate flow The default initial concentration outside of the subgrid is zero 2 Click OK to accept the default values and close the dialog box gt To assign the input rate of contaminants 1 Select Models MOC3D
448. ods When the Modflow Version is not set to gt MODFLOW 2000 MODFLOW 2005 the Transient column disappears and all stress periods are either steady state or tran sient which is controlled by the options of the Simulation Flow Type group Fig 2 17 The columns of this dialog box are described below e Period Active Length Time Step MODFLOW divides the simulation time into stress periods which are in turn divided into time steps Check the Active box to activate a stress period For each stress period the user has the option of changing parameters associated with head dependent boundary conditions in the River Stream Drain Evapotranspiration General Head Boundary and Time Variant Specified Head Boundary packages as well as the recharge rates in the Recharge package and pumping rates in the Well package For transport simulations the user may change mass loading rates MT3DMS only and source concentrations associated with the fluid sources and sinks 34 2 Modeling Environment Time Parameters afl jm fae fo fo fo fo jo a o o o oo o o o o an an Fig 2 17 The Time Parameters dialog box for MODFLOW 96 The length of stress periods and time steps is not relevant to steady state flow simulations However if transport simulations need to be done at a later time the actual period length should be entered e Transient Check the Transien
449. of the parameter upgrade vector i e the number of singular values remaining after truncation Singular value decomposition is carried out at least once per iteration corresponding to the testing of different Marquardt lambdas including the sole Marquardt lambda value of zero if RLAMBDAL is set to zero and NUMLAM is set to 1 as suggested above multiple incidences of singular value decomposition are required in any optimization iteration in which parameters hit their bounds The SVD output file can become very large not all of the information contained in it is always worth reading However an inspection of singular values can often provide assistance in determining best values for MAXSING and EIGTHRESH see below By clearing this box only singular values and not their correspond ing eigenvectors are written to modelname svd thus reducing its size consider ably The number of singular values used during each parameter upgrade is also recorded Number of singular values at which truncation occurs MAXSING In other words MAXSING is the maximum number of singular values to include in the inversion process equivalent to the maximum number of eigenvalues and the maximum number of degrees of freedom in parameter solution space This is problem dependent Experience with a particular problem may dictate its opti mal value set it high enough to obtain a good fit between model outputs and field data but not so high that numerical instabi
450. older for saving the model data such as C Models tutorial2 and type the file name TU TORIAL2 as the model name A model must always have the file extension PM5 All file names valid under MS Windows with up to 120 characters can be used It is a good idea to save every model in a separate folder where the model and its output data will be kept This will also allow PM to run several models simultaneously multitasking 2 Click OK PM takes a few seconds to create the new model The name of the new model name is shown in the title bar 4 2 2 2 Step2 Generate the Model Grid gt To generate the model grid 1 Select Grid Mesh Size A Model Grid and Coordinate System dialog box appears 2 Enter the values as shown in Fig 4 43 to the dialog box 3 Click OK to close the dialog box 4 2 Unconfined Aquifer System with Recharge 273 iigiiModel Grid and Coordinate System x Model Grid Coordinate System r Layer K Dimension Number of Layers 1 Model Thickness 25 Model Top Elevation 25 r Row I Dimension Number of Rows 20 Model Extent 10000 r Column J Dimension Number of Columns 12 Model Extent 6000 r Cross Sectional Display Vertical Exaggeration 20 Fig 4 43 The Model Grid and Coordinate System dialog box You are now in the Grid Editor of PM To help visualize the model site we can over lay a DXF file as a site map which gives us the locations of the bounda
451. olled by the Option tab see below 144 2 Modeling Environment The Options Tab The Statistic Option defines the physical meaning of Statistic specified in the Flow Observation tab It also defines how the weights are calculated Refer to Hill 62 for more details about the role of statistics and weights in solving regression problems 2 6 7 4 MODFLOW 2000 Parameter Estimation Run MODFLOW 2000 Select this menu item to start MODFLOW 2000 The available settings of the Run MODFLOW 2000 Sensitivity Analysis Parameter Estimation dialog box Fig 2 77 are described below e The File Table has three columns Generate Prior to running the program PM uses the user specified data to generate input files for MODFLOW 2000 An input file will be generated if it does not exist or if the corresponding Generate box is checked The user may click on a box to check or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Run MODFLOW 2000 Sensitivity Parameter Estimation Vv Basic Package c program files eit pmwin examples mf2k ex1 bas6 d Vv Layer Property Flow LPF c program files eit pmwin examples mf2k ex1 ipf6 da M Output Control c program files eit pmwin exa
452. olumns of the table are described below Number This column displays the read only species number Active Check the Active box to add a species to the simulation Description Type the name or description of the species here Density On This item is used by SEAWAT only Check the box to include the concentration of the simulated species in the fluid density calculation If the fluid density is independent of all simulated species i e Density On boxes of all species are cleared SEAWAT will run in a uncoupled mode and the user specified fluid density array see Section 2 6 2 7 will be used in the simulation DRHODC This item is used by SEAWAT only DRHODC i e 0p 0C is the slope that relates fluid density p to solute concentration C Separate values for DRHODC are entered for individual species DRHODC is ignored if the Density On box of the corresponding species is not checked Any mea 2 6 The Models Menu 87 Simulation Settings MT 3DMS SEAWAT Simulation Mode Constant Density Transport with MT3DMS Type of Reaction First order parent daughter chain reactions MT3D99 Only Species The following table defines the stoichiometric ratio or yield coefficient between species pairs The table is used when first order kinetic parent daughter chain reactions or instantaneous reaction among species is simulated MT3D99 Only Species Pair Stoichiometric ratio or yield coefficient a No 1 No 2 0 792
453. olution Note that the parameters for the confined leaky aquifer are the same as in the previous example so we can compare the results of these two examples Modeling Approach and Simulation Results The modeled domain is the same as in the previous example Three model lay ers are used to simulate the system The layer type of all three layers is 3 con fined unconfined transmissivity varies In the Layer Property dialog box the Stor age Coefficient flag is set to user specified and the Transmissivity flag is calculated All model cells in the first model layer are fixed head cells and all other cells are specified as active cells A transient flow simulation is performed for a stress period with the length of 49320 seconds 20 time steps and a time step multiplier of 1 3 For comparison the analytical solution is entered in the Drawdown Observation dialog box Fig 5 29 shows the numerical and analytical drawdown time curves at the ob servation borehole which is at a distance of 55 m from the pumping well The match of these two curves is very good While the use of the analytical solution is limited to the primary assumptions the numerical model can be used to evaluate pumping tests even if the confining aquitard Fig 5 28 has a higher value of the vertical hydraulic conductivity and the hydraulic head in the overlying aquifer is not constant during the pumping To do this simply specify all model cells as active cells This is allowed
454. on PEST tries lots of parameter sets and will consider that the goal of the iteration has been achieved if i lt PHIRATSUF 2 61 i l1 where i 1 is the lowest objective function calculated for optimization iteration i 1 and hence the starting value for the i th optimization iteration and is the 2 6 The Models Menu 169 objective function corresponding to a parameter set during optimization iteration i A value of 0 3 is often appropriate for PHIRATSUF If it is set too low model runs may be wasted in search of an objective function reduction which it is not possible to achieve If it is set too high PEST may not be given the opportunity of refining lambda in order that its value continues to be optimal as the parameter estimation process progresses NUMLAM is the maximum number of lambdas parameter sets that PEST can test during any optimization iteration It should normally be set between 5 and 10 For cases where parameters are being adjusted near their upper or lower limits and for which some parameters are consequently being frozen thus reducing the dimension of the problem in parameter space experience has shown that a value closer to 10 may be more appropriate than one closer to 5 RELPARMAX and FACPARMAX are used to limit parameter adjustments REL PARMAX is the maximum relative change that a parameter is allowed to undergo between iterations whereas FACPARMAX is the maximum factor change that a parameter is allow
455. on dialog box uses the following three formats for saving and loading data The formats are described in the following sections 6 2 File Formats 383 e Cell Group cell_group contains the data of the Cell Group table of the Flow Observation dialog box 2 75 e Flow Observations Data Flow_observations contains observation times ob served values and weights of a cell group Using the Flow Observation dialog box a Flow Observations Data file can be loaded to associate with a cell group at a time e Complete Information complete_flow_obs contains all cell groups and their observation data 6 2 7 1 Cell Group File 1 Data NCELLGROUPS The following data repeat for each cell group i e NCELLGROUPS times 2 Data OBSNAM GroupNumber Active Description Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NCELLGROUPS is the number of cell groups OBSNAM is the name of the cell group max 8 characters blank and special characters are not allowed GroupNumber is the number associated with the cell group Active A cell group is active if Active 1 A cell group is inactive if Active 0 Description Description of the cell group 6 2 7 2 Flow Observations Data File 1 Data NFOBS The following data repeat for each observation i e NFOBS times 2 Data Time FOBS STWT Explanation of Fields Used in Input Instructions
456. on is ne b Dzx k j 1 2 42 The output options for MOC3D are given in the Output Control MOC3D dialog box Fig 2 67 Most items in this dialog box are self explanatory The names of the separate ASCII or binary output files are given in Table 2 7 Table 2 7 Names of the MOC3D output files Output Term Filename Listing file Path MOC3D Ist Concentration file ASCII Path mocconc asc Concentration file binary Path mocconc bin Velocity ASCII Path mocvel asc Velocity binary Path mocvel bin Particle location ASCII Path mocprt asc Particle location binary Path mocprt bin Path is the folder in which the model is saved 2 6 The Models Menu 125 2 6 5 9 MOC3D Concentration Observation Select this menu item from the MOC3D menu to specify the locations of the concen tration observation boreholes and their associated observed measurement data in a Concentration Observations dialog box Its use is identical to the Head Observation dialog box see Section 2 6 1 14 The only difference is that the head observations are replaced by concentration observations 2 6 5 10 MOC3D Run Select this menu item to open the Run Moc3d dialog box Fig 2 68 The available settings of this dialog box are described below e The File Table has three columns Generate Prior to running a flow simulation PM uses the user specified data to generate input files for MODFLOW and MOC3D An input file will be generated if it does not exist o
457. on of the fourth order Runge Kutta algorithm for particles located in cells which contain or are ad jacent to sinks or sources and automatic selection of the first order Euler algorithm for particles located elsewhere Simulation Parameters Depends on the selected Solution Scheme one or more of the following parameters may be required Maximum number of total moving particles MXPART is the number of par ticles allowed in a simulation Courant number PERCEL is the number of cells or a fraction of a cell any particle will be allowed to move in any direction in one transport step Generally 0 5 lt PERCEL lt 1 Concentration weighting factor WD lies between 0 and 1 The value of 0 5 is normally a good choice This number can be adjusted to achieve better mass balance Generally it can be increased toward 1 as advection becomes more dominant Negligible relative concentration gradient DCEPS is a criterion for placing particles A value around 10 is generally adequate If DCEPS is greater than the relative cell concentration gradient DCCELL i equation 2 36 NPH particles are placed in the cell k i j otherwise NPL particles are placed see NPH and NPL below CMAX 5 CMINk i j CMAX CMIN DCCELL ij 2 36 where CMAX and CMIN ij are the maximum and minimum con centration values in the immediate vicinity of the cell k i j CMIN and CMAX are the minimum and maximum concentration values in the entir
458. on steps The value of Parameter Number is assigned to all model cells downstream from a vertex until the next vertex redefines the parameter number Density of River Fluid M L This value represents the prescribed density of fluid entering the groundwater system from the river This value is used by SEAWAT only if it is running in a uncoupled mode i e the density effect of River Parameters Layer Option apply to the selected polyline Assign layer number manually Parameters Active SEAWAT apply to the selected vertex Hydraulic Conductivity of Riverbed L T Head in the River L Elevation of the Riverbed Bottom L Width of the River L Thickness of Riverbed Sediments L Parameter Number Layer Number Density of River Fluid M L 3 1000 ALL Cancel Help Fig 2 25 The River Parameters dialog box 2 6 The Models Menu 53 all species are turned off see 2 6 2 1 and the Density of river fluid options in the Simulation Settings MT3TMS SEAWAT dialog box see Fig 2 46 on p 89 is set as User Specified in the River Package The ALL button Click the ALL button of a property to copy the property value to all other active vertices e When using the Cell by cell or Polygon input methods the following values are to be assigned to model cells of a river See the explanations above for the defi nition of the input values Hydraulic Conductance of the riverbed Crio
459. on where groundwater flow varies from time step to time step the flowlines and pathlines do not coincide Use the option Pathlines use transient flow fields to calculate transient pathlines e Stop Conditions In general particles will stop when the allowed travel time de fined in Tracking Step is reached or when the particles reach specified head cells In addition to these conditions two stop conditions are available Particles stop when they enter cells with internal sinks The flow model MODFLOW includes the options to simulate wells drains rivers general head boundaries streams evapotranspiration and recharge Except the last two options they are treated as internal distributed sources or sinks by PM PATH If the internal sink of a cell is sufficiently strong flow will be into the 3 3 PMPATH Options Menu 221 cell from all cell faces In that case every particle that enters the cell will be discharged If the sink is weak flow will be into the cell from some cell faces and a part of the flow will leave the cell through other faces A particle entering such a cell may be discharged or may leave the cell again In the fi nite difference approach however it is impossible to determine whether that particle should be discharged or pass through the cell If this option is se lected particles will be discharged when they enter cells with internal sinks regardless of the flow condition Particles stop when the simula
460. ong columns Read one value for each of the NROW rows This is a single array with one value for each row X1 Y1 are the coordinates of the lower left corner of the model worksheet see Coordinate System for details X2 Y2 are the coordinates of the upper right corner of the model worksheet see Coordinate System for details NLAY is the number of model layers TOP is a 2D matrix contains the top elevation of each model cell of a model layer BOTTOM is a 2D matrix contains the bottom elevation of each model cell of a model layer 6 2 File Formats 379 6 2 4 Line Map File A line map file contains a series of polylines each polyline is defined by the number of vertices and a series of coordinate pairs File Format Repeat Data 1 and 2 for each polyline 1 Data NVERTEX The following data repeats NVERTEX times 2 Data X Y Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space NVERTEX is the number of vertices of a polyline X is the x coordinate of the i th vertex Y is the y coordinate of the i th vertex 6 2 5 ASCII Time Parameter File An ASCII time parameter file can be saved or loaded by the Time Parameters dialog box see Section 2 5 1 File Format 1 Data LABEL Data NPER ITMUNI Data Reserved Reserved Reserved Reserved Data Reserved Reserved Reserved Reserved Data Reserved Reserved Reserved Reserved
461. or Map View Click the assign value button LH and click the J button Move the mouse pointer into a polygon The boundary of the polygon will be highlighted The value s of the polygon will be displayed in the status bar Press the right mouse button once The Data Editor displays a dialog box which allows the user to assign parameter value s to the polygon In the dialog box type new parameter value s then click the E button to apply the parameter value s to the model cells within the polygon 2 2 The Data Editor 19 gt To modify a polygon 1 The user may drag vertices of a polygon by pointing the mouse pointer at a vertex node and pressing down the left mouse button while moving the mouse 2 If there are several polygons some polygons can intersect or even cover other polygons If the mouse pointer is moved into a covered polygon the boundary of the polygon will not be highlighted In this case simply move the mouse pointer into that polygon hold down the Ctrl key and press the left mouse button once The Data Editor will resort the order of the polygons and the lost polygon will be recovered 2 2 3 The Polyline Input Method The Polyline Input Method is available only for the Drain General head boundary River and Streamflow Routing packages This input method is not allowed in the cross sectional view To activate this method click on the button or the but ton to switch to Grid View or Map View a
462. or drainable porosity Specific yield is defined as the volume of water that an unconfined aquifer releases from storage per unit surface area of aquifer per unit decline in the water table Specific yield is a function of porosity and is not neces sarily equal to porosity because a certain amount of water is held in the soil matrix and cannot be removed by gravity drainage Refer to Spitz and Moreno 109 for a summary of values of specific yield Refer to Bear 12 13 or Freeze and Cherry 46 for detailed explanation of storage terms and their definitions 2 5 9 Bulk Density 2 5 9 1 Layer by Layer The layer by layer bulk density data are used by the Chemical Reaction package of MT3D or RT3D version 1 for calculating the retardation factor or for calculating the first order irreversible radioactive decay or biodegradation rate of the adsorbed phase Refer to Section 2 6 6 4 for details 2 5 9 2 Cell by Cell The cell by cell bulk density data are used by the Chemical Reaction package of MT3DMS MT3D99 PHT3D SEAWAT and RT3D version 2 and later for simu lating sorption effects 2 6 The Models Menu 39 2 6 The Models Menu 2 6 1 MODFLOW 2 6 1 1 MODFLOW Flow Packages Drain The Drain package is used to simulate effects of features such as agricultural drains which remove groundwater from aquifer at a rate proportional to the head difference between the aquifer and the drain When the hydraulic head in the aquifer is greater
463. orizontal flow barrier is defined by assigning the following values to a model cell in the Horizontal Flow Barrier Package dialog box Fig 2 20 The location and the parameters of the barrier are assumed to be constant for the entire simulation _ Horizontal Flow Barrier Package Barrier Direction 1 4 300 Transmissivity 7 Thickness of the Barrier L T 100 Parameter Number 9 Current Position Layer Row Column 1 13 24 Directions 3 1 e 1 4 O No Barrier Cancel Help Fig 2 20 The Horizontal Flow Barrier dialog box Barrier Direction The barrier direction indicates the cell face where the bar rier is located To erase an existing barrier use zero for the barrier direction 2 6 The Models Menu 45 e Hydraulic Conductivity Thickness of the barrier TDW Tt or Transmis sivity Thickness of the barrier TDW LT The TDW represents the hy draulic characteristic of the barrier If a layer is unconfined type 1 or 3 or if MODFLOW 2000 is used TDW is the barrier hydraulic conductivity divided by the thickness of the barrier If a layer is confined type 0 or 2 TDW is the barrier transmissivity divided by the thickness of the barrier e Parameter Number Parameter Number is used to group cells where the TDW values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation step
464. ort DXF map 223 DXF map 195 matrix 188 raster graphics 195 results 193 INCTYP 156 initial amp prescribed hydraulic heads 36 initial concentration MOC3D 119 MT3D 126 MT3DMS SEAWAT 89 rt3d 114 Input Method Cell by Cell 16 Polygon 17 Polyline 19 instantaneous reaction among species 86 Index 409 interbed storage 31 Interbed storage package 45 interface file to mt3d 75 interpolation methods 177 inverse distance 179 Kriging 177 label format 201 Langmuir isotherm 98 layer bottom 32 property 27 top 32 Layer Proportions 71 Layer Property Flow 24 Leakance 29 Limitation of PM 375 line map file 379 linear equilibrium isotherm 98 Log transform 138 longitudinal dispersivity 95 96 mass loading 103 matrix 188 import 188 reset 191 MAX CHANGE 140 MAX ITER 140 mesh size 27 Method of characteristics 126 MOC3D 2 25 118 394 advection 119 concentration observation 124 concentration time curves 126 dispersion 121 observation wells 122 output control 123 run 125 scatter diagram 126 sink source concentration 123 strong weak flag 122 model data checked 77 modeling environment 7 PMPATH 208 MODFLOW 1 25 39 compaction scatter diagram 81 drawdown scatter diagram 81 410 Index head scatter diagram 78 head time curves 81 run 75 subsidence scatter diagram 81 MODFLOW 2000 1 25 393 forward model run 141 parameter estimation 135 334 337 perform
465. ort step size in the table to zero or to a value greater than Deltat nq will cause Deltatmazx to be used for the simulation For details about the stability cri teria associated with the explicit transport solution refer to 74 117 or 118 For implicit solutions in MT3DMS i e when the Generalized Conjugate Gra dient solver is used the transport step sizes in the table are the initial transport step size in each flow time step The subsequent transport step size may increase or remain constant depending on the user specified transport step size multiplier see below If the transport step size is specified as zero the model calculated value based on the user specified Courant number in the Advection Package MT3DMS dialog box is used Max No of Transport Steps If the number of transport steps within a flow time step exceeds the maximum number the simulation is terminated Multiplier Transport is the multiplier for successive transport steps within a flow time step This value is used by MT3DMS for the case that the Generalized Conjugate Gradient solver and the solution option for the advection term is the finite difference method see Section 2 6 2 3 Simulation Time Unit Each time when the time unit in the Simulation Time Unit group is changed PM will update the period length in the table if Auto Update Period Length is checked Note that changing the time unit does not affect the user specified parameter values Simulatio
466. ort the POLYLINE feature Use this feature only if the user s graphics software pack age accepts the DXF entity POLYLINE 3 4 2 Hydraulic Heads Select File Save Heads As to save the hydraulic head values of the current layer at the current stress period and time step in an ASCII Matrix file see Section 6 2 1 3 4 3 Drawdowns Select File Save Heads As to save the drawdown values of the current layer at the current stress period and time step in an ASCII Matrix file see Section 6 2 1 3 4 4 Flow Velocities Select File Save Velocity As and specify a file name in a File Save As dialog box to save flow velocities of the current layer at the current stress period and time step in an ASCII Matrix file see Section 6 2 1 The file saves average pore velocities at the center of each cell In addition the velocity components along the I J and K axes are added to the end of the file The default velocity at inactive cells is 1 0 x 10 3 4 5 Particles Select File Save Particles As and specify a file name in a Save Particle As dialog box to save the particle position and attributes in a Particles file see Section 6 2 12 for the format By selecting a Save as type in this dialog box either the starting position or end position after backward or forward tracking of the particles can be saved A Particles file can be loaded by selecting File Load Particles When a parti cle file is loaded PMPATH just adds the additional
467. ort transport8 beft Generate Output Control c simcore pmwin8 examp les transport transport8 oc Well c simcorespmwin8 examp les transport transport8 well Solver PCG2 c simcore spmwin8 examp les transport transport8 peq Basic Transport Package c simcore pmwin8 examp les transport transport8 mtrr Advection Package c simcorespmwin8 examp les transport transport8 mtrr Dispersion Package c simcorespmwin8 examp les transport transport8 mtrr Generalized Conjugate Gradient Solver F c simcore pmwin8 examp les transport transport8 mtrr Sink 3090959979 d Source Mixing Package _ o and Soules _ c simcore pmwinB examples transport transport8 mtmr Variable Density Flow Package c simcore spmwin8 examples transport transport8 swe Options I Regenerate all input files Generate input files only don t start SEAWAT Cancel Fig 2 56 The Run SEAWAT dialog box 108 2 Modeling Environment Run SEAWAT dialog box The available settings of the Run SEAWAT dialog box are described below e The File Table has three columns Generate Prior to running a transport simulation PM uses the user specified data to generate input files for SEAWAT An input file will be generated if it does not exist or if the corresponding Generate box is checked Normally we do not need to worry about these boxes since PM will take care of the sett
468. osity Ne effective porosity VCONT vertical leakance T71 HANI horizontal anisotropy HANI x HK horizontal hydraulic conductivity along columns VANI vertical anisotropy HK VK x VANI 8 2 Modeling Environment Table 2 2 Summary of menus in PM Menu Description File Create new models open existing models convert models to the PM format Save and print plots Grid Generate or modify the size of a model grid input of the geometry of the aquifer Parameters Input of spatial aquifer parameters for example transmissivity Input of tem poral parameters for example simulation length or number of stress periods Models Specify model specific data using the module provided and call simulation programs For example the user can add wells use the recharge or river modules to MODFLOW or define the advection or dispersion parameters in MT3DMS The simulation programs are called by selecting Run from the corresponding model Tools Call the modeling tools Value Manipulate model data read or save model data in separate files import model results import an existing MODFLOW input file Options Modify the appearance of the model grid on the screen load site maps change display mode change input method Help Call Processing Modflow Pro Help menu system to help you control the modeling process If a model data set has been specified the corresponding item of the Grid Parameters and Models menus will be checked To
469. ot simulated First order irreversible reaction The required parameters are First order reaction rate for the dissolved phase 1 T First order reaction rate for the sorbed phase 1 T The concentration change due to the chemical reaction from one transport step to another transport step at cell k i j can be expressed as At Pb JA Ck ij Aa Re i j el Nk ij A CRCT k ij Chig 2 51 where T is the first order rate for the dissolved phase Az T7 is the first order rate for the sorbed phase At is the transport time step and Cki j is the mass of the solute species adsorbed on the solids per unit bulk dry mass of the porous medium at the beginning of each transport step Cr i j is in equilibrium with solute concentration C in the cell k i j The rate constant is usually given in terms of the half life t 2 equation 2 55 Generally if the reaction is radioactive decay 2 should be set equal to A1 However for certain types of biodegradation Az may be different from M1 Monod kinetics MT3D99 implements the Monod kinetics only for the dis solved phase of an organic compound The required parameters are Product of total microbial concentration and the maximum specific growth rate of the bacterium M max M L 3T Half Saturation constant K ML According to Rifai and others 103 and Zheng 122 the change in the sub strate concentration within a transport time step using the Monod g
470. ottom elevation and riverbed conductance be specified to each model cell The riverbed conductance is defined as Kriv ape Wriv Criy 4 4 where Criy hydraulic conductance of the riverbed L T Kriv hydraulic conductivity of the riverbed sediment LT L length of the river within a cell L W iy width of the river within a cell L M iy thickness of the riverbed within a cell L Entering the river data on a cell by cell basis is sometimes very cumbersome Fortu nately pmp provides a Polyline input method which dramatically facilitates the data input process We will use this input method to specify the river data gt To specify the river data Select Models Modflow River to open the Data Editor Click the 4 button if the display mode is not Grid View Click the El button to switch to the Polyline input method Left click on the upstream end of the river to anchor one end of the polyline Move the mouse pointer along the trace of the river and left click to anchor another vertex of the polyline Repeat steps 4 and 5 until the polyline looks similar to Fig 4 53 then click on the latest vertex again to complete to polyline While drawing the polyline you may press the right mouse button to abort 7 Right click on the first vertex of the polyline on the upstream side to open a River Parameters dialog box and enter the values as shown in Fig 4 54 then click OK to close the dialog box nkwW D
471. ould be at most equal to the number of observations available for model calibration It is important to note that parameters that are fixed or tied will remain fixed and tied when defining super parameters hence the SVD assisted parameter estimation process will respect their status Offset for super parameters In the SVD assisted parameter estimation process super parameters are provided with a starting value of zero signifying zero perturbation of initial base parame ters However zero valued parameters can create problems for PEST especially in the enforcement of parameter change limits Hence it is best to supply an off set for such parameters to keep their values away from zero A value of 10 is suitable on most occasions of SVD assisted parameter estimation Parameter relative change limit RELPARMAX Base parameters are designated as relative limited by SVDAPREP On most occasions a value of 0 1 will be adequate though you should be prepared to alter this upwards if PEST convergence is too slow or downwards if parameter oscillation occurs or parameters hit their bounds too quickly 2 6 The Models Menu 167 Parameter scaling control variable SVDA_SCALADJ PEST provides a variety of automatic base parameter scaling mechanisms to combat the problems associated with base parameter hypersensitivity described in Section 2 8 of Addendum to the PEST Manual 39 When some parameters are not log transformed parameter scaling is essen
472. ounds of the time axis are defined by Upper Bound and Lower Bound which are determined automatically if the check box Fix Bounds is clear or if the Reset Bounds button is pressed When editing the upper and lower bounds the chart will be updated accordantly if Fix Bounds is not checked Check it to fix the bounds at specified values Check Loga rithmic to display the time axis in the logarithmic scale Y Axis The bounds of this axis are defined by Upper Bound and Lower Bound which are determined automatically if the check box Fix Bounds is clear or if the Reset Bounds button is pressed When editing the upper and lower bounds the chart will be updated accordantly if Fix Bounds is not checked Check it to fix the bounds at specified values Check Logarithmic to display the Y axis in the logarithmic scale Data Type Check the Calculated or Observed box to display the time series curves based on the calculated or observed values respectively The chart uses solid lines for displaying calculated curves Observation curves are dashed Select Use results of all observations if all Plot marked observations Time Series Curves Hydraulic Head j x E r X Asis Time Head Time Curve T Fix Bounds P Logarithmic Lower Bound 1 Upper Bound 24439070 1507 Reset Bounds Y Axis I FixBounds Logarithmic Lower Bound maso Upper Bound 157 1483 Reset Bounds r Data Type M Calculated I Observed Hydraulic Head 6 w
473. ours Using the 2D Visualization you can create contour plots for the water levels at the end of each time step The water level at the end of the pumping period dry season corresponds to the heads in time step 12 of period 1 Fig 4 47a The water level at the end of the recharge period wet season corresponds to the heads in time step 6 of 4 2 Unconfined Aquifer System with Recharge 283 period 2 Fig 4 47b Both figures use the contour interval of 0 5 m The minimum and maximum contour levels are 12 5 m and 19 m respectively og st ossi oes ee S n Well PO gy Well 2 Well 3 C Co a Og n H N Well 4 Well 5 Well 6 b3 m n An a S o 2 o Dia Wall 7 Wall B Well 9 a m m b Fig 4 47 a Head distribution after 240 days of pumping period 1 time step 12 b Head distribution after 120 days of recharge period 2 time step 6 284 4 Tutorials 4 3 Aquifer System with River Folder pmdir examples tutorials tutorial3 4 3 1 Overview of the Hypothetical Problem A river flows through a valley Fig 4 48 which is bounded to the north and south by impermeable granite intrusions The hydraulic heads at the upstream and down stream constant head boundaries are known which are saved in a data file The river forms part of a permeable unconfined aquifer system horizontal hydraulic conductivity HK 5 m day vertical hydraulic conductivity VK 0 5m day specific yield S 0 05
474. out the simulation A constant head cell may or may not be a constant concentration cell The initial con centration is specified by selecting Models MT3D Initial Concentration Models MT3DMS Initial Concentration or Models RT3D Initial Concentration 2 4 4 Top of Layers TOP The top elevation of a layer is required when one of the following conditions ap plies PM will check these conditions except the last one prior to running a model simulation 1 The BCF package is selected and layer type 2 or 3 is used 2 The BCF package is selected and VCONT to the underlying layer is calculated by PM The BCF package is selected and T or S is calculated by PM The LPF package is used 5 One of the programs PMPATH MT3D MT3DMS MOC3D RT3D PHT3D or 3D Master for 3D Visualization will be used Kw 2 4 5 Bottom of Layers BOT The bottom elevation of a layer is required when one of the following conditions applies PM will check these conditions except the last one prior to running a model simulation 1 The BCF package is selected and layer type 2 or 3 is used 2 5 The Parameters Menu 33 2 The BCF package is selected and VCONT to the underlying layer is calculated by PM The BCF package is selected and T or S is calculated by PM The LPF package is used 5 One of the programs PMPATH MT3D MT3DMS MOC3D RT3D PHT3D or 3D Master for 3D Visualization will be used amp 2 5 The Parameters
475. ovements and bank storage due to flood stages in surface streams U S Geological Survey Water Supply Paper 1536 J 343 366 Council GW 1999 A lake package for MODFLOW LAK2 Documentation and user s manual HSI Geotrans Davis JC 1973 Statistics and data analysis in geology John Wiley amp Sons New York Deutsch CV and Journel AG 1998 GSLIB Geostatistical Software Library and User s Guide Second Edition Oxford University Press ISBN 0 19 510015 8 Doherty J 1990 MODINV Suite of software for MODFLOW pre processing post processing and parameter optimization User s manual Australian Centre for Tropical Freshwater Research Doherty J Brebber L and Whyte P 1994 PEST Model independent parameter esti mation User s manual Watermark Computing Australia Doherty J 2000 PEST Model independent parameter estimation User s manual Wa termark Computing Australia Doherty J 2001a MODFLOW ASP Using MODFLOW 2000 with PEST ASP Wa termark Computing Australia Doherty J 2001b PEST ASP upgrade notes Watermark Computing Australia Doherty J 2004 Model Independent Parameter Estimation User Manual 5th Edition Watermark Computing Australia Downloaded from http www pesthomepage org 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 59 56 57 References 401 Doherty J 2010 PEST Model independent parameter estimation V
476. ows When PMPATH is started from PM it will automatically load the model currently used by PM If the model data have been subsequently modified and a flow simulation has been performed the modified model must be re loaded into PMPATH to ensure that it can recognize the modifications 2 7 The Tools Menu 2 7 1 Digitizer The Digitizer is based on the Data Editor Using the Digitizer the user can digitize shift or delete points and assign values to the points The menu item Points in the Value menu allows the user to save delete or load points PM saves or loads points to from XYZ files An XYZ file stores the number of points the x y coordinates and the associated values of all points Refer to Section 6 2 10 for the format gt To digitize a point 1 Click the Digitize button E It is not necessary to click the button if it is already depressed 2 Click the mouse pointer on the desired position to set a point gt To shift a digitized point 2 7 The Tools Menu 177 1 Click the Digitize button E 2 Point the mouse pointer to a digitized point left click and hold down the mouse button and then move the mouse to drag the digitized point 3 Release the mouse button when the point is moved to the desired position gt To delete a digitized point 1 Click the Digitize button E 2 Hold down the Ctrl key and left click on the point to be deleted gt To assign a value to a digitized point 1 Click the Digitize b
477. p 1 Orientation Plan View x Layer 1 Columnwidth 14 7 Read Help Close Fig 4 9 The Results Extractor dialog box 244 4 Tutorials 4 6 7 Click Read Hydraulic heads in the first layer at time step 1 and stress period 1 will be read and put into the spreadsheet You can scroll the spreadsheet by clicking on the scrolling bars next to the spreadsheet Click Save A Save Matrix As dialog box appears By setting the Save as type option the result can be optionally saved as an ASCII matrix or a SURFER data file Specify the file name H1 DAT and select a folder in which H1 DAT should be saved Click OK when ready Repeat steps 3 4 and 5 to save the hydraulic heads of the second and third layer in the files H2 DAT and H3 DAT respectively Click Close to close the dialog box gt To generate contour maps of the calculated heads 1 2 3 4 Select Tools 2D Visualization The Result Selection dialog box Fig 4 10 appears Click OK to select the default result type Hydraulic Head PM displays the model grid and head contours Fig 4 11 By default PM sets 10 contour levels ranging from the minimum to the maximum value One can customize the appearance of the contour lines by using the Environment Options dialog box Refer to Section 2 9 2 for details about this dialog box To save or print the graphics select File Save Plot As or File Print Plot Select File Leave Editor or
478. particles per cell in case of DCCELL gt DCEPS NPH Minimum number of particles allowed per cell NPMIN Maximum number of particles allowed per cell NPMAX Pattern for placement of particles for sink cells NLSINK No of particles used to approximate sink cells NPSINK Critical relative concentration gradient DCHMOC OK Cancel Help Fig 2 47 The Advection Package MT3DMS dialog box e Solution Scheme MT3DMS provides five solution schemes for the advection term as described below The method of characteristics MOC scheme was implemented in the trans port models MOC 73 and MOC3D see Section 2 6 5 3 and has been widely used One of the most desirable features of the MOC technique is that it is virtually free of numerical dispersion which creates serious diffi culty in many numerical schemes The major drawback of the MOC scheme is that it can be slow and requires a large amount of computer memory when a large number of particles is required Also the computed concentrations sometimes tend to show artificial oscillations The modified method of characteristics MMOC uses one particle for each finite difference cell and is normally faster than the MOC technique At each new time level a particle is placed at the nodal point of each finite difference cell The particle is tracked backward to find its position at the old time level The concentration associated with that position is use
479. pe 10 in the dialog box and select the option Apply to the entire model then click OK to assign the value of 10 to all model cells Select File Leave Editor or click the leave editor button eel Advection Package MT3DMS x Max number of total moving particles MXPART Solution Scheme Method of Characteristics MOC x Weighting Scheme Upstream weighting Particle Tracking Algorithm First order Euler he imulation Parameters Courant number PERCEL Concentration weighting factor WD Negligible relative concentration gradient DCEPS Pattern for initial placement of particles NPLANE No of particles per cell in case of DCCELL lt DCEPS NPL No of particles per cell in case of DCCELL gt DCEPS NPH Minimum number of particles allowed per cell NPMIN Maximum number of particles allowed per cell NPMAX OK Cancel Help Fig 4 20 The Advection Package MT3DMS dialog box 4 1 Your First Groundwater Model with PM 253 Dispersion Package MT3D MT3DMS RT3D x You need to specify the following values for each layer When finished click OK to specify the longitudinal dispersivity L for each cell TRPT Horizontal transverse dispersivity Longitudinal dispersivity TRPY Vertical transverse dispersivity Longitudinal dispersivity DMCOEF The effective molecular diffusion coefficient L 2 T DMCOEF 0 0 Fig 4 21 The Dispersion Pac
480. pestctl par and svda bpa Once the parameter estimation process is complete the pestctl par file is re named to pestctl _par and svda bpa is copied to pestctl par When you click on Models PEST Parameter Estimation View Estimated Parameter Val ues the pestctl par file is displayed When you click on the Update button of Fig 2 82 the initial parameter values PARVAL of the Parameters tab are updated with the values stored in pestctl par Automatic calculation of first iteration super parameter derivatives If this box is cleared super parameter derivatives calculation takes place through finite differences in the usual manner during the first optimization iteration of the inversion process If this box is checked PEST calculates super parameter derivatives internally for the first iteration of the SVD assisted parameter esti mation process removing the necessity for any model runs to be undertaken in calculating these derivatives Computation of super parameters Super parameters can be calculated internally by PEST on the basis of sensitivi ties supplied in the Jacobian matrix 1 e the svda jco file mentioned above Four options are available here 166 2 Modeling Environment SVD on Q I 2 X This option sets SVDA EXTSUPER to 0 in the PEST control file i e the aforementioned pestctl pst file PEST will formulate super parameters through singular value decomposition of Q X where X represents the base parameter Jac
481. pointer x y z position of the mouse pointer k J Viewing Window CSS TT Ef zl il if 1 refinement of layer k refinement of row refinement of column J width of row width of column J Fig 2 3 The Grid Editor 2 Move the grid cursor to the desired cell by using the arrow keys or by clicking the mouse on the desired position The sizes of the current column and row are shown on the status bar 3 Press the right mouse button once The Grid Editor shows the Grid Size dialog box Fig 2 4 4 In the dialog box type new values then click OK gt To insert or delete a column and or a row 1 Inserting or deleting columns rows is only possible when using the Grid Editor for the first time Click the assign value button ES 2 Move the grid cursor to the desired cell by using the arrow keys or by clicking the mouse on the desired position 3 Hold down the Ctrl key and press the up or right arrow keys to insert a row or a column press the down or left arrow keys to delete the current row or column 12 2 Modeling Environment Table 2 3 Summary of the toolbar buttons of the Grid Editor Button Name Action ne Leave editor Leave the Grid Editor and return to the main menu of PM Assign value Allows the user to move the grid cursor and change the widths of grid columns and rows E Pan Moves the Viewing Window up down or sideways to display areas of the model domain which at the current viewing
482. port 00 92 Harbaugh AW 2005 MODFLOW 2005 the U S Geological Survey modular ground water model the Ground Water Flow Process U S Geological Survey Techniques and Methods 6 A16 402 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 13 74 75 76 References Higgins GH 1959 Evaluation of the groundwater contamination hazard from under ground nuclear explosives J Geophys Res 64 1509 1519 Hill MC 1990a Preconditioned Conjugate Gradient 2 PCG2 A computer program for solving groundwater flow equations U S Geological Survey Denver Hill MC 1990b Solving groundwater flow problems by conjugate gradient methods and the strongly implicit procedure Water Resour Res 26 9 1961 1969 Hill MC 1992 MODFLOW P A computer program for estimating parameters of a transient three dimensional groundwater flow model using nonlinear regression U S Geological Survey Open file report 91 484 Hill MC 1998 Methods and guidelines for effective model calibration U S Geological Survey Water Resources Investigations Report 98 4005 Hill MC Banta ER Harbaugh AW and Anderman ER 2000 MODFLOW 2000 The U S Geological Survey modular ground water model User guide to the observation sensitivity and parameter estimation processes and three post processing programs U S Geological Survey Open file report 00 184 Hoschek J and Lasser D 1992 Grundlagen der
483. portant to the estimation of different parameters and to com pare the sensitivity of hydraulic heads throughout the model to different parameters 62 MODFLOW 2000 Parameter Estimation View Scatter Diagram This menu item is available only if head observations see Section 2 6 1 14 or flow observations Section 2 6 7 3 have been defined Select this menu item to open a Scatter Diagram dialog box which is identical as the Scatter Diagram Hydraulic Head dialog box as described in Section 2 6 1 20 with two exceptions 2 6 The Models Menu 149 e The user specified observation times and observed values are given in the columns Simulation Time and Observed Value directly without interpolating to the times at the end of each stress period or time step The Calculated Value column contains the values calculated by MODFLOW 2000 i e the values are not calculated by pmp using equation 2 34 e A Result Type option appears in the Data tab The first result type is Observed values versus simulated values When the second result type Weighted ob served values versus weighted simulated values is chosen the observed and calculated values are multiplied by a weighting factor which is the square root of weight defined in the Option tab of the Head Observations Fig 4 36 or Flow Observation Fig 2 75 dialog boxes MODFLOW 2000 Parameter Estimation View Time Series Curves This menu item is available only if head observ
484. problems HCLOSE is ig nored if MXITER 1 Maximum number of inner PCG iterations IITER ITER defines the max imum number of PCG iterations for each linear solution A value of 100 is typically sufficient It is frequently useful to specify a smaller number for nonlinear problems so as to prevent an excessive number of inner iterations 2 6 The Models Menu 69 Budget Closure Criterion RCLOSE RCLOSE is the residual convergence criterion for the inner iteration The PCG algorithm computes the 12norm of the residual and compares it against RCLOSE Typically RCLOSE is set to the same value as HCLOSE If RCLOSE is set too high then additional outer iterations may be required due to the linear equation not being solved with sufficient accuracy On the other hand a too restrictive setting for RCLOSE for nonlinear problems may force an unnecessarily accurate linear solution This may be alleviated with the ITER parameter or with damping e Damping Control Damping Method Two damping methods are available Fixed Damping Value If this method is selected then the Damping Value see below is used as a constant damping parameter Cooley s method If this method is selected then the Damping Value is used for the first outer iteration nonlinear iteration The damping param eter is adaptively varied on the basis of the head change using Cooley s method as described in Mehl and Hill 87 for subsequent iterations Damping
485. provided by Rausch 99 and included in the folder Source analytical solution of the companion CD ROM This program is written in BASIC Try to use this program to compare the analytical and numerical solutions 355 5 5 Solute Transport 3 16E 1 w b uoljesjuaou0 of days ime t ion lat Fig 5 47 Comparison of the calculated breakthrough curves with different disper sivity values simu 356 5 Examples and Applications 5 5 2 Two dimensional Transport in a Uniform Flow Field Folder pmdir examples transport transport2 Overview of the Problem In this example transport of solute injected continuously from a point source in a steady state uniform flow field should be simulated The available parameters are listed below Layer thickness 10m Groundwater seepage velocity 1 3 m day Effective porosity 0 3 Longitudinal dispersivity 10m Ratio of transverse to longitudinal dispersivity 0 3 Volumetric injection rate 1m day Concentration of the injected water 1000 ppm The task is to construct a 2D model and use MT3DMS to calculate the concen tration distribution at the end of a 365 day simulation period Modeling Approach and Simulation Results A numerical model consisting of 1 layer 31 rows and 46 columns and was con structed to simulate the problem A regular grid spacing of 10 m is used for each column and row The configuration of the model is shown in Fig 5 48 The model layer is simulated as a
486. r e 4 v 1 Az y t2 y vy t1 ene ae Vy1 Ay 3 6 z t2 z1 v t1 eave vz Az where AT t t For steady state flow fields the location of the particle at time t must still be within the same cell as at time t Given any particle s starting location within a cell at time t Pollock s algorithm allows determining the particle s exit time tz and exiting point from the cell directly without having to calculate the actual path of the particle within the cell The particle tracking sequence is repeated until the particle reaches a discharge point or until a user specified time limit is reached Backward particle tracking is implemented by multiplying all velocity terms in equation 3 3 by 1 For transient flow fields in addition to the condition for steady state flow fields t and t must lie within the same time step In PMPATH each particle may be associated with a set of attributes i e the retardation factor the starting forward and backward travel times and positions If a particle is traveling across the end forward tracking or the beginning backward tracking of a time step of a flow simulation PMPATH sets t to the end or beginning time of this time step and forces the particle to wait until the flow field of the next time step forward tracking or the previous 3 1 The Semi analytical Particle Tracking Method 207 time step backward tracking is read If the end or beginning time of a
487. r 1 5 0 m day Layer 2 0 5 m day Layer 3 2 0 m day 3 Select File Leave Editor or click the leave editor button eel gt To specify the vertical hydraulic conductivity 1 Select Parameters Vertical Hydraulic Conductivity 2 Use Value Reset Matrix to enter the following data for each layer Layer 1 0 5 m day Layer 2 0 05 m day Layer 3 1 0 m day 3 Select File Leave Editor or click the leave editor button w gt To specify the effective porosity 1 Select Parameters Effective Porosity The effective porosity is used in PMPATH which will be used to define the capture zones of the pumping wells 2 Use Value Reset Matrix to enter the following data for each layer Layer 1 0 2 Layer 2 0 25 Layer 3 0 25 4 3 Aquifer System with River 291 3 Select File Leave Editor or click the leave editor button eel gt To specify the well data Select Models Modflow Well Click the button if the display mode is not Grid View Switch to Layer 3 by pressing the PgDn key twice Move the grid cursor to Well 1 press Enter or right click and set the pumping rate to 500 m day Repeat the above step with Well 2 and Well 3 6 Select File Leave Editor or click the leave editor button w AUN e Nn The last step before running the steady state simulation in this tutorial is to specify river data which is a little difficult to set up MODFLOW requires that the river data i e river stage river b
488. r Property Flow LPF and the Block Centered Flow BCF packages for formulating inter cell hydraulic conductance terms As the BCF or LPF packages require different aquifer parameters for formulating finite difference equations of groundwater flow it is important to notice the following major differences between these two packages The Block Centered Flow BCF package supports four layer types Depend on the selected layer type the required aquifer parameters of a model layer are different and listed below Layer type 0 T and S Layer type 1 HK and Sy Layer type 2 T S and Sy Layer type 3 HK Sy and S Note that S and Sy are required only for a transient flow simulation All layer types use VCONT to describe the vertical conductance between two layers The Layer Property Flow package has only two layer types confined and convertible i e convertible between confined and unconfined Independent of the selected layer type a model layer always requires HK Ss and VK or VANI The only exception is Sy which is required only if the layer is convert ible note that Ss and Sy are required only for a transient flow simulation When the Layer Property Flow package is selected the menu items Trans missivity Vertical Leakance and Storage Coefficient of the Parameters menu are dimmed and cannot be used don t need to be used Note All versions of Modflow and either BCF or LFP package can be used with PEST for estimating parameter
489. r following the in the prior information equation Coef can be specified with or without a decimal point and can be specified in scientific notation e g 3 123E 03 2 6 The Models Menu 139 e indicates multiplication e Pnamis the parameter name For aquifer parameters i e HK VK HANI VANI SS and SY Pnam is the same as PARNAM given in the Parameters tab see above For time varying parameters e g RCH WEL Pnam is a combination of PARNAM and the stress period number to which Pnam pertains For example for parameter number 2 of recharge RCH_2 in the stress period 3 Pnam RCH_2 3 If the parameter is designated as being log transformed the prior information equation may contain only one parameter name e STAT must be entered literally e Statp is the value from which the weight for prior information equation Eqnam is calculated as determined using Stat flag e Stat flag is a flag identifying how the weight for prior information equation Eq nam is to be calculated This depends both on whether the user chooses to specify the variance standard deviation or coefficient of variation and whether for log transformed parameters the user chooses to specify the statistic related to the native untransformed parameter or to the transformed parameter 1 Stat flag 0 Statp is the variance associated with Prm and is related to the native prior value Weight 1 Statp unless the parameter is defined as log transformed
490. r if the corresponding Generate box is checked The user may click on a box to check or clear it Normally we do not need to worry about these boxes since PM will take care of the settings Description gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs xi Destination File Basic Package c program files eit pmwinexamples transport transpor M __ Block Centered Flow c program files eit pmwin examples transport transpor Vv Output Control c program files eit pmwin examples transport transpor M well c program files eit pmuwin examples transport transpor Vv Solver SIP1 c program files eit pmwinexamples transport transpor M MOC3D Main Package c program files eit pmwin examples transport transpor Options J7 Check model data J Regenerate all input files I Generate input files only don t start MOC3D Cancel Help Fig 2 68 The Run Moc3d dialog box 126 2 Modeling Environment Check the model data If this option is checked PM will check the geometry of the model and the consistency of the model data as given in Table 2 6 before creating data files The errors if any are saved
491. r level to the highest contour level To change the colors correspond to the lowest or highest contour levels simply click on one of the colored buttons and select a color from a Color dialog box After clicking OK the contour colors levels in the table are updated to reflect the changes Label Defines whether a contour should be labeled The user may click on an individual box of the Label column to turn label on M or off C Click on the header to display the Contour Labels dialog box Fig 2 109 which can be used to define the display frequency of contour labels First labeled con tour line defines the first contour line to be labeled Labeled line frequency specifies how often the contour lines are labeled After clicking OK the flags in the table are Label height Specifies the appearance height of the label text It uses the same length unit as the model Label spacing Specifies the distance between two contour labels It uses the same length unit as the model e Label Format The Label Format dialog box Fig 2 110 allows the user to spec ify the format for the labels The elements of this dialog box are described below Fixed This option displays numbers at least one digit to the left and N digits to the right of the decimal separator where N is the value specified in Decimal digits i Color Spectrum x Minimum Color Maximum Color C OK Cancel Help Fig 2 108 The Color Spectrum dialog box x
492. r using the multicomponent reactive transport model PHT3D see Section 2 6 3 for details The required parameters for the selected chemical reaction type are specified by selecting MT3DMS SEAWAT Chemical Reaction see Section 2 6 2 6 No kinetic reaction is simulated Select this one to turn off the simulation of kinetic reactions First order irreversible reaction simulates radioactive decay or biodegrada tion Monod kinetics MT3D99 implements the Monod kinetics only for the dis solved phase of an organic compound First order parent daughter chain reactions can be used to model radioac tive chain reaction and biodegradation of chlorinated solvents for exam ple the transformation of perchloroethene PCE trichloroethene TCE dichloroethene DCE vinyl chloride VC The species are defined in the Species tab and the yield coefficients between species pairs are to be specified in the Stoichiometry tab of the Simulation Settings dialog box Fig 2 45 Instantaneous reaction among species MT3D99 uses the approach of Bor den and Bedient 15 and Rifai and others 102 103 to simulate the aerobic and anaerobic biodegradation of common hydrocarbon contaminants includ ing benzene touluene ethylbenzene and xylene BTEX Stoichiometric ra tios between the first species and other species are required to simulate this type of reaction and are to be specified in the Stoichiometry tab Fig 2 45 Species tab Fig 2 44 The c
493. ral Head Boundary Package Horizontal Flow Barrier Package Interbed Storage Package Recharge Package Reservoir Package River Package Streamflow Routing Package 194 2 Modeling Environment e Time Variant Specified Head Package e Well Package 2 9 The Options Menu There are five menu items in the Options menu Maps Environment Display Cell Information Display Mode and Input Method The menu item Display Cell In formation opens a Cell Information dialog box Fig 2 8 which displays the user specified data of the cell pointed by the grid cursor The menu items Display Mode and Input Method are described in Section 2 2 The use of the menu items Maps and Environment is described below 2 9 1 Map The Maps Options dialog box Fig 2 101 allows the user to display up to 5 DXF maps 3 Line maps and one geo referenced raster bitmap graphics The options in this dialog box are grouped under two tabs described below The Vector Graphics Tab The Vector Graphics Tab is used to import DXF or Line maps A DXF file contains detailed data describing numerous CAD entities An entity is a line or symbol placed on a drawing by the CAD system PM supports the following entities LINE POLY LINE POINT ARC SOLID CIRCLE and TEXT The other entities are ignored There is no size limit to the number of the acceptable entities x Vector Graphics Raster Graphics r DXF File Filename x Factor hg MEW JeAprogram fleswt360 pmwin
494. rameter or flow package the spatial extent of an adjustable parameter is defined by assigning a parameter number to the cells of interest PARNAM is a combination of that parameter number and the short name of the aquifer parameter i e HK HANI VK VANI SS SY T S or VCONT or package For example if parameter numbers 1 and 2 are specified for the Recharge package then RCH 1 and RCH_2 are assigned to PARNAM Fig 2 79 Modification of the assigned names is not allowed Active The value of an estimated parameter will only be adjusted if Active is checked Otherwise the user specified cell value will be used for the simulation When switching from the BCF to LPF or from LPF to BCF package some aquifer parameters might become unadjustable e g T S are not adjustable when using the LPF package and they will be indicated by gray background color Normally the total number of active parameters should not exceed 10 although PM allows 500 parameters Description A text describing the parameter can be entered here optional for example recharge zone one A maximum of 120 characters is allowed PARVAL is a parameter s initial value For a fixed parameter this value remains invariant during the optimization process For a tied parameter see PARTRANS below the ratio of PARVAL1 to the parent parameter s PARVAL sets the ra tio between these two parameters to be maintained throughout the optimization process For an adjustable p
495. rate inflow into the mining site for holding the head at 21 m and 2 Use the calculated steady state head as the initial hydraulic head and calculate the temporal development curve of the water level head vs time in the arti ficial lake for the case that the abstraction within the mining site is turned off Modeling Approach and Simulation Results The aquifer is simulated using five model layers 21 rows and 25 columns The thick ness of each model layer is 20 m The elevation of the top of the first model layer is 100 m A regular grid spacing of 100 m is used for each column and row The layer type 3 confined unconfined transmissivity varies is used for every layer For task 1 the cells within the mining pit in the 4th model layer are set as fixed head cells with the initial hydraulic head of 21 m The cells of all 5 layers at the west boundary are fixed head cells with the initial head h 100 m The cells of the layers 3 to 5 at the east boundary are fixed head cells with the initial head h 95 m The initial hydraulic head values at all other cells have been set at 100 m To ensure that there is no resistance to the groundwater flow within the mining pit a very high value say 1 m s is used for the vertical and horizontal hydraulic conductivities of the cells within the pit A steady state flow simulation was performed Fig 5 20 shows the two cross sections and the head contours of layer 4 It is obvious that the cells a
496. rd se lector J before the first column of the table then press the Del key Note that the user cannot manually add a parameter to the table If a parameter is deleted by mis take simply click the Cancel button to discard all changes or click the OK button to accept changes and then open the Simulation Settings MODFLOW 2000 dialog box again to recover the lost parameter The meaning of each column of the table is described below By clicking on a column header the parameters can be sorted in ascending order using the values of that column e PARNAM While editing data of a certain aquifer parameter or flow package the spatial extent of an estimated parameter is defined by assigning a parameter number to the cells of interest PM automatically assigns a PARNAM by com bining that parameter number with the short names of the aquifer parameter i e HK VK VANI HANI SS and SY or package For example if parameter num bers 1 and 2 are specified for the Recharge package then RCH_1 and RCH_2 are assigned to PARNAM Fig 2 74 Modification of the assigned names is not allowed e Active The value of an estimated parameter will only be adjusted if Active is checked Otherwise the user specified cell values will be used for the simulation Simulation Settings MODFLOW 2000 Operation Mode Parameter Estimation Parameters Prior Information Control Data Flow Package Layer Properties Flow LPF HK Parameter No 1 HK
497. reach in each segment and then computing stream flow to adjacent downstream reaches in each segment as inflow in the upstream reach plus or minus leakage from or to the aquifer in the upstream reach The accounting scheme used in this package assumes that streamflow entering the modelled reach is instantly avail able to downstream reaches This assumption is generally reasonable because of the relatively slow rates of groundwater flow Streamflow into a segment that is formed from tributary streams is computed by adding the outflows from the last reach in each of the specified tributary segments If a segment is a diversion then the specified flow into the first reach of the segment 54 2 Modeling Environment is subtracted from flow in the main stream However if the specified flow of the diversion is greater than the flow out of the segment from which flow is to be diverted then no flow is diverted from that segment Using the Data Editor a stream is defined by using the Cell by Cell or Polygon input methods to assign parameters to model cells or by using the Polyline input method and assigning parameters to vertices of the polylines along the trace of the stream The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress periods the input parameters can be different from period to period The input methods require different parame ters as described below e When usin
498. reakthrough curves at the observation borehole The numerical solution is obtained by using the 3rd order TVD Calculated concentration distribution 005 358 Comparison of the breakthrough curves at the observation borehole The numerical solution is obtained by using the upstream finite difference method ies eroria Liebe eiiean de ee ey eat bee cad 358 Calculated concentration values for one dimensional transport from a constant source in a uniform flow field 0 4 360 Calculated concentration values of hydrocarbon 362 Calculated concentration values of oxygen 05 362 Comparison of calculated concentration values of four species in a uniform flow field undergoing first order sequential transformation 364 Model domain and the measured hydraulic head values 369 Contours produced by Shepard s inverse distance method 370 Contours produced by the Kriging method 370 Contours produced by Akima s bivariate interpolation 371 Contours produced by Renka s triangulation algorithm 371 Calculation of the mean safety criterion by the Monte Carlo method 373 Local coordinates within a cell 0 0 0 ccc cc eee es 389 List of Tables 2 1 2 2 2 3 2 4 2 6 2 7 2 8 2 9 2 10 3 1 4 1 4 2 4 3 4 4 4 5 5 6 5 7 5 8 6 1 Symbols used in the present text
499. reater than zero A value of 0 001 is often adequate PHIREDSWH is a criterion for switching the calculation method of derivatives between the forward finite difference method and the central finite difference method If for the i th iteration the relative reduction in the objective func tion between successive optimization iterations is less than PHIREDSWH PEST will switch to three point derivatives calculation for those parameter groups with FORCEN Switch The relative reduction in the objective function is defined by d 1 i 1 where is the objective function calculated on the basis of the upgraded parameter set determined in the i th iteration A value of 0 1 is often suitable for PHIREDSWH If it is set too high PEST may make the switch to three point derivatives calculation too early The result will be that more model runs will be required than are really needed at that stage of the estimation process If PHIREDSWH is set too low PEST may waste an optimization iteration or two in lowering the objective function to a smaller ex tent than would have been possible if it had made an earlier switch to central derivatives calculation Note that PHIREDSWH should be set considerably higher than PHIREDSTP see below which sets one of the termination criteria on the ba sis of the relative objective function reduction between optimization iterations NOPTMAX is the maximum number of optimization iterations A value of 20 to 30 i
500. recharge pond is in the upper left corner of the grid the quarter of the pond that is simulated occupies a square area that is 16 rows long and 16 columns wide The boundaries along row 1 and along column 1 are no flow boundaries as a result of the symmetry Model layer 1 simulates the upper geohydrologic unit and is assigned a hydraulic conductivity of 5 feet per day The bottom of layer 1 is at an elevation of 20 feet The lower geohydrologic unit is simulated as model layer 2 This layer is simulated as a confined unconfined layer with constant transmissivity layer type 2 The top and bottom elevations of layer 2 are set at 10 and 0 feet respectively Because the head in this layer is always below the layer top the flow from above is limited as described by McDonald and Harbaugh 85 p 5 19 Thus there is no direct hydraulic connection between the perched layer and the lower layer but the perched heads have a direct impact on the recharge into the lower layer All cells in layer 2 are assigned a constant head of 1 foot because there is no need to simulate heads in this layer for the purpose of estimating recharge The middle geohydrologic unit is not simulated as a separate model layer because it is assumed 5 1 Basic Flow Problems 309 Cross Section infiltration pond 60 FETTER VERON pond leakage Perched groundwater 407 mound Layer Elevation in feet above arbitrary datum
501. regular shape of the interconnected pore space and the velocity variations at the microscopic level as well as the unresolved macroscopic level See Section 2 6 2 4 for details Retardation factor R For a linear isotherm R is independent of the concen tration field R is calculated by R 1 Ka 2 56 e where ne is the effective porosity and rho is the bulk density of the porous medium 2 6 5 5 MOC3D Strong Weak Flag A flag is required for each cell within the transport subgrid Where a fluid source is strong new particles are added to replace old particles as they are advected out of that cell Where a fluid sink is strong particles are removed after they enter that cell and their effect has been accounted for Where sources or sinks are weak particles are neither added nor removed and the source sink effects are incorporated directly into appropriate changes in particle positions and concentrations A strong source or sink cell is indicated by the cell value of 1 2 6 The Models Menu 123 2 6 5 6 MOC3D Observation Wells Cells of the transport subgrid can be designated as observation wells by assigning the value of 1 to the cells At each observation well the time head and concentration after each particle move will be written to the separate output file MOCOBS OUT saved in the same folder as your model data Note that this feature is to facilitate graphical post processing of the calculated data using other soft
502. remains constant during the simulation Varying the streambed conductance value shows that for this problem streambed conductance values greater than 10 ft d produce nearly the same results Annual recharge to the aquifer is 1 5 ft However the daily recharge rate varied according to a sinusoidal distribution for the first 180 days while no recharge was allowed for the following 180 days The distribution of the recharge over time is shown in Fig 5 14 Annual recharge is 1 5 feet SS MAiAKSH 8B8 i ANVAHOOM RQA amp amp i AAASLNDA recharge for analytical solution SJ recharge rate assigned to each 15 day period in model simulation ANANN op O fo _ l Recharge rate in hundreths of a foot per day MRQQQQAANM Aaa RAOGOi ALAA AAO VA VA 2 20 180 240 300 360 Time in days since start of infiltration period Fig 5 14 Distribution of recharge used for analytical solution and the model after Prudic 98 5 1 Basic Flow Problems 313 Modeling Approach and Simulation Results The aquifer is simulated using one model layer Specification of the elevations of layer top and bottom are not necessary because the layer is confined and transmis sivity and confined storage coefficient are specified directly as defined in the Layer Property dialog box The sinusoidal distribution of the recharge rate was divided into 15 day intervals for the model simulation and the rate for the middle of each in
503. requency 75 packages DE45 solver 63 Drain 39 Evapotranspiration 41 General head boundary 42 GMG solver 68 Horizontal flow barrier 44 Interbed storage 45 modflow solvers 61 PCG2 solver 65 Recharge 47 Reservoir 48 river 51 SIP solver 67 SSOR solver 67 Streamflow routing 53 Time variant specified head 58 Well 59 Wetting capability 59 parameter anisotropy 36 bulk density 38 effective porosity 37 horizontal anisotropy 36 horizontal hydraulic conductivity 36 initial amp prescribed hydraulic heads 36 specific storage 38 specific yield 38 storage coefficient 38 time 33 vertical hydraulic conductivity 37 vertical leakance 37 parameter estimation MODFLOW 2000 135 PEST 149 Parameters MODFLOW 2000 136 Parameters Menu 33 PARCHGLIM 154 parent daughter chain reactions 363 PARGP 154 PARLBND 154 PARNAM 137 PEST 153 particle location 124 particle tracking 203 219 particle tracking algorithm 91 128 particle velocity 119 Particles file format 388 PARTIED 154 PARTRANS 154 PARUBND 154 PARVAL 138 PARVALI PEST 153 pathline file format 387 pathlines 220 Paths to Simulation Program File 26 PCE sequential degradation of 114 PCG2 solver package 65 Peclet number 91 127 Perchloroethene sequential degradation of 114 PEST 2 25 395 Index 411 Control Data 167 drawdown scatter diagram 175 drawdown time curves 176 estimated parameter values 175 head scatter diagra
504. reservoir boundary is not activated If reservoir stage 2 6 The Models Menu 49 drops below the lowest land surface elevation for all cells within the specified reser voir area water exchange is not simulated between the reservoir and the underlying groundwater system In active cells water exchange between surface water and groundwater is com puted in a manner identical to the River package see Section 2 6 1 8 The Reservoir package is ideally suited for cases where leakage from or to reservoirs may be a sig nificant component of flow in a groundwater system however if reservoir stage is unknown then a more complex conceptualization would be needed in which reser voir stage would be computed as part of the simulation rather than having stage specified as model input Programs that compute the lake stages based on inflows and outflows exist for example Cheng and Anderson 16 or Council 29 Three options are available for simulating leakage between a reservoir and the underlying groundwater system The first option simulates leakage only to layer 1 the second option simulates leakage to the uppermost active cell and the third option simulates leakage to a specified layer for each active reservoir cell Inherent in the simulation of reservoirs is that the reservoir only partially penetrates an active model cell If the reservoir fully penetrates a cell the reservoir leakage will be simulated in a lower cell Thus water exchange between
505. respective residual and then squared before being assimilated into the objective function e Obgnme Obgnme is observation group to which the prior information belongs and Obgnme must be twelve characters or less in length When running PEST in the Regularization mode see Regularization tab below Obgnme of at least one of the prior information equations must be regul PEST can ac commodate multiple regularization groups Any observation group name Obgnme begins with the letters regul is considered to be a regularization group See Sec 8 2 of the PEST manual for details about multiple regular ization groups Some examples of prior information equations are given below refer to the PEST manual 37 for more details The parameter factor must never be omitted Suppose for example that a prior information equation consists of only a single term viz that an untransformed ad justable parameter named par1 has a preferred value of 2 305 and that you would like PEST to include this information in the optimization process with a weight of 1 0 If this article of prior information is given the label pil the pertinent prior information line can be written as pil 1 0 parl 2 305 1 0 pr_info If a parameter is log transformed you must provide prior information pertinent to the log of that parameter rather than to the parameter itself Furthermore the parameter name must be placed in brackets and preceded by log not
506. ric flux per unit volume and represents internal sources and or sinks of water S L71 is the specific storage coefficient of saturated porous media h L is the hydraulic head and t L is time For a three dimensional finite difference cell as shown in Fig 3 2b the finite difference form of equation 3 1 can be written as Qx2 T3 Qz1 a Qy2 T Qy1 ae Q22 a Qz1 Ay Az Ax Az Az Ay Ag Ay Az Ww s Ah ArAnA N 3 2 where Qaz Qx2 Qui Qy2 Qui and Q 2 L3T are are volume flow rates across the six cell faces Az Ay and Az L are the dimensions of the cell in the respective coordinate directions W L T is flow to internal sources or sinks within the cell and Ah L is the change in hydraulic head over a time interval of length At T Equation 3 2 is the volume balance equation for a finite difference cell The left hand side of equation 3 2 represents the net rate of outflow per unit volume of the porous medium and the right hand side is the rate production per unit volume due to internal sources sinks and storage Substitution of Darcy s law for each flow term in equation 3 2 i e Q Ah K A Az yields an equation expressed in terms of unknown heads at the center of the cell itself and adjacent cells An equation of this form is written for every cell in the mesh in which head is free to vary with time Once the system of equations is solved and the head
507. ries and the pumping wells gt To load a map 1 Select Options Map to open the Map Options dialog box 2 Right click on the first DXF File field to bring up the Map Files dialog box and then select the file BASEMAP DXF from the folder examples tutorials tutorial2 3 Check the box at the front of the DXF File field The map will be displayed only if the box is checked 4 Click OK to close the Map Options dialog box 5 Select File Leave Editor or click the leave editor button E 4 2 2 3 Step 3 Refine the Model Grid It is a good practice to use a smaller grid in areas where the hydraulic gradient is expected to be large which are normally located around the wells In PM grid re finement takes place within the Grid Editor and it is quite easy to add additional rows and columns to an existing model grid This is done by using a combination of holding down the CTRL key and using the arrow keys as follows CTRL Up arrow add a row CTRL Down arrow remove an added row CTRL Right arrow add a column 274 4 Tutorials CTRL Left arrow remove an added column It is also possible to specify the row and column spacing of individual cells by click ing the right mouse button within the cell of interest however we will not be doing that in this exercise gt To refine the model grid around the pumping wells 1 Select Grid Mesh Size to open the Grid Editor 2 Zoom in around Well 1 by clicking on
508. rix A is changed with each iteration and Gaussian elimination is required after each change This is called external iteration For a linear equation iteration is significantly faster because A is changed at most once per time step Thus Gaussian elimination is required at most once per time step This is called internal iteration e Max equations in upper part of A This is the maximum number of equations in the upper part of the equations to be solved This value impacts the amount of memory used by the solver If specified as 0 the program will calculate the value as half the number of cells in the model which is an upper limit The actual number of equations in the upper part will be less than half the number of cells whenever there are no flow and constant head cells because flow equations are Direct Solution DE45 Iteration Parameters Maximum Iterations external or internal s0 Max equations in upper patt of A 0 Max equations in lower part of A fo r te Max bandwidth of AL 0 Head change closure criterion L 001 Relaxation Acceleration Parameter 1 Printout from the Solver Problem Type All available information Cli C The number of iterations only Linear C None Nonlinear Printout Interval 1 Cancel Help Fig 2 30 The Direct Solution DE45 dialog box 64 2 Modeling Environment not formulated for these cells The solver prints the actual number of equations in the upper part
509. rization and is incorporated in PEST In its broadest sense regularization is a term used to describe the process whereby a large number of parameters can be simultaneously estimated without incurring the numerical instability that normally accompanies parameter non uniqueness Numerical stability is normally achieved through the provision of supplementary information to the parameter estimation process Such supplementary information often takes the form of preferred values for parameters or for relation ships between parameters i e prior information Thus if for a particular parameter the information content of the observation dataset is such that a unique value cannot be estimated for that parameter on the basis of that dataset alone uniqueness can nevertheless be achieved by using the supplementary information provided for that parameter through the regularization process Regularization is particularly useful in estimating values for parameters which describe the spatial distribution of some property over a two or three dimensional model domain of a ground water model The user is no longer required to subdivide the model domain into a small number of zones of piecewise parameter constancy Rather a large number of parameters can be used to describe the distribution of the spatial property and PEST s regularization functionality can be used to estimate values for these parameters To run PEST in the regularization mode select Regulariz
510. rizes the use of the tool bar buttons which are described in the following sections 3 2 3 1 Open model The Open model button J opens an existing model created by PM A model file for PM always has the extension PMS Prior to opening a model the flow simula tion must be performed By default PMPATH reads the unformatted binary files HEADS DAT and BUDGET DAT from the same folder as the loaded model Note The first time PMPATH is started from PM the model currently used by PM will be loaded into PMPATH automatically If model data has been modified and a flow simulation has been performed the modified model must be re loaded into PMPATH to ensure that it can recognize the modifications 3 2 PMPATH Modeling Environment 211 Table 3 1 Summary of the toolbar buttons of PMPATH Button Name Action E Open model Opens a model created by PMWIN Set Particle Allows the user to place particles in the model domain x Erase particle Activates the erase particle tool R Zoom in Allows the user to drag a zoom window over a part of the model domain Zoom out Forces PMPATH to display the entire model grid le A Particle color Allow the user to select a color for new particles from a color dialog box B Run particles back Execute backward particle tracking for a time length ward The product of the number of particle tracking steps and the particle tracking step length defines the time length 4 Run particles ba
511. rowth function is calculated as follows AC _ C AO Maian an e 2 52 At AOA Resi 2 2 6 The Models Menu 101 Where C ML is the substrate concentration At T is the length of a transport time step M M L is the total microbial concentration Hmaz T71 is the maximum specific growth rate of the bacterium and the half saturation constant K ML represents the substrate concentration at which the rate of growth is half the maximum rate 4 First order parent daughter chain reactions The first order parent daughter chain reactions is implemented in MT3D99 for both dissolved and sorbed phases In addition to the yield coefficients between species pairs see Section 2 6 2 1 the required parameters for each involved species are First order reaction rate coefficient for the dissolved phase T7 First order reaction rate coefficient for the sorbed phase T7 Considering the dissolved phase the changes in the concentration values of involved species within a transport time step are calculated in the following sequential order a Cc A 2 C Yi j2A C 2 53 AC k k k 1 k 1 A A OF Ypi yp AT OTL Where Cp ML is the concentration of species k At T is the length of a transport time step Ay T71 is the first order reaction rate coefficient for the dissolved phase for species k and Y _ 1 is the yield coefficient between species k 1 and k Instantaneous reaction amo
512. rs should be displayed e Contour level table The user may click on each cell of the table and modify the values or click on the column header of the table to change the values for all cells of that column Level To produce contours on regular intervals click the header of this col umn A Contour Levels dialog box allows the user to specify the contour range and interval By default this dialog box displays the lowest and high est values found in the current layer After clicking OK the contour levels in the table are updated to reflect the changes Color Defines the color of a contour line Click on the header to display the Color Spectrum dialog box Fig 3 9 which can be used to assign a grada tional change of contour colors from the lowest contour level to the highest contour level To change the colors correspond to the lowest or highest con Environment Options x Appearance Cross Sections Velocity vectors V Orient labels uphill I Visible Head Drawdown B 254 5584 2545 584 254 5584 2545 584 254 5584 2545 584 254 5584 2545 584 B 254 5584 2545 584 B 254 5584 2545 584 B 254 5584 2545 584 254 5584 2545 584 _ 254 5584 2545 504 254 5584 2545 584 254 5584 2545 584 Label Format Restore Defaults Load Save OK Cancel Fig 3 8 The Contours tab of the Environment Options dialog box of PMPATH
513. rtical hydraulic conductivity within the un saturated zone can provide a mechanism for the formation of perched ground wa ter tables The conceptual model is rectangular and consists of three geohydrologic units The upper and lower units have higher hydraulic conductivities than the middle unit Fig 5 11 There is a regional water table in which the head is below the bottom of the middle unit Natural recharge occurs over the entire area at a rate of 0 001 foot per day This recharge can percolate through the two upper units without the forma tion of a water table above the middle because the vertical hydraulic conductivity of this unit is 0 002 foot per day Recharge at a rate of 0 01 foot per day from a pond covering 6 acres 23225 m will cause a perched ground water body to form in the top two units The total pond leakage is about 2 360 cubic feet per day 66 8 m3 d The perched water table spreads out over an area much larger than the area covered by the pond This has an impact on the distribution of recharge to the lower unit The task is to calculate the long term head distribution resulting from the pond recharge Modeling Approach and Simulation Results Because of the rectangular symmetry of the system there is no flow between quad rants Therefore only one quarter of the system must be simulated The problem is simulated using a grid of 50 rows 50 columns and 2 model layers A uniform grid spacing of 16 feet is used The
514. rvoirs that include two or more areas of lower elevation separated by areas of higher elevation the filling of part of the reservoir may occur before spill ing over to an adjacent area The package can simulate this process by specifying two or more reservoirs in the area of a single reservoir Using the Data Editor reservoirs are defined by using the Cell by Cell or Poly gon input methods to assign the following parameters to model cells Reservoir Number regs Land surface elevation of the reservoir Berg L Vertical hydraulic conductivity of the reservoir bed HCrrg LT 1 Thickness of the reservoir bed Ry L Layer Indicator TRESL Parameter Number Parameter Number is used to group cells where the HCRrzs values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps The water table elevations of reservoirs are specified in the Stage Time Table of Reservoirs dialog box see below The land surface elevation within the specified area of potential inundation for each reservoir is typically defined by the average land surface elevation of individual cells within the area At cells in which reservoir stage exceeds land surface elevation within the specified reservoir area the reser voir boundary is activated Similarly wherever reservoir stage is less than the land surface elevation of a cell the
515. ry GHB package is used to simulate head dependent flow boundaries Cauchy boundary conditions where flow into or out of a GHB cell from an external source is provided in proportion to the difference between the head in the cell and the head assigned to the external source Using the Data Editor a general head boundary is defined by using the Cell by Cell or Polygon input methods to assign parameters to model cells or by using the Polyline input method and assigning parameters to vertices of the polylines along the trace of the boundary The input parameters are assumed to be constant during a given stress period For transient flow simulations involving several stress peri ods the input parameters can be different from period to period The input methods require different parameters as described below e When using the Polyline input method right click on a vertex to specify its prop erties in the General Head Boundary Parameters dialog box Fig 2 19 If the properties are assigned to one vertex only the properties of all vertices of the polyline are assumed to be the same The settings of the dialog box are described below Layer Option and Layer Number Layer Option controls how the layer num ber of a general head boundary is determined W General Head Boundary Parameters Layer Option apply to the selected polyline Assign layer number manually Parameters apply to the selected vertex Active Equivalent Hydraulic Co
516. s 2 6 1 5 MODFLOW Flow Packages Interbed Storage For steady state flow simulations this menu item is not used and is therefore dimmed Groundwater is released from storage under conditions of decreasing hydraulic head The released water volume is proportional to the compressibility of the soil matrix and water because a reduction of the hydraulic head results in an increase in the effective stress on the soil skeleton and a decrease of the water pressure In creasing effective stress on the soil skeleton results in deformation compaction of the soil matrix The Interbed Storage IBS package 78 calculates the water volume released from storage and simulates elastic and inelastic compaction of compressible fine grained beds in an aquifer due to groundwater extraction The term interbed is used to denote a poorly permeable bed within a relatively permeable aquifer Fig 2 21 The interbeds are assumed to consist primarily of highly compressible clay and silt beds from which water flows vertically to adjacent coarse grained beds To incorporate the calculation of interbed storage of a layer check the Interbed Storage flag in the Layer Property dialog box see Section 2 4 2 Using the Cell Fig 2 21 Types of fine grained beds in or adjacent to aquifers Beds may be dis continuous interbeds or continuous confining beds Adapted from Leake and Prudic 78 46 2 Modeling Environment by cell or Polygon input methods of the D
517. s However one can only estimate the required aquifer parameters of the BCF or LPF package as given above As the BCF package does the not support the required parameterization method of MODFLOW 2000 this package cannot be used with the built in model calibration capability of MODFLOW 2000 That is the user cannot estimate aquifer parameters when using BCF with MODFLOW 2000 The settings of Modflow Version and Flow Package are saved with the model i e if the model is used on another computer these settings will remain the same Table 2 5 Versions and Filenames of MODFLOW Version Filename MODFLOW 96 pmdir modflw96 Ikmt2 modflow2i exe MODFLOW 2000 pmdir mf2k mf2ki exe MODFLOW 2005 pmdir modflow2005 mf2005 exe is the folder in which PM is installed for example C Simcore PM8 pmdir 2 3 The File Menu 25 Module Models The supported modules or models are listed below Each mod ule model is associated with a program Note that some modules are optional and may not appear on the user s computer MODFLOW is groundwater flow simulation program which is used when selecting the menu item Modflow Run PMPATH isa particle tracking model also referred to as advective transport included in PM Text Viewer which can be any text editors is used to display simulation result files which are saved in ASCII MODFLOW 2000 Parameter Estimation The associated program is used when selecting the menu item MOD
518. s However values exceeding 16 in two dimensional simu lations or 32 in three dimensional simulations are rarely necessary If the random pattern is chosen NPH particles are randomly distributed within the cell If the fixed pattern is chosen NPH is divided by NPLANE to yield the number of par ticles to be placed per plane which is rounded to one of the values shown in Fig 2 49 on page 94 Minimum number of particles allowed per cell NPMIN If the number of par ticles in a cell at the end of a transport step is fewer than NPMIN new particles are inserted into that cell to maintain a sufficient number of particles NPMIN can be set to 0 in relatively uniform flow fields and a number greater than zero in diverging converging flow fields Generally a value between zero and four is adequate 130 2 Modeling Environment e Maximum number of particles allowed per cell NPMAX If the number of particles in a cell exceeds NPMAX particles are removed from that cell until NPMAX is met Generally NPMAX 2 x NPH e SRMULT is a multiplier for the particle number at source cells SRMULT gt 1 In most cases SRMULT 1 is sufficient However better results may be obtained by increasing SRMULT e Pattern for placement of particles for sink cells NLSINK is used to select a pattern for initial placement of particles to approximate sink cells in the MMOC scheme The convention is the same as that for NPLANE and it is generally adequate to set NLS
519. s The spread sheet displays a series of columns and rows which corresponds to the columns and rows of the finite difference grid The cell data are shown in the spreadsheet If the user is editing a particular package in which a cell has more than one value for ex ample the River package requires three values for each cell the parameter type can be selected from the Parameter drop down box The Column Width drop down box is used to change the appearance width of the columns of the spread sheet The cell data may be edited within the Browse Matrix dialog box The user may also assign a value to a group of cells by using the mouse to mark the cells and then enter the desired value The user may save the cell data by clicking the Save button and spec ifying the file name and the file type in a Save Matrix As dialog box There are four file types ASCII Matrix Wrap form ASCII Matrix SURFER files and SURFER files real world An ASCII Matrix file may be loaded into the spreadsheet at a later time The format of the ASCII matrix file is described in Section 6 2 1 A SURFER file has three columns containing the x y coordinates and the value of each cell If the file type is SURFER files the origin of the coordinate system for saving the file is set at the lower left corner of the model grid If the file type is SURFER files real world the coordinate system defined in the the Environment Options dialog box see Section 2 9 2 will be saved
520. s robust as ILU smoothing additional iterations are likely to be required in reducing the residuals In extreme cases the solver may fail to converge as the residuals cannot be reduced sufficiently Semi Coarsening This option controls semi coarsening in the multigrid pre conditioner The possible options and their meanings are given as follows Coarsen Rows Columns Layers rows columns and layers are all coars ened Coarsen Rows Columns rows and columns are coarsened but the layers are not Coarsen Columns Layers columns and layers are coarsened but the rows are not Coarsen Rows Layers rows and layers are coarsened but the columns are not No Coarsening there is no coarsening Typically the options Coarsen Rows Columns Layers or Coarsen Rows Col umns should be selected In the case that there are large vertical variations in the hydraulic conductivities then the option Coarsen Rows Columns should be used If no coarsening is implemented the GMG solver is comparable to the PCG2 ILU 0 solver described in Hill 59 and uses the least amount of memory Relaxation Parameter This parameter can be used to improve the spectral condition number of the ILU preconditioned system The value of relaxation parameter should be approximately one However the relaxation parameter can cause the factorization to break down If this happens then the GMG solver will report an assembly error and a value smaller than one for relax
521. s a number that acts as a flag to indicate if the charge im balance carried by a solution is to be transported If CBLOFFSET 0 the charge imbalance of solutions is transported This is achieved by adding CB_OFFSET to the charge imbalance of all solution The resulting val ues are used as the concentrations in the transport equations to calculate the redistribution of the charge imbalance If CB_OFFSET 0 the charge imbalance is not transported Default value for CB_OFFSET is 0 05 Threshold values for executing PHREEQC Changes in aqueous concentration values is the PHREEQC 2 activa tion deactivation criteria as described in the PHT3D manual At the be 2 6 The Models Menu 113 ginning of each reaction step PHT3D checks for each cell by which amount the concentration of the mobile species have changed during the previous reaction step If the change in a cell is smaller than Changes in aqueous concentration values no reactions are calculated for that cell The user should always verify that the selected value has negligible effect on the simulation outcome If the value is set to 0 PHREEQC 2 will be executed for all grid cells except fixed concentration boundaries in all reaction steps Changes in pH is the PHREEQC activation deacvtivation as described in the PHT3D manual This value is only used when greater than zero and when Changes in aqueous concentration values is greater than zero 2 6 4 RT3D 2 6 4 1 RT3D Simul
522. s are obtained the volume flow rates across the cell faces can be computed from Darcy s law The average pore velocity components across each cell face are Uri Qr1 Ne Ay Az Ur2 Qr2 Ne Ay Az Vy1 Qyi Ne Ax Az Vy2 Qy2 Me Ax Az 3 3 Ver Q21 Ne Ax Ay Vz2 Qza Ne Ax Ay where 206 3 The Advective Transport Model PMPATH Ne is the effective porosity and Uz1 Vze2 Vy1 Vy2 Vz1 and Vz2 LT are the average pore velocity components across each cell face Pollock s semi analytical particle tracking scheme is based on the assumption that each velocity component varies linearly within a model cell in its own coor dinate direction The semi analytical particle tracking algorithm uses simple linear interpolation to compute the principal velocity components at any points within a cell Given the starting location x y z of the particle and the starting time t the velocity components are expressed in the form Ua ty Ay z1 Vat Vy t1 Ay y y1 vy 3 4 vz ty A z a z T Uz1 where x1 i and z are defined in Fig 3 2b Az Ay and A T are the compo nents of the velocity gradient within the cell Az Ux2 ag vgs Ax Ay vy2 vyi Ay 3 5 Az Uz2 Vz1 Az Using a direct integration method described in Pollock 93 and considering the movement of the particle within a cell the particle location at time t is a to 21 v2 t
523. s considered insignificant under the condition DCCELL lt DCEPS Setting NPL equal to NPH causes a uniform number of particles to be placed in every cell over the entire grid i e the uniform approach No of particles per cell in case of DCCELL gt DCEPS NPH is the number of initial particles per cell to be placed at cells where the relative cell con centration gradient DCCELL is greater than DCEPS The selection of NPH depends on the nature of the flow field and also the computer memory limita tion Generally use a smaller number in relatively uniform flow fields and a larger number in relatively nonuniform flow fields However values exceed ing 16 in two dimensional simulations or 32 in three dimensional simulations are rarely necessary If the random pattern is chosen NPH particles are ran domly distributed within the cell If the fixed pattern is chosen NPH is di vided by NPLANE to yield the number of particles to be placed per plane which is rounded to one of the values shown in Fig 2 49 Minimum number of particles allowed per cell NPMIN If the number of particles in a cell at the end of a transport step is fewer than NPMIN new particles are inserted into that cell to maintain a sufficient number of particles NPMIN can be set to 0 in relatively uniform flow fields and a number greater than zero in diverging converging flow fields Generally a value between zero and four is adequate 94 2 Modeling Environment Fixed
524. s observations for which the current value of pertinent relationships is calculated by the model can be linear or nonlinear in either case derivatives of these relationships with respect to adjustable parameters are re evaluated by PEST during each optimization iteration If regularization infor mation is entirely linear there are many matrix operations carried out as part of PEST s regularization functionality which do not need to be repeated from iter ation to iteration If repetition of these calculations can be avoided in parameter estimation contexts involving many regularization constraints significant gains in efficiency can be made e Perform inter regularization group weight factor adjustment IREGADJ If this box is checked the variable MEMSAVE of the PEST control data file will be set to 1 In this case PEST takes account of both the number and sensitivities of regularization observations and prior information equations in each group in determining relative inter regularization group weighting so that the contribution made by each group to the overall set of regularization constraints is balanced The SVD SVD Assist Tab SVD Truncated Singular Value Decomposition 2 6 The Models Menu 163 Truncated singular value decomposition i e truncated SVD is another popular method of solving inverse problems Using SVD the dimensionality of parameter space is reduced to that point at which a unique solution to the parameter estim
525. s often adequate If you want to ensure that PEST termination is triggered by other criteria more indicative of parameter convergence to an optimal set or of the futility of further processing you should set this variable very high PHIREDSTP and NPHISTP are convergence criteria For many cases 0 01 and 3 are suitable values for PHIREDSTP and NPHISTP respectively If in the course of the parameter estimation process there have been NPHISTP optimization it erations for which 2 6 The Models Menu 171 erta lt PHIREDSTP 2 64 Qi being the objective function value at the end of the i th optimization iteration and min being the lowest objective function achieved to date PEST will end the optimization process e NPHINORED is the first termination criterion A value of 3 is often suitable If PEST has failed to lower the objective function over NPHINORED successive iterations the program stops e RELPARSTP and NRELPAR represent the second termination criterion If the magnitude of the maximum relative parameter change between optimization it erations is less than RELPARSTP over NRELPAR successive iterations the pro gram stops The relative parameter change between optimization iterations for any parameter is calculated using equation 3 55 For many cases a value of 0 01 for RELPARSTP and a value of 3 for NRELPAR are adequate e Output Options When the optimization process is complete one of the termi nation criteria having been
526. s used only if the Flow and transport coupling procedure is Non linear Iterative SEAWAT will stop execution after the given number iterations for the flow and transport solutions if convergence has not occurred Density change convergence criterion for coupling iterations M L This value is used only if the Flow and transport coupling procedure is Non linear Iterative If the maximum fluid density difference between two consecutive implicit coupling iterations is less than then given value SEAWAT will ad vance to the next timestep Otherwise SEAWAT will continue to iterate on the flow and transport equations or will terminate if Maximum number of non linear coupling iterations is reached Density change threshold for recalculating flow solution M L This value is used only if the Flow and transport coupling procedure is Conditional If the fluid density change between the present transport timestep and the last flow solution at one or more cells is greater than the given value then SEAWAT will update the flow field by solving the flow equation with the updated density field Length of the first transport time step FIRSTDT This is the length of the first transport timestep used to start the simulation Reference fluid density DENSEREF DENSEREF is the fluid density at the reference concentration temperature and pressure For most simulations DENSEREF is specified as the density of freshwater at 25 C and at
527. scale lie outside the Viewing Window By dragging the mouse the model grid and sitemaps will be moved in the same direction as the mouse cursor When the left mouse button is released the grid and maps will be redrawn o Zoom in Allows the user to zoom in by dragging a window over a part of the model domain Zoom out Display the entire worksheet e Rotate grid To rotate the model grid point the mouse pointer to the grid left click and hold down the mouse button and move the mouse Fal Shift grid Allows the user to move the model grid to another position To shift the model grid point the mouse pointer to the grid left click and hold down the mouse button and move the mouse Map View Switch to the Map View display mode Column View Switch to the column cross sectional display mode p g0 Row View Switch to the row cross sectional display mode Duplication If duplication is turned on the size of the current row or column on off will be copied to all rows or columns passed by the grid cursor Duplication is on when this button is depressed gt To refine a layer a row or a column 1 Refining a grid is only possible when the grid has already been saved Click the assign value button 2 Move the grid cursor to the desired cell by using the arrow keys or by clicking the mouse on the desired position 3 Press the right mouse button once The Grid Editor shows the Grid Size dialog box Fig 2 4 4
528. se the Data Editor to define subregions for which a water budget is to be calculated A subregion is indicated by a subregion number ranging from 0 to 50 A subre gion number must be assigned to each model cell The number 0 indicates that a cell is not associated with any subregion 4 Once the desired subregions are defined in the Data Editor select File Leave Editor and save the changes 5 Click OK in the Water Budget dialog box to perform the water budget calcula tion PM calculates and saves the flows in the file WATERBDG DAT as shown in Table 2 10 The unit of the flows is LT Flows are calculated for each subregion in each layer and each time step Flows are considered IN if they are entering a subregion Flows between subregions are given in a Flow Matrix The term HORIZ EXCHANGE gives the flow rate horizontally across the boundary of a subregion The term EXCHANGE UPPER gives the flow rate coming from IN or going to OUT to the upper adjacent layer The term EXCHANGE LOWER gives the flow Ne 188 2 Modeling Environment rate coming from IN or going to OUT to the lower adjacent layer For example consider EXCHANGE LOWER of REGION 1 and LAYER 1 the flow rate from the first layer to the second layer is 2 6107365E 03 m s The percent discrepancy is calculated by 100 IN OUT IN OUT 2 2 71 2 8 The Value Menu 2 8 1 Matrix Use the Browse Matrix dialog box Fig 2 95 to examine cell value
529. see Section 2 3 4 to display the global listing file MF2K GLOBAL LISTING which contains the parameter values and statistics for parameter estimation iterations the optimized value of each adjustable parameter together with that parameter s 95 confidence interval It tabulates the set of field measurements their optimized model calculated counterparts the difference between each pair and certain functions of these differences MODFLOW 2000 Parameter Estimation View Forward Run Listing File During a parameter estimation process forward runs are repeated and the run record is saved in the listing file OUTPUT DAT Listing files are overwritten during sub sequent forward model runs and thus only the listing file unique to final parameter values is available for inspection with the Text Viewer see Section 2 3 4 Parameter estimation processes are often terminated unexpectedly because the groundwater flow process of MODFLOW 2000 fails to complete a flow calcula tion due to an unsuitable parameter combination used by an estimation iteration In that case MODFLOW 2000 writes error messages to the OUTPUT DAT file and terminates the simulation It is therefore recommended to check this file when MODFLOW 2000 fails to complete the parameter estimation iterations MODFLOW 2000 Parameter Estimation View Estimated Parameter Values At the end of each optimization iteration MODFLOW 2000 writes the estimated pa rameter set to a file named
530. select the cell and then right click to set the pumping rate to 3888 m d in the Cell Value dialog box This pumping rate is equivalent to 45 l s the negative sign means that water is being extracted from the system A recharge well would have a positive sign Click the Change Stress Period button E to open a Temporal Data dialog box this allows you to select and edit the data so that different values can apply during different Stress Periods In the Temporal Data dialog box select Period 2 and click the Edit Data button The status bar displays Period 2 indicating that you are entering data for stress period 2 For each well in the system set the pumping rate to 0 Select File Leave Editor or click the leave editor button eel There are two recharge periods namely the dry season when recharge is zero and the wet season when recharge is 7 5 x 10 4m day gt To set the recharge rate 1 Select Models MODFLOW Recharge 282 4 Tutorials 2 The status bar displays Period 1 indicating that you are entering data for stress period 1 3 Set the entire grid to a uniform value for the first stress period by selecting Value Reset Matrix to open a Reset Matrix dialog box 4 In the Reset Matrix dialog box enter the following values then click OK to close the dialog box Recharge Flux LT 0 0 Layer Indicator IRCH 0 Recharge Options Recharge is applied to the highest active cell 5 Click the Ch
531. ser specified data to generate input files for MODFLOW and MODPATH An input file will be generated if it does not exist or if the corresponding Generate box is checked Normally we do not need to worry about these boxes since PM will take care of the settings Note that MODPATH 94 95 and or MODPATH PLOT 95 cannot be started from PMWIN directly In most cases however the user does not need to use these programs since PMPATH includes all their features and is far easier to use Refer to Section 6 4 for how to run MODPATH Description gives the names of the packages used in the flow model Destination File shows the paths and names of the input files of the flow model e Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start MODFLOW Check this option if the user does not want to run MODFLOW The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file MODFLOW BAT Check the model data If this option is checked PM will check the geometry of the model and the consistency of the model data as given in Table 2 6 before creating data files The errors if any are saved in the file CHECK LIS located in the same folder as the model data e OK Click OK
532. served Reserved Reserved Oo Pe WN FR The following data repeat for each borehole i e NBOREHOLES times 6 Data OBSNAM Active x y NHOBS 7 Data PR 1 PR 2 PR NLAYERS The following data repeat NHOBS times for each borehole 8 Data Time HOBS statistic weight Explanation of Fields Used in Input Instructions All data in the same record are separated by at least one space The text string PMWIN_OBSERVATION_FILE must be entered literally NBOREHOLES is the number of observation boreholes EVH default 1 for MODFLOW 2000 not used by PEST ITT default 1 for MODFLOW 2000 not used by PEST STAT_FLAG default 0 for MODFLOW 2000 not used by PEST OBSNAM name of the observation borehole max 8 characters blank and spe cial characters are not allowed Active A borehole is active if Active 1 A borehole is inactive if Active 0 x x coordinate of the borehole y y coordinate of the borehole NHOBS number of observations of a borehole PR layer proportion values for layer i NLAYERS Number of layers in the model Time Observation time HOBS observed value at Time Statistic statistic value for the observation used by MODFLOW 2000 weight weighting factor for the observation used by PEST Reserved Reserved for future use Enter 0 in the file 6 2 7 Flow Observation Files The Flow Observati
533. signed to a model cell although the STR package allows the user to assign more than one reach in different segments to the same model cell Stream Stage hs L Streambed Hydraulic Conductance C L T71 Elevation of the Streambed Top TO P str L Elevation of the Streambed Bottom BOTstr L Width of the Stream Channel Wtr L Slope of the Streambed Channel Str Manning s roughness coeff n C Parameter Number 2 6 1 10 MODFLOW Flow Packages Time Variant Specified Head For transient simulations the Time Variant Specified Head package 78 allows con stant head cells to take on different head values for each time step A time variant specified head boundary is defined by using the Cell by Cell or Polygon input methods of the Data Editor to assign the following parameters to model cells e Flag A non zero value indicates that a cell is specified as a time variant specified head boundary e Start Head h L This value is the prescribed hydraulic head of a cell at the start of the stress period e End Head he L This value is the prescribed hydraulic head of a cell for the last time step of a stress period This package does not alter the way contant head boundaries are formulated in the finite difference equations of MODFLOW It simply sets the element in the IBOUND array to a negative value for all cells where a time variant specified head boundary is s
534. solve the advection term E E 2 1 u l Injection well z E Q 1 m day E o E Kag 5 amp m i 2 o amp Observation E borehole 2 3 l 3 E 4 450 m Fig 5 48 Configuration of the model and the location of an observation borehole 1 89E 1 numerical solution analytical solution Fi trati y concentration ppm 1 E 0 is 3 65E 2 Simulation time days Fig 5 50 Comparison of the breakthrough curves at the observation borehole The numerical solution is obtained by using the 3rd order TVD scheme 358 5 Examples and Applications Fig 5 49 Calculated concentration distribution 1 63E 1 numerical solution analytical solution m concentration ppm 1 E 0 3 65E 2 Simulation time days Fig 5 51 Comparison of the breakthrough curves at the observation borehole The numerical solution is obtained by using the upstream finite difference method 5 5 Solute Transport 359 5 5 3 Monod Kinetics Folder pmdir examples transport transport3 Overview of the Problem The example problem considered in this section is adapted from Zheng 122 It involves one dimensional transport from a constant source in a uniform flow fie
535. ss Sections iV Visible IV Show grid i IV Show groundwater surface potential Exaggeration fi Projection Row Projection Column fi Minimum Elevation fo Maximum Elevation i773 Fig 3 7 The Cross Sections tab of the Environment Options dialog box of PMPATH thickness on the screen is smaller than pixel PMPATH will clear this box and turn off the display of the cross sections In this case the Visible check box will be cleared automatically Show grid Check this box to display the model grid Show Groundwater surface Potential Check this box to display the ground water surface or the hydraulic heads of the highest active cells on the cross sections e Exaggeration scaling factor for the height Use this value to change the appear ance height of the cross sections A larger exaggeration value lets PMPATH draw the projection of the pathlines on the cross section windows in greater details The exaggeration value can range from 0 01 to 1000 e Projection Row and Projection Column PMPATH uses the grid cursor Fig 3 4 to define the column and row for which the cross sectional plots should be made The grid cursor can be moved by holding down the Ctrl key and click the left mouse button on the desired position Alternatively type the row and column in the Projection Row and Projection Column edit boxes e Minimum Elevation and Maximum Elevation The visible part on the cross sec tional plots is defi
536. ssociated with the fluid of point or spatially distributed sources or sinks The concentration value of a particular source or sink is specified in the Data Editor Point sources include wells general head boundary cells fixed head cells rivers and streams Recharge is the only spa tially distributed source whereas evapotranspiration is the only sink whose concen tration can be specified The concentration of a sink cannot be greater than that of the groundwater at the sink cell If the sink concentration is specified greater than that of the groundwater it is automatically set equal to the concentration of the groundwater Therefore setting a big sink concentration value e g 1 x 10 to evapotranspiration ensures that the groundwater concentration is used for the computation Note that MT3DMS does not allow the concurrent use of the rivers and the streams This does not cause problems in any case because the Streamflow Rout ing package has all functions of the River package Menu items of this menu are dimmed if the corresponding hydraulic features given in the Models MODFLOW menu are not used checked The user may or may not specify the concentration for the sources or sinks when they are used in the flow simulation The specified concentration will be used in the transport simulation if a corresponding menu item is checked If a checked item is no longer necessary for a transport simulation simply select the item again and deactivate
537. stem with River 287 2 Refine the grid around each of the three wells by halving the size of the following rows and columns Columns 8 through 14 Rows 7 through 12 The grid should now be refined around the wells and appear similar to Fig 4 50 3 Select File Leave Editor or click the leave editor button ee 4 3 1 4 Step 4 Assign Model Data gt To define the layer properties 1 Select Grid Layer Property to open the Layer Property dialog box 2 Make sure that for layer 1 the type is set to unconfined and layers 2 and 3 are set to 3 confined unconfined Note that MODFLOW requires horizontal hy draulic conductivity for layers of type 1 or 3 and transmissivity for layers of type 0 or 2 Refer to Section 2 4 2 page 27 for details of the Layer Property dialog box 3 Click OK to close the Layer Property dialog box gt To define the model boundaries 1 Select Grid Cell Status IBOUND Modflow 2 Click the button if the display mode is not Grid View 3 Set no flow boundaries in the first layer in the areas defined by the Granite and South Granite Hills T ite Hills in SS He Granite Hills J Fig 4 50 Model grid after the refinement 288 Nn 4 Tutorials Turn layer copy on by click the layer copy button ac Layer Copy is on if the layer copy button is sunk The cell values o
538. sub region This means that the difference between total inflow and total outflow should equal the total change in storage It is recommended to read the listing file by selecting Models Modflow View Run Listing File The run listing file also contains other essential informa tion In case of difficulties this supplementary information could be very helpful If the computational accuracy is inadequate decrease the convergence criterion in the selected solver In addition to the run listing file various simulation results can be saved by checking the corresponding output terms in the MODFLOW Output Control dialog box Fig 2 36 The settings are described below e Output Terms The output terms and the corresponding result files are described below All result files are saved in the folder in which the model data are saved Hydraulic Heads are the primary result of a MODFLOW simulation Hy draulic heads in each finite difference cell are saved in the unformatted bi nary file HEADS DAT E Modflow Output Control Output Terms Output Frequency Stress period Drawdowns Time step Vv Always include the result of the first time step of Cell by cell Flow Terms a poe seeneers ram GU Always include the result of the last time step of Compaction of Individual Layers from IBS1 each stress period Preconsolidation Heads from IBS1 Predefined Head Values Echo Print of Input Values For noflow calle 999 99 Interface file to MT
539. sumes that the concentration outside of the subgrid is the same within each layer so only one concentration value is specified for each layer within or adjacent to the subgrid by using the C Outside of Subgrid table of this dialog box The values of other layers which are not within or adjacent to the subgrid are ignored Subgrid for Transport MOC3D 4 x Subgrid C Outside of Subarid Number of first layer for transport ae Number of last layer for transport hB Number of first row for transport mo Number of last row for transport phs Number of first column for transport moO o Number of last column for transport pes Fig 2 63 The Subgrid for Transport MOC3D dialog box 2 6 5 2 MOC3D Initial Concentration MOC3D requires initial concentration of each cell within the transport subgrid at the beginning of a transport simulation The values specified here are shared with MT3D 120 2 Modeling Environment 2 6 5 3 MOCS3D Advection Use the Parameter for Advective Transport MOC3D dialog box Fig 2 64 to spec ify the required data as described below Parameters for Advective Transport MOC3D xj Interpolation scheme for particle velocity In MOC3D the advection term of a solute transport process is simulated by the Method of Characteristics MOC Using the MOC scheme a set of moving particles is distributed in the flow field at the beginning of the simulation A concentration and a position in the Car
540. t 0 so that equation 2 49 is reduced to linear sorp tion equation 2 42 If the first order mass transfer rate is infinitely large the right hand side of equation 2 49 is equal to zero which also leads to lin ear sorption For very small values of 3 the left hand side of equation 2 48 becomes negligible i e there is no change in the sorbed concentration and sorption is negligible Dual domain mass transfer without sorption and Dual domain mass trans fer with sorption Dual domain means that two kinds of continuum e g a fractured medium and the porous medium exist simultaneously in the same spatial region i e the same model cells In fractured aquifers the water moves faster along fractures than it does in a rock formation and the solute transport is often controlled by advection along the fractures and dominated by dispersion in the porous block along the fractures MT3DMS uses the dual domain concept to approach extremely heteroge neous porous media or media composed of fractures and pores In this ap proach the effective porosity specified in Parameters Effective Porosity is used as the primary porosity for the pore spaces filled with mobile water i e fractures and the secondary porosity for the pore spaces filled with immobile water i e rock formation is defined in the Chemical Reaction MT3DMS dialog box Fig 2 51 The sum of the primary and the secondary porosi ties is the total porosity of the medium The exc
541. t and is given by Fick s first law 96 2 Modeling Environment z3 F D VC 2 37 where F ML T is the mass flux of solute per unit area per unit time D L T is the diffusion coefficient C M L is the solute concentration and VC ML 3L is the concentration gradient In porous media the solute mass cannot diffuse as fast as in free water because the ions must move along longer pathways through the pore space To account for this tortuosity effect an effective diffusion coefficient D must be used D w D 2 38 According to Freeze and Cherry 46 w ranges from 0 5 to 0 01 for labora tory studies of diffusion of non adsorbed ions in porous geologic materials The diffusion coefficients D of the major ions Nat K Mg t Ca t CU COs HCO so are temperature dependent and range from 1 x 107 to 2 x 10 m s at 25 C 83 104 At 5 C the coefficients are about 50 smaller The molecular diffusion coefficient is generally very small and negli gible compared to the mechanical dispersion see below and is only important when groundwater velocity is very low In MT3DMS the concentration change due to dispersion alone is solved with a fully explicit central finite difference scheme There is a certain stability criterion associ ated with this scheme To retain stability the transport step size cannot exceed an upper limit defined by equation 2 39 0 5 R Dex i Dyy i Diz Ar Ay 4z At lt 2 39
542. t box if a stress period is transient Clear the Tran sient box if a stress period is steady state 2 5 The Parameters Menu 35 Multiplier Flow MODFLOW allows the time step to increase as the simulation progresses It uses the following equations to increase the lengths of time steps as a geometric progression TSMULT 1 Aty PERLEN oorr P 4 2 3 Atm 1 TSMULT Atm 2 4 where PERLEN is the length of a stress period TSMULT is the time step multiplier N ST P is the number of time steps and Atm is the length of the m th time step within a stress period Transport Step size The transport models further divide each time step into smaller time increments called transport steps Because the explicit numerical solution of the solute transport equation has certain stability criteria associated with it the length of a time step used for a flow solution may be too large for a transport solution Each time step must therefore be divided into smaller trans port steps For explicit solutions e g when the Generalized Conjugate Gradient solver is not used in MT3DMS the transport step sizes in the table are used for the simulation Considering stability criteria the transport models always cal culate a maximum allowed transport step size Deltatmaz Usually the smallest cell containing sinks will be the one which determines Deltatma Therefore in transport simulations variable cell sizes are not always beneficial Setting the transp
543. t sorption can be represented by a first order reversible kinetic sorption defined by equation 2 48 OC C mF e c E 2 48 where 3 T7 is the first order mass transfer rate between the dissolved and sorbed phases pp M L is the bulk density of the porous medium C is the sorbed concentration and Kg L3 MT is the distribution coefficient 2 6 The Models Menu 99 that depends on the solute species nature of the porous medium and other conditions of the system Using the First order kinetic sorption option the user has the choice of specifying the initial concentration for the sorbed or immobile phase for each species To do this simply check Use the initial concentration for the nonequibrilium sorbed or immobile liquid phase and specify the concentra tion value to Jnitial concentration for the sorbed phase or Initial concen tration for the immobile liquid phase in the Chemical Reaction MT3DMS dialog box If the box Use the initial concentration for the nonequibrilium sorbed or immobile liquid phase is not checked it is assumed that the initial concentration of the sorbed or immobile liquid phase is in equilibrium with the initial concentration of the dissolved phase Equation 2 48 can be rearranged in C Pb OC ee g ae 2 49 If sufficient time is available for the system to reach equilibrium for exam ple the flow velocity of groundwater is very slow then there is no further change in C and C
544. t the end of each time step and saves it in the list ing file output dat see Table 4 2 The water budget provides an indication of the overall acceptability of the numerical solution If the accuracy is insufficient a new run should be made using a smaller convergence criterion in the iterative solver see Section 2 6 1 13 It is recommended to check the listing file by selecting Models MODFLOW View Run Listing File This file contains other further essential infor mation In case of difficulties this supplementary information could be very helpful 4 1 Your First Groundwater Model with PM 239 Table 4 1 Output files from MODFLOW File Contents path OUTPUT DAT Detailed run record and simulation report path HEADS DAT Hydraulic heads path DDOWN DAT Drawdowns the difference between the starting heads and the calculated hydraulic heads path BUDGET DAT Cell by Cell flow terms path INTERBED DAT Subsidence of the entire aquifer and compaction and precon solidation heads in individual layers path MT3D FLO Interface file to MT3D MT3DMS This file is created by the LKMT package provided by MT3D MT3DMS Zheng 1990 1998 path is the folder in which the model data are saved Table 4 2 Volumetric budget for the entire model written by MODFLOW CUMULATIVE VOLUMES Le 3 RATES FOR THIS TIME STEP L 3 T IN IN CONSTANT HEAD 209924 1410 CONSTANT HEAD 2 2174E 03 WELLS 0 0000 WELLS 0 0000 RECHARGE 254170 0160 RECHARGE
545. t we shall do in this case gt To set the initial hydraulic heads Select Parameters Initial amp Prescribed Hydraulic Heads First set the entire grid to a uniform value by selecting Value Reset Matrix Enter 16 in the Reset Matrix dialog box and click OK to exit Now set hydraulic head of the northern constant head boundary to 15 meters by first selecting the top left cell 1 1 1 with the left mouse button and then assigning a value of 15 by pressing Enter or right clicking and entering 15 in the Cell Value dialog box 5 Copy the value of 15 to the remainder of the northern boundary using the Dupli cation button and the left mouse button 6 Select File Leave Editor or click the leave editor button ee BRWN re gt To specify the time parameters 1 Select Parameters Time 2 In the Time Parameters dialog box change the Simulation Time Unit to DAYS and check that Steady State is selected in the Simulation Flow Type box 3 Click OK to leave the Time Parameters dialog box gt To specify the recharge rate 1 Select Models MODFLOW Recharge 2 Set the entire grid to a uniform value by selecting Value Reset Matrix 3 In the Reset Matrix dialog box enter Recharge Flux LT 1 0 00025 this is the mean recharge rate of the two seasons Layer Indicator IRCH 0 Recharge Options Recharge is applied to the highest active cell 4 Click OK to exit the dialog box 5 Select File L
546. tary Information 6 3 2 MODFLOW 96 Basic Package Block Centered Flow Package Density Package DEN1 Direct Solution Package DE45 Drain Package Evapotranspiration Package General Head Boundary Package Horizontal Flow Barrier Package Interbed Storage Package Output Control Preconditioned Conjugate Gradient 2 Package PCG2 River Package Recharge Package Reservoir Package Strongly Implicit Procedure Package Slice Successive Overrelaxation Package Stream Routing Flow Package Time Variant Specified Head Well Package BAS DAT BCE DAT DEN1 DAT DE45 DAT DRN DAT EVT DAT GHB DAT HFB1 DAT IBS1 DAT OC DAT PCG2 DAT RIV DAT RCH DAT RES1 DAT SIP DAT SOR DAT STR1 DAT CHD1 DAT WEL DAT 6 3 Input Data Files of the supported Model 6 3 3 MODFLOW 2000 2005 Discretization File Basic Package Zone Array File Multiplier Array File Layer Property Flow Package Block Centered Flow Package Drain Package Evapotranspiration Package General Head Boundary Package Horizontal Flow Barrier Package Interbed Storage Package Recharge Package Stream Routing Flow Package Reservoir Package River Package Time Variant Specified Head Well Package Strongly Implicit Procedure Package Slice Successive Overrelaxation Package Direct Solution Package DE45 Link Algebraic Multigrid Solver Package Preconditioned Conjugate Gradient 2 Package PCG2 Output Control Observation Process Sensitivity Process Parameter Es
547. te sian coordinate system are associated with each of these particles Particles are tracked forward through the flow field using a small time increment At the end of each time increment the average concentration at a cell due to advection alone is evaluated from the concentrations of particles which happen to be located within the cell The other terms in the governing equation i e dispersion chemical re action and decay are accounted for by adjusting the concentrations associated with each particle after the redistribution of mass due to those processes on the grid A moving particle in a ground water flow system will change velocity as it moves due to both spatial variation in velocity and temporal variations during transient flow During a flow time step advection is determined from velocities computed at the end of the flow time step Temporal changes in velocity are accounted for by a step change in velocity at the start of each new flow time step After the flow equation is solved for a new time step the specific discharge across every face of each finite difference cell is recomputed on the basis of the new head distribution and the movement of particles during this flow time step is based only on these specific discharges MOC3D provides two interpolation options linear and bilinear interpolation for calculating the spatial variation of the particle velocity from the specific dis charges Konikow and others 74 indicate that if
548. te convective modeling procedure based on quadratic upstream interpolation Computer Methods Appl Mech Engng 19 Leonard BP 1988 Universal Limiter for transient interpolation modeling of the advec tive transport equations the ULTIMATE conservative difference scheme NASA Tech nical Memorandum 100916 ICOMP 88 11 Leonard BP and Niknafs HS 1990 Cost effective accurate coarse grid method for highly convective multidimensional unsteady flows NASA Conference Publication 3078 Computational Fluid Dynamics Symposium on Aeropropulsion April 1990 Leonard BP and Niknafs HS 1991 Sharp monotonic resolution of discontinuities with out clipping of narrow extrema Computer amp Fluids 19 1 141 154 Li YH and Gregory S 1974 Diffusion of ions in seawater and in deep sea sediments Pergamon Press Math ron G 1963 Principles of geostatistics Economic Geology 58 1246 1266 McDonald MG and Harbaugh AW 1988 MODFLOW A modular three dimensional finite difference ground water flow model U S Geological Survey Open file report 83 875 Chapter Al McDonald MG Harbaugh AW Orr BR and Ackerman DJ 1991 BCF2 A method of converting no flow cells to variable head cells for the U S Geological Survey Modular Finite Difference Ground water Flow Model U S Geological Survey Open File Report 91 536 Denver Mehl SW and Hill MC 2001 User guide to the Link AMG LMG package for solving matrix equations using an algebraic multigrid solver U S G
549. ters 1 Select Parameters Time 2 In the Time Parameters dialog box change the Simulation Time Unit to DAYS 3 and select Steady State in the Simulation Flow Type box Click OK to close the Time Parameters dialog box 290 4 Tutorials The groundwater flows naturally under a gentle gradient towards the river from both sets of hills and also in an easterly direction The values of starting heads which include the required values for the fixed head cells are saved in examples tutori als tutorial3 t2sh dat We will import this file to the initial hydraulic head gt To specify the initial amp prescribed hydraulic heads 1 Select Parameters Initial amp Prescribed Hydraulic Heads 2 Select Value Matrix to open the Browse Matrix dialog box 3 Click the button select the file examples tutorials tutorial3 t2sh dat and then click OK The data will appear in the Browse Matrix dialog box click OK to close this dialog box and return to the Data Editor The data is now loaded into layer 1 4 Turn on layer copy by pressing down the layer copy button 5 Move to the second layer and the third layer Now the data of layer is copied to the second and third layers 6 Select File Leave Editor or click the leave editor button w gt To specify the horizontal hydraulic conductivity 1 Select Parameters Horizontal Hydraulic Conductivity 2 Use Value Reset Matrix to enter the following data for each layer Laye
550. th a tran sient simulation The transient simulation is run for one stress period with a length of 500 000 days The stress period is divided into 50 time steps with a time step multiplier of 1 3 The first time step is 0 3 days and the last time step is 115 385 days The specific yield is 20 percent and the confined storage coefficient is 0 001 The PCG2 solver is used and cells are activated by comparison of the wetting thresh old to heads in underlying cells The head change criterion for closure is 0 001 foot and the residual change criterion is 10 000 cubic feet the wet ting threshold is 0 5 foot the wetting factor is 0 5 and the wetting iteration interval is 1 Fig 5 10 shows simulated water table heads along row 1 at several times during the transient sim ulation Steady state conditions were reached at the 44th time step of the transient simulation as indicated by storage flow terms being zero see the simulation listing file OUTPUT DAT Simulated Water Table Distance from center of pond in feet Steady State 190 days sss 7O8days eee 2630 days Fig 5 10 Simulated water table along row 1 beneath a leaking pond after 190 708 2630 days and steady state conditions 308 5 Examples and Applications 5 1 5 Perched Water Table Folder pmdir examples basic basic5 Overview of the Problem This example is adapted from the the third test problem of the BCF2 package Mc Donald and others 86 Contrasts in ve
551. th the Block Centered Flow BCF package When Vertical Anisotropy of a layer in the Layer Property dialog box Fig 2 14 is VK the cell by cell vertical hydraulic conductivity of that layer is used in the simulation When Vertical Anisotropy is VANI the cell by cell vertical anisotropy of the layer is used 2 5 7 Effective Porosity If the total unit volume V of a soil matrix is divided into the volume of the solid portion V and the volume of voids V the porosity n is defined as n V V Ef fective porosity with the respect to flow through the medium is normally smaller than porosity because part of the fluid in the pore space is immobile or partially im mobile This may occur when the flow takes place in a fine textured medium where adhesion i e the attraction to the solid surface of the porous matrix by the fluid molecules adjacent to it is important On a more macroscopic scale the effective porosity also has to accommodate the fact that unresolved conductivity variations lead to a reduction of effective porosity Transport models for example PMPATH or MT3DMS use effective porosity to calculate the average velocity of the flow through the porous medium If a dual porosity system is simulated by MT3DMS effective porosity should be specified as the portion of total porosity filled with mobile water and the immobile porosity is defined through Models MT3DMS Chemical Reaction A summary of representa tive porosity valu
552. the button and then dragging a box around the area of Well 1 Click the I button and click on the cell containing Well 1 4 Divide this column into three by adding two additional columns with CTRL Right arrow followed by CTRL Right arrow 5 Divide the row also into three by adding two additional rows with CTRL Up arrow followed by CTRL Up arrow You should see dashed lines where the new rows and columns will be placed W 6 Zoom out by pressing the 4 button You will notice that the rows and columns added extend throughout the model domain and form part of the fine discretiza tion around some of the other wells 7 Repeat the above refinement around Well 2 to Well 9 remember some of the discretization has already been done when you added rows and columns around Well 1 8 At this stage the model cells change from a size of 167 m to 500 m abruptly In order to have a more gradual size change we need to half the size of the following rows and columns again using the CTRL key and the arrow keys Columns 3 and 11 Rows 7 9 10 12 17 and 19 Upon completion of the refinement your grid should look like that in Fig 4 44 9 Select File Leave Editor or click the leave editor button w 4 2 2 4 Step 4 Assign Model Data The Data Editor is accessed each time when spatial data such as recharge hydraulic conductivity etc need to be input to the model The format and commands of the Data Editor are the same for each param
553. the aquifer It depends on the material and characteristics of the streambed itself and the imme diate environment Since the STR package requires the input of stream hydraulic conductance C str to each reach of a stream the input param eters at active vertices are linearly interpolated or extrapolated to each cell along the trace of the polyline and C str is obtained by K strs L Wer oe Topstr Bot str oe where L is the length of the stream within a cell Stream Stage hs L is the head in the stream In a model cell containing a stream reach the leakage rate Q str between the reach and groundwater is calculated by equations 2 23 and 2 24 By default MODFLOW saves the calculated leakage rates in the BUDGET DAT which can be used for water balance calculations Os Cotr he h if h gt Bote 2 23 Qstr Cstr i hs Botstr if h lt Bot str 2 24 Slope of the Streambed Channel Sstr and Manning s roughness coeff n C These parameters are used only when the option Calculate 56 2 Modeling Environment stream stages in reaches is selected To obtain the stream stage the stream water depth dstr is calculated using the Manning s equation under the assumption of a rectangular stream channel The calculated water depth is added to the streambed top to get the stream stage The Manning s equation for a rectangular stream channel is Q 3 5 n C Wstr str 2 25 dstr where Q L T
554. the cell 2 Click on the J button and select a color from a Color dialog box gt To Change the color using the Color Spectrum dialog box 1 Click the header button Color A Color Spectrum dialog box appears Using the Color Spectrum dialog box the color of each layer can be automatically assigned to get a gradational change from one color to another 2 In the Color Spectrum dialog box click the Minimum Color button to display a Color dialog box In the Color dialog box select a color and click OK Repeat this procedure for the Maximum Color button 3 In the Color Spectrum dialog box click OK A gradation of colors from the minimum to the maximum is assigned to each layer 222 3 The Advective Transport Model PMPATH Particle Tracking Time Properties Fig 3 13 The Pathline Colors tab of the Particle Tracking Time dialog box Particle Tracking Time Properties 2 2 9 Evapotranspiration Fig 3 14 The RCH EVT Options tab of the Particle Tracking Time dialog box The RCH EVT Options Tab The RCH EVT Options tab 3 14 provides two options e Recharge The option is disabled if recharge is not used MODFLOW treats recharge as an internal distributed source of a cell and does not assign it to any of the six cell faces The distributed source approximation is usually only appropri ate for two dimensional areal flow models The flow velocity across the top face of a cell in the top model layer is
555. the contour level table e Orient label uphill If this box is checked the contour labels are displayed so that they are always oriented uphill i e oriented towards places with higher cell values e Ignore inactive cells If this box is checked the data of inactive cells will not be used for creating contours e Parameter When editing a particular package in which a cell has more than one value for example the River package requires three values for each cell the user can select the parameter type from this drop down box PM uses the data associated with the selected parameter type to create contours e Contour level table The user may click on each cell of the table and modify the values or click on the column header of the table to change the values for all cells of that column Level To produce contours on regular intervals click the header of this col umn A Contour Levels dialog box allows the user to specify the contour range and interval By default this dialog box displays the lowest and high 2 9 The Options Menu 201 est values found in the current layer After clicking OK the contour levels in the table are updated to reflect the changes Line and Fill Define the color of a contour line and the fill color between two contour lines Click on the headers Line or Fill to display the Color Spectrum dialog box Fig 2 108 which can be used to assign a gradational change of contour colors from the lowest contou
556. the grid cursor from the upper left cell 1 1 1 to the lower left cell 1 30 1 of the model grid The value of 1 has now been duplicated to all cells on the west side of the model Move the grid cursor to the upper right cell 1 1 30 by clicking on this cell Move the grid cursor from the upper right cell 1 1 30 to the lower right cell 1 30 30 The value of 1 has now been duplicated to all cells on the east side of the model Turn on layer copy by clicking the layer copy button ac Layer copy is on if the layer copy button is depressed The cell values of the current layer will be copied to other layers if model layer is changed while layer copy is on Layer copy can be turned off by clicking the layer copy button again Move to the second layer and then to the third layer by pressing the PgDn key twice The cell values of the first layer are copied to the second and third layers Select File Leave Editor or click the leave editor button w The next step is to specify the geometry of the model gt To specify the elevation of the top of model layers 1 Ww Select Grid Top of Layers TOP A Top of Layers TOP dialog box appears and asks if the layer bottom elevation should be used for the layer top elevation In the Top of Layers TOP dialog box click No PM displays the model grid Move the grid cursor to the first layer if it is not in the first layer Select Value Reset Matr
557. the status of the model data of each stress period The boxes in the Data Status column have three states B Model data has been specified and will be used for the simulation O Model data has been specified but will not be used The model data from the previous stress period will be used for the simulation Q Model data has not been specified The model data from the previous stress period will be used for the simulation Click on the Data boxes to toggle between and O Fig 2 10 shows an example in which the model data for the periods 1 3 4 are specified The specified data of the first period will be used throughout the first three periods The data of the fourth period will be used for the rest of the simulation The model data of the third period has been specified but will not be used for the simulation since the Data Status is 0 2 3 The File Menu 21 Temporal Data x To edit the model data for a specific stress period select a period from the table below then press Edit Data Edit Data m Data Status a im a Copy Data D i 0 Close mi m Help Fig 2 10 The Temporal Data dialog box e Edit Data To edit model data for a particular stress period select a row of the table and click the Edit Data button After having specified the model data of a stress period the Data status changes to B e Copy Data To copy model data from one stress period to ano
558. the table If a parameter is deleted by mis take simply click the Cancel button to discard all changes or click the OK button to Simulation Settings PEST Operation Mode Parameter Estimation X Parameter Groups Prior Information Regularization SVD SVD Assist Control Data Modflow Version MODFLOW 2000 MODFLOW 2005 Flow Package Layer Properties Flow LPF Description PARVAL Minimum Maximum PARTRANS HK Parameter No 1 0 0003 0 000003 0 03 Log transformed HK Parameter No 3 0 00004 0 000002 Log transformed SS Parameter No 1 0 000026 2 60001E 07 2 60001E 03 Log transformed SS Parameter No 3 0 000004 4E 08 0 002 Log transformed RCH Parameter No 1 1 9E 08 9 99992E 11 0 00001 None RCH Parameter No 2 9 5E 09 1 50001E 10 0 00001 None RIV Parameter No 1 1 2 0 01 100 Log transformed WEL Parameter No 1 1 1 4 0 011 None VK Parameter No 2 0 0000001 2 00001E 09 2 00001E 05 Log transformed ANA Cancel Help Fig 2 79 The Simulation Settings PEST dialog box 2 6 The Models Menu 153 accept changes and then open the Simulation Settings PEST dialog box again to recover the lost parameter The meaning of each column of the table is described below By clicking on a column header the parameters can be sorted in ascending order using the values of that column PARNAM While editing data of a certain aquifer pa
559. ther 2 3 The File Menu 2 3 1 New Model Select New Model to create a new model A New Model dialog box allows the user to specify a filename on any available folder or drive for the new model A PM model must always have the file extension pm5 which has been kept consistent since PMWIN version 5 All file names valid under the MS Windows operating system with up to 120 characters can be used It is a good idea to save every model in a separate folder where the model and its output data will be kept This will also allow the user to run several models simultaneously multitasking 2 3 2 Open Model Use Open Model to load an existing PM model Once a model is opened PM dis plays the filename of the model on the title bar 2 3 3 Convert Model A Convert Models dialog box appears after selecting this menu item The options in this dialog box are grouped under 4 tabs PMWIN 4 x MODFLOW 88 96 22 2 Modeling Environment PMWIN 4 x MODFLOW 88 96 MODFLOW 2000 2005 Telescoping Flow Model PMWIN 4 x Model mall Click the open file button to select a PMWIN4 x model Refinement factor for columns Refinement factor for rows Fig 2 11 The Convert Model dialog box MODFLOW 2000 2005 and Telescoping Flow Model Fig 2 11 The tabs are de scribed below In addition the user can specify refinement factors for both column and row directions In this way one can load or create a model with a higher reso
560. tial Permissible values of SVDA_SCALADJ are 4 3 2 1 0 1 2 3 and 4 No base parameter scal ing is undertaken if SVDA_SCALADJ is set to zero Save Multiple BPA files If this box is checked SVDA_MULBPA in the PEST control file i e pestctl pst is set to 1 meaning that a series of BPA files will be recorded in the course of the parameter estimation process Each BPA file contains base parameter values as estimated during subsequent optimization iterations i e svda bpa 0 contains the initial base parameters svda bpa contains the base parameters after the first optimization iteration and so on In addition a final BPA file i e svda bpa will created at the end of optimization iterations Note that not all optimization iterations will be represented in this sequence only those iterations will be rep resented where base parameters are improved from those previously achieved during the current parameter estimation process In normal operation when the parameter estimation process is complete PEST undertakes a single model run using optimized parameters before terminating execution thus model input and output files contain best fit parameter values and corresponding best fit model outputs This is not possible when undertak ing SVD assisted parameter estimation However based on the contents of the svda bpa file which is copied to PESTCTL PAR by PM at the end of the pa rameter estimation process the user can carry out su
561. tical solution to describe the drawdown with time during pumping with a well in a leaky confined aquifer In addition to the assumptions in the Theis solution the analytical solution requires two assumptions the hydraulic head in the overlying or underlying aquifer is constant during pumping in the leaky confined aquifer and the rate of leakage into the pumped aquifer is proportional to drawdown In this example a pumping well withdraws water at a constant rate from the leaky confined aquifer The drawdown of the hydraulic head is monitored with time at a borehole 55 m from the pumping well The borehole is located in the leaky confined aquifer The initial hydraulic head is 8 m everywhere Specific yield and effective porosity are 0 1 The other aquifer parameters are given in Fig 5 28 The analytical solution for this case is given in Table 5 4 Pumping rate Q 0 004 m3 s impervious K 1 0E5 m s Ky 1 0E 6 m s S 3 75E 4 Overlying aquifer K 1E 7 mis Ky 1 5E 8 mis 1 5E4 Aquitard K 2 3E 4 m s Kv 2 3E5 mis 7 5E4 Leaky confined aquifer 10m impervious K horizontal hydraulic conductivity Kv vertical hydraulic conductivity S confined storage coefficient Fig 5 28 Configuration of the leaky aquifer system and the aquifer parameters 332 5 Examples and Applications The task is to construct a numerical model calculate the drawdown curve at the borehole and compare it with the Hantush Jacob s
562. timation Process Head Observation Package Observed flows to features represented by the Drain package Observed flows to features represented by the General Head Boundary package Observed flows to features represented by the River package Observed flows to features represented by the Streamflow Routing package Observed flows to features represented by the Time Variant Specified Head package DISCRET DAT BAS6 DAT ZONE DAT MULTIPLE DAT LPF6 DAT BCF6 DAT DRN6 DAT EVT6 DAT GHB6 DAT HFB6 DAT IBS1 DAT RCH6 DAT STR6 DAT RES1 DAT RIV6 DAT CHD6 DAT WEL6 DAT SIP DAT SOR DAT DE45 DAT LMG DAT PCG2 DAT OC DAT OBS_MAIN DAT SEN DAT PES DAT HOB DAT DROB DAT GBOB DAT RVOB DAT STOB DAT CHOB DAT 6 3 4 MODPATH and MODPATH PLOT version 1 x Main data file MAIN DAT 393 Other files required by MODPATH such as RIV DAT or WEL DAT are the same as those of MODFLOW 88 96 394 6 Supplementary Information 6 3 5 MODPATH and MODPATH PLOT version 3 x Main data file MAIN30 DAT Other files required by MODPATH such as RIV DAT or WEL DAT are the same as those of MODFLOW 88 96 6 3 6 MOC3D Main MOC3D Package MOCMAIN DAT Source Concentration in Recharge MOCCRCH DAT Observation Well File MOCOBS DAT Other files required by the flow simulation such as RIV DAT or WEL DAT are the same as those of MODFLOW 88 96 6 3 7 MT3D Advection Package MTADV1 DAT Basic Transport Package MTBTN1I DAT Chemical Reaction Packag
563. tion 15m Width of each cell _ 50 m 400 m 400 m Fig 5 45 Model grid and boundary conditions 5 4 Geotechnical Problems 353 Fig 5 46 Distribution of the land Mu subsidence maximum 0 11 m 354 5 Examples and Applications 5 5 Solute Transport 5 5 1 One dimensional Dispersive Transport Folder pmdir examples transport transport1 Overview of the Problem This example demonstrates the use of the numerical transport model and compares the numerical results with an analytical solution A uniform flow with a hydraulic gradient of 0 2 exists in a sand column The hydraulic conductivity of the sand column is 100 m d The effective porosity is 0 2 The longitudinal dispersivity is 1 m A pollutant mass of 1 gram is injected into the sand column instantaneously The task is to construct a one dimensional numerical model and calculate the breakthrough curve time series curve of concentration at 20 m downstream of the injection point Calculate the breakthrough curve by using a longitudinal dispersivity of 4 m and compare these two curves Will the peak arrival time of the concentration be changed if only the longitudinal dispersivity is changed Modeling Approach and Simulation Results The numerical model of this example consists of one layer one row and 51 columns The thickness of the layer and the width of the row and column is m To obtain a hydraulic gradient of
564. tion MOC3D dialog box Fig 2 65 to specify the required data for each model layer as described below Simulate Dispersion Check this option if dispersion should be included in the simulation First order decay rate A T typically represents radioactive decay of both the free and sorbed solute A radioactive decay rate is usually expressed as a half life 12 The half life is the time required for the concentration to decrease to one half of the original value The decay rate A is calculated by 122 2 Modeling Environment Dispersion Chemical Reaction MOC3D x Vv Simulate Dispersion First order decay rate 1 T 00027 Effective molecular diffusion coefficient L 2 T 0 kes Longitudinal Horizontal Vertical transverse Retardation dispersivity L dispersi IL dispersivity L factor 1 10 Al 2 2 10 1 2 if it Fig 2 65 The Dispersion Chemical Reaction MOC3D dialog box In2 yas 2 55 t 2 Effective molecular diffusion coefficient L T describes the diffusive flux of a solute in water from an area of greater concentration toward an area where it is less concentrated Refer to Section 2 6 2 4 page 94 for more about the molecular diffusion coefficient and dispersivity Longitudinal dispersivity az L horizontal transverse dispersivity ary L and vertical transverse dispersivity arv L describe the spreading of the solute concentration in groundwater caused by the ir
565. tion gives the names of the packages used in the model Destination File shows the paths and names of the input files of the model Options Regenerate all input files Check this option to force PM to generate all input files regardless the setting of the Generate boxes This is useful if the input files have been deleted or overwritten by other programs Generate input files only don t start MT3DMS Check this option if the user does not want to run MT3DMS The simulation can be started at a later time or can be started at the Command Prompt DOS box by executing the batch file MT3DMS BAT Use Legacy Name File Format e g MT3D99 The Name File of later ver sions of MT3DMS uses the same format as MODFLOW 2000 However old versions of MT3D MT3DMS and its variants such as MT3D99 use an older format Check this box if you are running MT3D99 or older versions of MT3DMS OK Click OK to generate MT3DMS input files In addition to the input files PM creates a batch file MT3DMS BAT in the model folder When all input files are generated PM automatically runs MT3DMS BAT in a Command Prompt window DOS box During a simulation MT3DMS writes a detailed run record to the file OUTPUT MTM saved in the model folder See Section 2 6 2 12 on page 104 for details about the output terms Run SEAWAT Basic Package Block Centered Flow BCF6 Destination File c simcore pmwin8 examples transport transport8 bas c simcorespmwin8 examples transp
566. tion of the ET surface exceeds the ET extinction depth d and 3 In between these two extremes evapotranspiration varies linearly with the ground water table elevation These assumptions can be expressed in the equation form Rer Rerum if h gt hs Rgr 0 f h lt h d 2 7 h h d Rer Reru if hs d lt h lt hs where Rpr LTT is the evapotranspiration rate per unit surface area of groundwa ter table The evapotranspiration flow rate Q gr LT t drawn from a model cell is Qer Rer DELR DELC 2 8 where DELR DELC is the map area of a model cell Q gr is drawn from only one cell in the vertical column beneath the map area The Evapotranspiration package provides two options for specifying the cell in each vertical column of cells where evapotranspiration is drawn from 42 2 Modeling Environment 1 Evapotranspiration is always drawn from the top layer of the model 2 Vertical distribution of evapotranspiration is specified in the Layer Indicator Ar ray Ipr defines the layer where evapotranspiration is drawn from the ground water table elevation In either case the Q gr has no influence on the simulation if the designated cell is either a no flow inactive cell or a constant head cell You can select an option in the Evapotranspiration Package dialog box The layer indicator array is needed only when the second option is used 2 6 1 3 MODFLOW Flow Packages General Head Boundary The General Head Bounda
567. tion time limit is reached This option is avail able only if the simulation mode Pathlines use transient flow fields is se lected In PMPATH the starting time of each particle is always the beginning of the time step defined in Current Time For the forward particle tracking scheme the simulation time limit is the end of a transient flow simulation For the backward particle tracking scheme on the other hand the simulation time limit is the beginning of the simulation Backward particle tracking will not work if this stop option is checked and particles are started from the be ginning of a transient flow simulation In this case particles will be stopped immediately after the start Note that PMPATH cannot start backward parti cle tracking from the end of a transient flow simulation rather PMPATH can only start particles from the beginning of the last simulation time step If the simulation time limit is reached and this option is not checked PMPATH cal culates flowlines by assuming that the flow field of the first or last time step is steady state The Pathline Colors Tab Normally the color of each pathline is the same as the color of each particle How ever it is sometimes useful when the colors of pathlines are distinguished by layers instead of particles There are two ways to change the color of each layer gt To change the color individually 1 Click on a colored cell of the table Fig 3 13 a Zl button appears in
568. tions involving several stress periods the in put parameters can be different from period to period Note that the user may move to other layers within the Data Editor and examine the grid configuration in each layer although the values are specified for each vertical column of cells e Recharge Flux Ip LT e Layer Indicator Irc e Parameter Number Parameter Number is used to group cells where the Ir values are to be estimated by the parameter estimation programs PEST Section 2 6 8 or MODFLOW 2000 Section 2 6 7 Refer to the corresponding sections for parameter estimation steps MODFLOW uses Ip to calculate the recharge flow rate Qr L T applied to the model cell Qr Ir DELR DELC 2 15 where DELR DELC is the map area of a model cell In MODFLOW the recharge rate Qp is applied to a single cell within a vertical column of cells In the simplest situation the water table is located in the top layer of the model the top layer is designated as unconfined and an array of Recharge Flux Ip is specified for that layer Problems may arise when the water table cuts across layers To solve this kind of problems the Recharge package provides three options for specifying the cell in each vertical column of cells that receives the recharge The user can select an option from the Recharge Package dialog box Fig 2 22 1 Recharge is only applied to the top grid layer 2 Vertical distribution of recharge is specified i
569. tions of the head observation boreholes and their associated observed measurement data in a Head Observation dialog box see Section 2 6 1 14 on page 70 for details When this menu item is selected and checked the Head Observation package of MODFLOW 2000 will use the head observation data for the parameter estimation If you do not want to use the Head Observation package and the head observation data select the menu item again and click the Deactivate button 2 6 7 3 MODFLOW 2000 Parameter Estimation Flow Observations This menu is used for specifying the flow observation data associated with drain general head boundary river or constant head boundary cells Each sub menu is en abled only if the corresponding flow package is in use When a sub menu is selected and checked its flow observation data will be used for the parameter estimation If the user does not want to use the flow observation data select the sub menu again and click the Deactivate button 142 2 Modeling Environment Flow Observation River x Group Number Flow Observation Options Multiplicative Factor 1 Group Number f0 j Position Layer Row Column 1 6 11 Fig 2 75 The Flow Observation River dialog box Flow observations are defined by assigning parameters to model cells using the Flow Observation dialog box Fig 2 75 of the Data Editor The dialog box consists of two tabs as described below The Group Number Ta
570. tno wre E Se Rte a ote Fs 210 3 2 3 1 Open modelis srann tia gia A EA 210 Contents IX 32 3 2 Set particle ss is aces satan a S 211 3 2 3 3 Efase Particle messien dats ees Ge bea ae 213 32 34 ZOOM coe aaa ede ee ee 213 32 35 Zoom OUT s eea a E o OREN Atlee TS bs 213 3 2 3 0 Particl Color a3 csseue eenn o a A ASE ks 214 3 2 3 7 Run Particles Backward 0 214 3 2 3 8 Run Particles Backward Step by Step 214 3 2 3 9 Stop Particle Tracking 0 214 3 2 3 10 Run Particles Forward Step by Step 214 3 2 3 11 Run Particles Forward 004 215 3 3 PMPATH Options Menu 0 0 00 e eee eee eee 215 333 1 Environment osser ccs ese Mig noes dads ote da eek 215 3 3 2 Particle Tracking Time 0 0 ce eee ee eee eee 219 33 3 J MApS asc ie ee eee poate awew eae ean UN S EEO 223 3 4 PMPATH Output Piles s vos e55 c ee ened be coin Bee eee as 224 SAA Plots suigtent tie sani ht Gen a iit com aa atte se eae bt 224 3 4 2 Hydraulic Heads 0 2 eee eee eee 225 3 4 3 Drawdowns 0 cece cece cet eee eens 225 3 4 4 Flow Velocities 0 0 0 ccc enerne eren 225 Sided Particles rea a ate tae Pe ea eo a eee Geers 225 Tutorials nne a eA esa pat at cet abet a da hehe 227 4 1 Your First Groundwater Model with PM 227 4 1 1 Overview of the Hypothetical Problem 227 4 1 2 Runa Stea
571. to 0 This means that these two boreholes are screened at the first layer For boreholes 3 and 4 set the proportion value of the second layer to 1 and other layers to 0 For boreholes 5 and 6 set the proportion value of the third layer to and other layers to 0 2 Click OK to close the dialog box 4 1 3 1 Perform Transport Simulation with MT3DMS MT3DMS requires a cell status code for each model cell which indicates whether 1 solute concentration varies with time active concentration cell 2 the concentra tion is kept fixed at a constant value constant concentration cell or 3 the cell is an inactive concentration cell Use 1 for an active concentration cell 1 for a constant concentration cell and 0 for an inactive concentration cell Active variable head cells can be treated as inactive concentration cells to minimize the area needed for transport simulation as long as the solute concentration is insignificant near those cells Similar to the flow model you must specify the initial concentration for each model cell The initial concentration value at a constant concentration cell will be kept constant during a transport simulation The other concentration values are used as starting values in a transport simulation gt To assign the cell status to MT3DMS 1 Select Grid Cell Status ICBUND MT3D MT3DMS For the current example we accept the default value 1 for all cells Concentration Observation xj Observations
572. tral difference method to cal culate the derivatives In this case twice as many model runs as there are parameters within the group will be required however the derivatives will be calculated with greater accuracy and this will probably have a beneficial effect on the performance of PEST FORCEN Switch Derivatives calculations for all adjustable group mem bers will begin using the forward difference method switching to the central method for the remainder of the estimation process after the relative objective function reduction between successive iterations is less than PHIREDSWH as defined in the Control Data below Experience has shown that in most instances the most appropriate value for FORCEN is Switch This allows speed to take precedence over accuracy in the early stages of the optimization process when accuracy is not critical to objective 2 6 The Models Menu 157 function improvement and accuracy to take precedence over speed later in the process when realization of a normally smaller objective function improvement requires that derivatives be calculated with as much accuracy as possible espe cially if parameters are highly correlated and the normal matrix thus approaches singularity e DERINCMUL If a three point derivatives calculation is employed the value of DERINC is multiplied by DERINCMUL Set DERINCMUL to a value of 1 0 if the user does not wish the parameter increment DERINC to be changed Alter natively if
573. truct the numerical model and use PMPATH to compute the capture zone of the pumping well Based on the calculated groundwater flow field we will use MT3DMS to simulate the contaminant transport We will show how to use PEST to calibrate the flow model and finally we will create an animation sequence displaying the development of the contaminant plume To demonstrate the use of the transport models we assume that the contami nant is dissolved into groundwater at a rate of 1x104 ug s m The longitudinal and transverse dispersivity values of the aquifer are 10 m and 1 m respectively The distribution coefficient for the linear equilibrium sorption is 0 000125 The bulk den sity of the porous medium is 2000 kg m The initial concentration molecular diffusion coefficient and decay rate are assumed to be zero We will calculate the concentration distribution after a simulation time of 3 years and display the break through curves concentration time series at two points X Y 290 310 390 310 in both units no flow boundary E E D pumping well L L lt x gt contaminated area Fa E D 5 _ unit 1 T pumping well lt unit 2 S I5 5 fo oj 2 2 T E g Q Q Sa a 1 no mo g fhan no flow boundary lt 580 m 5 Fig 4 1 Configuration of the hypothetical model 4 1 Your First Groundwater Model with PM 229 4 1 2 Runa Steady State Flow Simulation Six main steps must b
574. ts dialog box 3 Click OK to import the hydraulic head it is the default result type from the first time step of the first stress period 4 4 2 Unconfined Aquifer System with Recharge 281 Select File Leave Editor or click the leave editor button ee We now need to change from a steady state simulation to a transient simulation In the transient simulation there are two stress periods one of 240 days when pumping is occurring and no recharge and the other of 120 days when there is recharge only It is possible to have different conditions for each stress period as will be demonstrated below gt To change to a transient simulation 1 2 ay Select Parameters Time to open the Time Parameters dialog box Change the model to transient by clicking on Transient in the Simulation Flow Type box Activate the second period by checking the Active box in the second row of the table Change the length of periods and numbers of time steps such that For period 1 Period Length 240 Time Steps 12 For period 2 Period Length 120 Time Steps 6 Click OK to close the Time Parameters dialog box Now we need to set the pumping rate for each well during stress period 1 gt To set the pumping rate l 2 Select Models MODFLOW Well The status bar displays Period 1 indicating that you are entering data for stress period 1 At each of the wells marked by a little shaded box on the DXF Map left click to
575. tt 118 describe the design of 2 1 The Grid Editor 9 model grids which are intended for use both in flow and transport simulations These sources provide valuable general information relating to spatial discretization and grid design in numerical groundwater modeling In the block centered finite difference method an aquifer system is replaced by a discretized domain consisting of an array of nodes and associated finite difference blocks cells Fig 2 1 shows the spatial discretization scheme of an aquifer system with a mesh of cells and nodes at which hydraulic heads are calculated The nodal grid forms the framework of the numerical model Hydrostratigraphic units can be represented by one or more model layers The thickness of each model cell and the width of each column and row can be specified The locations of cells are described in terms of layers rows and columns PM uses an index notation Layer Row Column for locating the cells For example the cell located in the first layer 6th row and 2nd column is denoted by 1 6 2 To generate or modify a model grid select Grid Columns J 1 23456789 10 iI ha a a i i TD LOL OLLLLLSAL LK q NWY Were BS Layers K Fig 2 1 Spatial discretization of an aquifer system and the cell incides Mesh Size If a grid does not exist a Model Dimension dialog box Fig 2 2 appears for specifying the extent and number of layers rows and columns of the model
576. udgets This time we only assign the cell 1 15 25 to zone 1 the cell 2 15 25 to zone 2 and the cell 3 15 25 to zone 3 All other cells are assigned to zone 0 The water budget is shown in Table 4 4 The pumping well 242 4 Tutorials Table 4 4 Output from the Water Budget Calculator for the pumping well FLOWS ARE CONSIDERED IN IF THEY ARE ENTERING A SUBREGION THE UNIT OF THE FLOWS IS L 3 T FLOW TERM IN OUT IN OUT STORAGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 CONSTANT HEAD 0 0000000E 00 0 0000000E 00 0 0000000E 00 HORIZ EXCHANGE 7 8003708E 05 0 0000000E 00 7 8003708E 05 EXCHANGE UPPER 0 0000000E 00 0 0000000E 00 0 0000000E 00 EXCHANGE LOWER 0 0000000E 00 7 9934180E 05 7 9934180E 05 WELLS 0 0000000E 00 1 0000000E 10 1 0000000E 10 DRAINS 0 0000000E 00 0 0000000E 00 0 0000000E 00 RECHARGE 3 1999998E 06 0 0000000E 00 3 1999998E 06 SUM OF THE LAYER 8 1203711E 05 7 9934282E 05 1 2694290E 06 REGION 2 IN LAYER 2 FLOW TERM IN OUT IN OUT STORAGE 0 0000000E 00 0 0000000E 00 0 0000000E 00 CONSTANT HEAD 0 0000000E 00 0 0000000E 00 0 0000000E 00 HORIZ EXCHANGE 5 6002894E 04 0 0000000E 00 5 6002894E 04 EXCHANGE UPPER 7 9934180E 05 0 0000000E 00 7 9934180E 05 EXCHANGE LOWER 0 0000000E 00 6 3981197E 04 6 3981197E 04 WELLS 0 0000000E 00 1 0000000E 10 1 0000000E 10 SUM OF THE LAYER 6 3996314E 04 3981209E 04 1 5104888E 07 a REGION 3 IN LAYER 3 FLOW TERM IN OUT IN OUT STORAGE 0 0000000E 00 0 0000000E
577. ue PARVAL1 must lie between these two bounds For fixed and tied parameters PARLBND and PARUBND are ignored PARTRANS controls the parameter transformation By clicking on a cell of the PARTRANS column this flag can be set as None Log transformed Tied or Fixed Use Log transformed if you wish that a parameter be log transformed throughout the estimation process this is recommended for transmissivities and hydraulic conductivities A parameter which can become zero or negative in the course of the parameter estimation process must not be log transformed hence if a parameter s lower bound is zero or less PEST will disallow logarithmic trans formation for that parameter Note that by using an appropriate scale and offset you can ensure that parameters never become negative Thus if you are estimat ing the value for a parameter whose domain as far as the model is concerned is the interval 9 99 10 you can shift this domain to 0 01 20 for PEST by designating a scale of 1 0 and an offset of 10 0 Similarly if a parameter s model domain is entirely negative you can make this domain entirely positive for PEST by supplying a scale of 1 0 and an offset of 0 0 See the discussion on the SCALE and OFFSET variables below If a parameter is fixed taking no part in the optimization process PARTRANS must be specified as Fixed If a parameter is linked to another parameter this is signified by a PARTRANS value of Tied In the latter case t
578. ulation of existing PM model must be performed The sub region is de fined by the starting and ending columns and rows PM automatically transfers the model parameters and the calculated heads from the regional model to the sub model The boundary of the sub model will be set to constant head bound ary for steady state simulations or time variant specified head boundary for transient simulations Convert Models PMWIN 4 x MODFLOW 88 96 MODFLOW 2000 2005 Telescoping Flow Model PM Model pm5 Start Column End Column c simcore pmB examples tutorials tutorial3 tutorial3 pm5 Start Row End Row 22 Type in the starting and ending columns and rows then Click the Convert button to start the conversion The converted model will be saved in c simcore pm8 enamples tutorials tutori pm_11 PM will load the converted model if the conversion is successful Refinement factor for columns Refinement factor for rows 2 3 The File Menu 23 Fig 2 12 Telescoping a flow model using the Convert Model dialog box 2 3 4 Preferences The Preferences dialog box Fig 2 13 defines the MODFLOW version and manages the paths to the simulation programs of an opened PM model The settings of the dialog box are described below gi Preferences MODFLOW Groundwater Flow Process Modflow Version ZIE pe Flow Package Modules MODFLOW Active Path to Simulation Program F
579. um eigenvalue is only avail able when POLCG is selected Check this box if the solver should calculate the upper bound on the maximum eigenvalue of A Otherwise a value of 2 will be used The upper bound is estimated as the largest sum of the absolute values of the components in any row of A Estimation of the upper bound uses slightly more execution time per iteration Allowed Iteration Numbers MXITER is the maximum number of outer iterations For each outer iter ation A and b equation 2 32 are updated by using the newly calculated hydraulic heads For a linear problem MXITER should be 1 unless more that ITER1 inner iterations are required A larger number generally less than 100 is required for a nonlinear problem Outer iterations continue until the final convergence criteria see below are met on the first inner iteration ITER1 is the maximum number of inner iterations Equation 2 32 with a new set of A and b is solved in inner iterations The inner iterations continue until ITER iterations are executed or the final convergence criteria see below are met Convergence Criteria Head Change L is the head change criterion for convergence When the maximum absolute value of the head change at all nodes during an iteration is less than or equal to the specified Head Change and the criterion for Residual is satisfied see below iteration stops Residual L T is the residual criterion for convergence Resi
580. urrent layer 2 8 3 Polygons The Polygons menu allows the user to save or load the zones in or from a Polygon file All polygons in the layer being edited can be deleted by selecting Polygons Delete All Using Polygon files the user can transfer polygon information between parameters or between models with different grid configurations The format of the polygon file is given in Section 6 2 9 192 2 Modeling Environment i Search And Modify x Parameter Horizontal Hydr Conductivity 7 IV Ignore Inactive Cells Active Color Minimum Maximum Value fOptions lal Vv 5 75 0 Display Only M 75 10 0 Display Only v 10 125 0 Display Only v 12 5 15 0 Display Only M 15 17 5 0 Display Only Vv 17 5 20 0 Display Only O 0 0 0 Display Only O 0 0 0 Display Only O 0 0 0 Display Only O 0 0 0 Display Only O 0 0 0 Display Only O 0 0 0 Display Only m 0 h O Display Only O 0 0 0 Display Only 0 0 0 Display Oni C a n n EE R z Fig 2 99 The Search and Modify dialog box 2 8 4 Points The Points menu appears only in the Digitizer Refer to Section 2 7 1 for details about the Digitizer and the Points menu 2 8 5 Search and Modify Use the Search and Modify dialog box Fig 2 99 to modify cell data of the current layer or to create solid fill plots based on the cell data The options of the dialog box are described below e The Trace Table The user defines a search range a
581. ute transport A uniform horizontal grid of 10 rows and 15 columns is used Aquifer parameters are specified as shown in Fig 5 8 Two steady state solutions were obtained to simulate natural conditions and pumping conditions The steady state solutions were obtained through a single simu lation consisting of two stress periods The first stress period simulates natural condi tions and the second period simulates the addition of pumping wells with extraction rates of 30000 ft d 850 m d The simulation is declared to be steady state so no storage values are specified and each stress period requires only a single time 304 5 Examples and Applications 1507 areal recharge T 0 004 ft d Potentiometric ote a EEA A surface if upper aquifer A WIM yg rT confining unit YY 0 lower aquifer 50 Cross sectional model configuration 100 Layer 1 Hydraulic conductivity 10 feet d 50 L Yy Confining unit Uy Vertical leakance 0 001 1 day Layer 2 2 Transmissivity 500 feet day Well Cell dimension 500 feet by 500 fe t Well se OOo SSeS logos RERRRES stones Fig 5 8 Configuration of the hypothetical model after McDonald and others 86 step to produce a steady state result The PCG2 Package is used to solve the flow equations for the simulat
582. utput terms by checking the corresponding output terms in this tab All output terms denoted by ASCII are also saved in the listing file The calculated concentration values are saved in the unformatted binary file MT3D UCN In addition MT3D96 can save the mass contained in each cell in the unformatted binary file MT3D CBM All output files are located in the same folder as your model You can use the Result Extractor to read the unformatted binary files e Output Times The value of the output frequency NPRS indicates whether the output is produced in terms of total elapsed simulation time or the transport step number If NPRS 0 simulation results will only be saved at the end of simu lation If NPRS lt 0 simulation results will be saved whenever the number of transport steps is an even multiple of NPRS If NPRS gt 0 simulation results will be saved at times as specified in the table shown in Fig 2 72 There are two ways for specifying the output times The user may click the table header Output Time and then enter a minimum time a maximum time and a time interval between each output into an Output Time dialog box PM will use these entries to calcu late NPRS and the output times The other way is to specify a positive NPRS and press the Tab key then enter the output times into the table Note that the output times are measured from the beginning of the simulation e Misc E Output Control M13D MT3DMS Output Terms Output Tim
583. utton E 2 Move the mouse pointer to the point to be assigned a value 3 Right click on the point The Digitizer shows a dialog box 4 In the dialog box type a new value then click OK 2 7 2 The Field Interpolator 2 7 2 1 Interpolation Methods for Irregularly Spaced Data Numerical groundwater models require parameters e g hydraulic conductivity hy draulic heads elevations of geological layers etc assigned to each model cell Hy drogeologists however often obtain a parameter distribution in the form of scattered irregular data points x Yi fi i 1 N N is the number of measurement points x and y are the coordinates and f is the parameter value at point i A fundamental problem is how to estimate the parameter values for each model cell from these data A number of interpolation or extrapolation methods for solving this kind of problems do exist Some of the methods are used by commercial contouring soft ware e g GEOKRIG GRIDZO SURFER or TECKONEM Some implementations are published and available at no cost e g GSLIB 31 In an earlier time a com mon approach used by many modelers is that contour maps are first created either by using software packages or manually then overlaid on the model grid for assigning parameter values to model cells The process is indirect and somewhat cumbersome The Field Interpolator provides a more direct way for assigning cell values by using the Kriging method and methods deve
584. value This defines the value of the damping parameter For linear problems a value of 1 0 should be used For nonlinear problems a value less than 1 0 but greater than 0 0 may be necessary to achieve convergence A typical value for nonlinear problems is 0 5 Damping also helps to alleviate excessive inner PCG iterations e Preconditioner Control Smoother Type E Geometric Multigrid Solver Iteration Control Maximum Number of Outer lteration MxITER 50 Head change Closure Criterion HCLOSE L 001 Maximum number of inner PCG iterations ITER 100 Budget Closure Criterion RCLOSE L 3 T i Damping Control Damping Method Fixed Damping Value Ne Damping Value 1 Preconditioner Control Smoother Type ILU Smoothing zi Semi Coarsening Coarsen Rows Columns x m Fig 2 34 The Geometric Multigrid Solver dialog box 70 2 Modeling Environment ILU Smoothing Select this option to implement ILU 0 smoothing in the multigrid preconditioner This smoothing requires an additional vector on each multigrid level to store the pivots in the ILU factorization Symmetric Gauss Seidel SGS Smoothing Select this option to imple ment the Symmetric Gauss Seidel SGS smoothing in the multigrid pre conditioner No additional storage is required for this smoother users may want to use this option if available memory is exceeded or nearly exceeded when using ILU Smoothing Using SGS smoothing is not a
585. vapotranspiration Package HFB for the Horizontal Flow Barrier Package of MODFLOW GHB for the General Head Boundary Package IBS for the Interbed Storage package OC for the Output Control Option PCG for the Preconditioned Conjugate Gradient 2 Package RCH for the Recharge Package RIV for the River Package SIP for the Strongly Implicit Procedure Package SOR for the Slice Successive Over Relaxation Package STR for the Streamflow Routing Package WEL for the Well Package DIS for the discretization file BAS6 for the Basic Package of MODFLOW 2000 BCF6 for the Block Centered Flow Package of MODFLOW 2000 2005 LPF for the Layer Property Flow package of MODFLOW 2000 2005 HFB6 for the Horizontal Flow Barrier Package of MODFLOW 2000 2005 LMG for the Link Algebraic Multigrid Solver Package of MODFLOW 2000 2005 OBS for the main input file to the Observation Process of MODFLOW 2000 HOB for the Head Observation Package of MODFLOW 2000 DROB contains the observed flows to features represented by the Drain package This file is used by the Observation Process of MODFLOW 2000 GBOB contains the observed flows to features represented by the General Head Boundary package This file is used by the Observation Process of MODFLOW 2000 RVOB contains the observed flows to features represented by the River package This file is used by the
586. vity and recharge values on the basis of observed heads or drawdowns only is of little value in steady state problems due to the non uniqueness of such a fit The parameters to be estimated are defined in the following steps gt To define an adjustable parameter for estimation 1 Select a parameter from the Parameters menu or select a package from the Mod els Flow Simulation MODFLOW Flow Packages menu for example Trans missivity or Well 150 2 Modeling Environment 2 Assign an initial guess of the parameter value and a parameter number to cells within an area where the parameter value should be estimated The parameter number needs to be unique within a parameter type e g T S or Ss and may be any integer ranging between 1 and 500 Set the parameter number to zero if the specified parameter value should not be estimated 3 Select PEST Parameter Estimation Simulation Settings to open a Simulation Settings PEST dialog box which provides an overview of all parameters de fined in previous steps and interfaces for setting control parameters The dialog box also allows selecting or deselecting parameters for estimation see Section 2 6 8 1 Note 1 Using the Calculated settings in the Layer Options dialog box PM allows the user to specify HK VK or Ss instead of T VCONT and S values to layers of types 0 or 2 However when using PEST to estimate T VCONT or S values the user must define the adjustable parameters by s
587. ware packages out side of PM 2 6 5 7 MOC3D Sink Source Concentration This menu is used for specifying the concentrations of point or distributed sources including constant head cells general head boundary cells rivers wells and recharge cells Except the concentrations associated with constant head cells all source con centration values are specified in the Data Editor If the concentration of a fluid source is not specified the default value for the concentration is zero The source concentra tion associated with the constant head cells are specified in the Source Concentration Constant Head dialog box Fig 2 66 The constant head cells are grouped into zones which are defined by specifying unique negative values to the IBOUND array see Section 2 4 3 1 Each zone has an associated source concentration value Source Concentration Constant Head xj Zones are defined within the IBOUND array by specifying unique negative values for constant head cells to be associated with seperate fluid source concentration Max 200 zones are allowed here Source Concentration M L 3 a 1 2 3 4 5 6 7 a Fig 2 66 The Source Concentration Constant Head dialog box The concentration in the fluid leaving the aquifer at fluid sinks is assumed to have the same concentration as the fluid in the aquifer However if the fluid sink is associated with evaporation or transpiration it is assumed that the fluid discharge
588. where Ax Ay and Az are the widths of the cell along the row column and layer directions R is the retardation factor The components of the hydrodynamic dispersion coefficient D z Dyy and D are calculated by equation 2 40 2 v2 2 Decors Searg hee 2 lvl u u 2 2 2 v Dy ar arH Ln aryo Z D 2 40 u u u 2 2 v2 De ar hag pop AFD v u u where ay L is the longitudinal dispersivity apy L is the horizontal trans verse dispersivity ary L is the vertical transverse dispersivity vz vy and vz LT are components of the flow velocity vector along the x y and z axes and lv v2 up v2 2 41 2 6 The Models Menu 97 Equation 2 39 is calculated for each active cell and the minimum At is taken as the maximum allowed step size for solving the dispersion term This criterion is compared with other transport step size constraints to determine the minimum step size for the simulation Generally a higher flow velocity for example the velocity in the immediate vicinity of a pumping well will cause larger values of Dzz Dyy and D which in turn result in a smaller At in equation 2 39 When At is too small the required CPU time will become enormous To overcome this problem an implicit formulation is implemented in MT3DMS See Section 2 6 2 10 for details 2 6 2 5 MT3DMS SEAWAT Species Dependent Diffusion Select this item to enter diffusion coefficient for individual species The speci
589. which contains composite scaled sensitivity values that indicate the total amount of information provided by the observations for the estimation of one parameter If some parameters have composite scaled sensitivities that are less than about 0 01 times the largest composite scaled sensitivity it is likely that the regression will have trouble converging Hill 62 A parameter with large composite scaled sensitivity and many large dimensionless scaled sensitivities is probably more reliably estimated than a parameter with a large composite scaled sensitivity and one large dimensionless scaled sensitivity because the error of the single important observation is propagated directly into the estimate Hill 63 MODFLOW 2000 Parameter Estimation View One Percent Scaled Sensi tivities Select this menu item to use the Text Viewer see Section 2 3 4 for linking a Text Viewer with PM to display the file MF2KOUT _S1 which contains one percent scaled sensitivity values that indicate an approximate amount of information pro vided by the observations for the estimation of one parameter MODFLOW 2000 Parameter Estimation View One Percent Scaled Sensi tivities Arrays The one percent sensitivities for hydraulic heads are calculated for the entire grid and can be contoured just like hydraulic heads can be contoured The one percent scaled sensitivity map can be used to identify where additional observations of hydraulic head would be most im
590. wing the location of the particles should appear Select Options Particle Tracking Time to open the Particle Tracking Time Properties dialog box for setting up the particle tracking parameters In the Tracking Steps group change the time unit to years step length to 10 and maximum number of steps to 200 Click OK to close the Particle Tracking Time Properties dialog box Start the backward particle tracking by clicking on the J button You can easily see that the flowlines intersect with the river in numerous places Fig 4 58 Fig 4 58 Steady state hydraulic head distribution in the 3rd model layer and capture zones of the pumping wells gt To run forward particle tracking We will now introduce a contaminant source upstream of Well 2 and see how far the contamination moves through the steady state flow field after 75 100 and 125 years 1 Since the contamination is a surface source we need to place the particles in layer 1 If you aren t already in Layer change to it by using the PgUp key 296 2 3 Nn oo 4 Tutorials To place the particles on the ground surface drag a box around the cell 1 5 6 In the Cell Faces tab of the Add New Particles dialog box you will notice that the figure defines the various faces of an individual cell since the contamination is a surface source we only want to place particles on cell face 5 Click the Particles tab and set the
591. x Specify the starting position As shown in Fig 2 97 the starting position indicates the column and row at which a matrix will be loaded Numbers of rows and columns of the loaded matrix need not to be identical to those of the finite difference grid This allows to replace only part of the cell data by the matrix For example the user can use the Field Generator to generate a matrix with heterogeneously distributed data from statistic parameters and load it into the grid as a subregion Select an option from the Options group Before a matrix is loaded to the spread sheet its values will be modified according to the following options 190 2 Modeling Environment a Replace The cell data in the spreadsheet are replaced by those of the ASCII Matrix b Add The cell values of the ASCII Matrix are added to those of the spread sheet c Subtract The cell data in the spreadsheet are subtracted from those of the loaded matrix d Multiply The cell data in the spreadsheet are multiplied by those of the loaded matrix e Divide The cell data in the spreadsheet are divided by those of the loaded matrix If a cell value of the loaded matrix is equal to zero the corresponding cell value in the spreadsheet remains unchanged Note A SURFER GRD file may only be used with regularly spaced model grids since SURFER is limited to regular spaced grids Furthermore PM only accepts SURFER GRD files saved in ASCII Consider using the Field Interpo
592. ze The following rules apply 1 Pumping rates mass loading rate see Section 2 6 2 9 and cell by cell conduc tance values of the river drain general head boundary and stream are scaled by the cell volume For example if a well cell is refined to four cells all four refined cells will be treated as wells each with 1 4 of the original pumping rate The sum of their pumping rates remain the same as that of the previous single well 2 The parameters of polylines which are used to define river drain general head boundary or stream remain the same since they are grid independent If a stream of the Stream Routing package is defined by using cell by cell values you must redefine the segment and reach number of the stream 3 Transmissivity T and storage coefficient S values are scaled by the thickness 4 All other model parameters remain the same gt To change the width of a column and or a row 1 Click the assign value button E The grid cursor appears only if the Assign Value button is pressed down You do not need to click this button if it is already depressed 2 1 The Grid Editor 11 Z SAMPLE PMS EIT Processing Modflow Pro File Value Options Help eff ojejo sjeo mle irp position of the grid cursor k J grid cursor no flow bounde a rn ann eontemiraced area PIAZZA AOE constant hecd aal h corstunt hecd bour dary tr nos flow bourrdd position of the mouse
593. zero if the existing recharge is not assigned to the top face Consequently particles cannot be tracked backwards to the top 3 3 PMPATH Options Menu 223 face In PMPATH recharge may be treated as a distributed source or assigned to the top face or bottom face of a cell by selecting a corresponding option from the dialog box If the option Assign recharge to top and bottom cell faces is chosen positive recharge values will be assigned to the top face and negative recharge values will be assigned to the bottom face e Evapotranspiration The option is disabled if evapotranspiration is not used Sim ilar to Recharge evapotranspiration can be assigned to top face of a cell or treated as a distributed sink 3 3 3 Maps The Maps Options dialog box Fig 3 15 allows the user to display up to 5 DXF maps and 3 Line Maps A DXF file contains detailed data describing numerous CAD entities An entity is a line or symbol placed on a drawing by the CAD system PMPATH supports the following entities LINE POLYLINE POINT ARC SOLID CIRCLE and TEXT The other entities are ignored There is no size limit to the number of the acceptable entities A Line Map consists of a series of polylines Each polyline is defined by a header line and a series of coordinate pairs The header line only contains the number of the coordinate pairs Refer to Section 6 2 4 for the format of the Line Map files gt To import a DXF map or a Line Map 1 Ri
594. zontal Flow Barrier ite ate ead chan Wawaooue sata s 44 2 6 1 5 MODFLOW Flow Packages Interbed Storage 45 2 6 1 6 MODFLOW Flow Packages Recharge 47 2 6 1 7 MODFLOW Flow Packages Reservoir 48 2 6 1 8 MODFLOW Flow Packages River 51 2 6 1 9 MODFLOW Flow Packages Streamflow Routing 53 2 6 1 10 MODFLOW Flow Packages Time Variant Specified Head sopo eot ineho peonon eee 58 2 6 1 11 MODFLOW Flow Packages Well 59 2 6 1 12 MODFLOW Flow Packages Wetting Capability 59 2 6 1 13 MODFLOW Solvers 004 61 2 6 1 14 MODFLOW Head Observations 70 2 6 1 15 MODFLOW Drawdown Observations 73 2 6 1 16 MODFLOW Subsidence Observations 73 2 6 1 17 MODFLOW Compaction Observations 73 2 6 1 18 MODFLOW Output Control 74 2 6 1 19 MODFLOW Run 000000 75 2 6 1 20 MODFLOW View 0 0008 78 2 6 2 MT3DMS SEAWAT 00 000 84 2 6 2 1 MT3DMS SEAWAT Simulation Settings 85 2 6 2 2 MT3DMS SEAWAT Initial Concentration 89 2 6 2 3 MT3DMS SEAWAT Advection 89 2 6 2 4 MT3DMS SEAWAT Dispersion 94 2 6 2 5 MT3DMS SEAWAT Species Dependent Diffusion 97 2 6 2 6 MT3DMS SEAWAT Chemical Reaction 97 2 6 2 7 MT3DMS SEAWAT Prescribed Fluid Density 102 2 6 2 8 MT3DMS SEAWAT Sink Source Concentration 102 2 6 2 9 MT3DM

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