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1. Data Structure View 0 ptions 4 Domain Geometry Data Structure X Furrow o i Furrow H Domain Geometry A Domain Geometry 3 FE Mesh Sections H Flow Parameters faa Flow Parameters E O FA Domain Properties H FE Mesh H B FE Mesh g Initial Conditions aj Domain Properties Domain Properties Gq Pressure Head Material Distribution Fs Initial Conditions Temperature G3 Nodal Recharge Boundary Conditions a Concentration 1 H Scaling Factors ay Auxiliary Objects Concentration 2 Anisotropy Al Angle E 1st Component A 2nd Component A Subregions E Observation Nodes E Flowing Particles 4 Initial Conditions E Boundary Conditions E Auxiliary Objects E gt Results Graphical Display Results Other Information amp Concentration 3 d Boundary Conditions 000 Results B FE Mesh CEE Numbering Dig Auxiliary Objects E Rendering E144 Graph Type E gt Lighting GIBE Color Scale Se pResults Graphical Display 00 Pressure Head 000 Water Content 000 Velocity 000 Velocity Vectors 00 Temperature 000 Concentration 1 000 Concentration 2 000 Concentration 3 Results Other Information Ge Ee Ge ee E lt l ii gt ite Daa E Daia View Figure 152 Selected Navigator Bars Data Tabs on the left and in the middle the View Tab on the right 236 8 3 Edit Bars The
2. ok Cancel Figure 168 The HYDRUS Authorization Status dialog window Tab History of Activation 9 2 2 1 On Line Activation Online activation is the fastest and most convenient way to activate HYDRUS The Online Activation window Fig 169 appears after clicking on the Activate on line button on the HYDRUS Activation Status window Here you need to enter information about the License Number and the appropriate Activation Key that you received together with an invoice from the HYDRUS Customer Support This Activation Key is used for all Workplaces of a particular license For special purposes different Activation Keys can be generated for individual 278 Workplaces e g when a particular Workplace has an authorization for a different HYDRUS Level or a specific HYDRUS module In the section Specify the required authorization level select the required HYDRUS Level to Activate i e 2D Lite 2D Standard 3D Lite 3D Standard or 3D Professional please note that this Level has to correspond with the purchased Level and the Type of License to activate e g Time Limited Authorization with the Expiration Date or the Network Installation with the Number of Clients If no checkbox is selected a Time Unlimited Single User License is authorized With regard to a possible loss of authorization due to failure of hardware it is recommended to choose a shorter period of validity default is 0 5 years An item Computer Descr
3. Figure 2 The project Manager with the Project Groups tab 27 E Project Manager gt aro peo Papas Current Project Group Name 3D_Tests Description Three Dimensional Examples Level 3D Standard Directory C ussl HYDRUS3D 2 0 Examples 3D_Tests Descripti Flow and transport through a dike with a see Multiple hysteretic loops Lenhard et al 199 Column test One dimensional infiltration test Grass Field Problem Hupselse Beek 1982 Comparison with the 2 D analytical solution Solute transport with nitrification chain Solute transport with nonlinear cation adsom Solute transport with kinetic linear cation ads Solute transport with first order attachment Contaminant transport from a waste disposal 12 26 2010 a ome n E n ee Project Details Project Name Dike Description How and transport through a dike with a seepage face root uptake Program Name HYDRUS 22 Project Type 3D L Water Flow Solute Transport Root Water Uptake Yes 14 6 MB 12 26 2010 Figure 3 The Project Manager with the Projects tab The Project Manager gives users considerable freedom in organizing their projects The projects are grouped into Project Groups Fig 2 which can be placed anywhere in accessible memory i e on local and or network hard drives Project Groups serve to organize projects into logical groups defined by a user Each Project G
4. ccccccccesesssessssesesesssssssessssssseseseseeees 169 Example of FE Mesh Refinements top and FE Mesh bottom eee 170 Circular left and rectangular right refinements around a node eeeeeee 171 12 Figure 109 Figure 110 Figure 111 Figure 112 Figure 113 Figure 114 Figure 115 Figure 116 Figure 117 Figure 118 Figure 119 Figure 120 Figure 121 Figure 122 Figure 123 Figure 124 Figure 125 Figure 126 Figure 127 Figure 128 Figure 129 Figure 130 Figure 131 Figure 132 Figure 133 Figure 134 Refinement on a line by defining either the size or the number of finite elements alons a AIM Vice esnan cova tinet oa ccaneoaua dust aeu cnet avaeagesatac anata yesan E N R 172 Refinements on a surface left or solid right ssssesssessesssesssesessseessresseesseesees 172 The FE Mesh Refinement dialog window for the Genex T3D module with six different types of refinements applied to a Circular or a Rectangular Point a Line with a given FE size or a number of points to a Surface and to a Solid 174 Example of mesh stretching using a stretching factor of 3 in the x direction 177 The FE Mesh Information dialog window for a two dimensional problem top and a three dimensional problem bottom sssssssssessssssessessssseesseessersseesseressseesseese 178 The FE Mesh Sections dialog Window c cccssscecesececseeeec
5. 182 with the pressure head of the lowest point in the selected region Hydrostatic Equilibrium from the lowest located nodal point c a distribution versus depth that is in hydrostatic equilibrium with the pressure head at the soil surface Hydrostatic Equilibrium from the domain top surface d a Linear distribution with depth and e equal to the field capacity see below When options a b or c are selected only one value of the pressure head needs to be specified For option d one needs to provide values of the pressure head or water content for the top and bottom of the selected domain Option c is currently available only for 2D Simple and 3D Layered Geometries and the vertical lines connecting different layers of FE nodes have to be vertical P E E Distribution Values in selected nodes Same value for all nodes No of Sel Nodes 2601 Hydrostatic Equilibrium from the lowest located nodal point Minimum value 200 5 Hydrostatic Equilibrium from the domain top surface Maximum value 100 Linear distribution with depth Set to Field Capacity Other Options Constant Internal Pressure Head Sink Source Time Variable Internal Pressure Head Sink Source values in Var H4 Slope in Y direction Pressure Head Time Variable Internal Flux Sink Source values in Var FI4 Bottom Pressure Head Value Figure 116 The Water Flow Initial Condition dialog window To simplify definition of the initial
6. 3D_Tests Dike H3D 4 C USSL Dike_1 H3D 5 C USSL 3D_Tests Test8 H3D 6 C USSL 3D_Tests Test6 H3D 7 C ussl ANNEMIEK 001 H3D 8 C USSL ANNEMIEK 000 H3D Exit Ctri P Ctrl C Ctri F4 ndo Ctrl Z Ctrl A Copy Ctrl C Paste Ctrl V Select Properties Alt Enter Find Ctrl F Delete Del Delete AIl Domain Geometry Flow and Transport Parameters FE Mesh Domain Properties Initial condition Boundary Conditions Sections Cross Sections Auxiliary Objects Background Layers Nui wae ae ee oe a kee ae View Insert Calculation Resulf View Insert Calculation Results Tools C A Geometry FE Mesh Domain Properties g Initial Conditions Boundary Conditions w Results Ej Navigator EI Edit bar Tabs in View Status bar 3 Toolbars 3 Arrange toolbars 38 Customize toolbars Standard View Zoom by Rectangle View all Previous View S Dynamic View Scroll Zoom Rotate GE View Stretching il Perspective Auto Rotate View in Direction oy iy w m a D Figure 158 The HYDRUS Menus I File Edit and View 246 eae Calculation Results Domain Geometry Display Quantity gt Boundary Information E5 FE Mesh Parameters FE Mesh Refinement gt SW Generate FE Mesh Domain Properties X Delete FE Mesh Initial conditi gt Observation Points nitial condition a ie gt 4
7. Material Observation Node Boundary Condition or Initial Condition 6 5 1 Materials on Geometric Objects Let s assign three different materials to three Surfaces in Figure 123 When only one material is defined which is a default option in each new project one needs to first define multiple materials and or their soil hydraulic properties This can be done as usual using the Menu command Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Soil Hydraulic Parameters The same dialog window Fig 19 can be also displayed by clicking on the New Material or Edit Materials commands on the Edit Bar Fig 124 Note that in Version 2 0 of HYDRUS one can name materials Materials Mi 1 Sand Gi 2 Loam Hl 3 Sit modified Commands Vex New Material HE Set Material f Sort Materials Transfer to FE mesh 23 Edit Materials Options C Numbering KA Edit Properties on FE mesh Figure 124 The upper part of the Edit Bar which displays defined materials and commands for various actions with materials There are three different ways of assigning materials to particular geometric objects Surfaces a Click on a particular Surface Geo Object to select it and then on a Material 1 2 or 3 in the Materials section of the Edit Bar to assign it 195 b Click on a Material 1 2 or 3 in the Materials section to select it of the Edit Bar and then on a particular Surf
8. Distribution Constant T Slope in X direction 5 00 Linear distribution with depth Slope in Y direction 0 00 i Specification of the Concentration IC Specification of the Pressure Head IC Top Concentration IC o oo H Bottom Concentration IC o o00 Bottom Pressure Head IC 190 00 cm Assigned to Surfaces No Assigned to Surfaces No 2 All Surfaces with no other assigned Concentration IC Remark Remark Default Concentration IC m Cancel Figure 130 The Edit Pressure Head left and Concentration right Initial Conditions dialog window 6 5 4 Boundary Conditions at Geometric Objects New Property Objects for Boundary Conditions must be selected from existing boundary conditions used in HYDRUS For example for Water Flow Boundary Conditions new Objects are selected from the list box Boundary Condition Type displayed in Figure 131 Similarly as for other Properties in this dialog one can define Name Color register a Remark assigned Boundary Condition at selected Boundary Curves and if needed specify required parameters e g for Deep Drainage BC Notes 1 When the same pressure head initial or boundary condition involving either Equilibrium from the lowest located point or A linear distribution is chosen for multiple surfaces or curves then this condition is applied globally to all selected surfaces e g a single point with
9. HYDRUS calculates and reports surface runoff evaporation and infiltration fluxes for the atmospheric boundary Water content dependence of solute reactions parameters using the Walker s 1974 formula was implemented A new option to consider root solute uptake including both passive and active uptake im nek and Hopmans 2009 The Per Moldrup s tortuosity models Moldrup et al 1997 2000 were implemented as an alternative to the Millington and Quirk 1961 model An option to use a set of Boundary Condition records multiple times Executable programs are about 1 5 3 times faster than in the standard version due to the loop vectorization 10 Options related to the fumigant transport e g removal of tarp temperature dependent tarp properties additional injection of fumigant 11 Anew CWM1 constructed wetland module Langergraber et al 2009 Version 2 02 additionally supports several add on modules that have their own user manuals such 20 as the DualPerm module im nek et al 2012e the UNSATCHEM module im nek et al 2012c the Wetland module Langergraber and Simunek 2011 the C Ride module Sim nek et al 2012b and the HP2 module Simunek et al 2012a Version 2 03 offers some new functionality with respect to the import of various properties from either existing HYDRUS projects or from text files see Section 6 6 allows users to import definition of isolines only in 3D Professional and
10. N2 2 v Comment Figure 79 The Thickness dialog window 140 The height of a solid is defined using one or more Thickness vectors Each thickness vector is defined by an Anchor Point P and two Boundary Points N1 and N2 The anchor point P must be part of the base surface i e it must be either a defining point of the external boundary or the internal curve or an internal point in the base surface Boundary points N1 and N2 are arbitrary points in 3D space Coordinates of these points can be edited thus allowing one to specify the thickness vector in an arbitrary direction i e not necessarily perpendicular to the base surface Usually the anchor point P is the same as boundary point N1 so that one can use the same index for both P and N1 If for whatever reason we do not want to have the base surface on the bottom of the transport domain Solid e g when the bottom of the transport domain is not in the same plane users can make the N1 node be different from P the red part in Fig 80 Figure 80 A solid with several thickness vectors AWN FANN PANNAN DANNY VALN ANNI YA NN ANN lA Ne SI AA d 4 SS Ls f tA aA ANSNI ZAN NNN SSA WS AVA J S 4 2 Z Z J AVIS A TAVAT AS SJ SIS Figure 81 FE Mesh for the solid in Figure 80 The height of a solid is constant when less than three thickness vectors are used Three thickness vec
11. V Automatic Apply OK Cancel Insert Points on Curve Line No Type of Points Split Curve at Inserted Points Insert Parametric Points O Insert Intermediate Points Distance related to Length 0 00 Distance between new node and 000 Line Stat 000 fem 0 000 0 00 Line End 0 00 cm 0 000 0 00 Numbering starts with 0 00 No 0 00 Point Automattic 0 00 Line Automatic cant rT Figure 60 The Insert Point on Curve dialog window 117 4 2 Surfaces 4 2 1 General Definitions An object Surface refers to depending on the problem type and the selection made in the Domain Type and Units dialog window e 2D General For two dimensional problems a Surface serves to define the shape of the computational domain or its parts See also Geometry Information e 3D Layered In this case the term Surface is used to define the Base Surface for Solid 3D Layered domains This type of Solids is available in the 3D Standard version e 3D General The term Surface serves to define boundary surfaces of a general 3D solid This type of Solids is available only in the 3D Professional version More detailed information can be found in the section about Solid General Section 4 4 In the 3D Standard version the only available type of a Surface is a Planar Surface This type of the Surface is defined by its boundary cu
12. nodes lines or surfaces which can for example occur when selection is made by a Rectangle or a Rhomboid then the command is located in the submenu Surfaces B Intersection of Solids this option not yet available Select two or more Solids click with the right mouse button on these selected Solids and select the command Create Intersection When more types of different objects are selected e g nodes lines or surfaces which can for example occur when selection is made by a Rectangle or a Rhomboid then the command is located in the submenu Solids For the Intersection Solids A B Fig 84 the Solid A will remain in its original shape and the Solid B will be cut off For the Intersection Solids B A the Solid B will remain in its original shape and the Solid A will be cut off C Intersection of Surfaces and Solids this option not yet available It is possible to create this intersection using the menu command Insert gt Domain Geometry gt Intersection or by clicking with the right mouse button on the item Intersections in the data tree of the Navigator bar and selecting Insert Intersections from the displayed popup menu In the dialog select desired type of Intersection e g surfaces or solids Edit Intersection x Edit Intersection Intersection No Intersection No Intersection of Surfaces S1 x S2 Intersection Type Intersection Type Partial Surface surf compo
13. up menu Fig 154 that allows users to choose different display options such as Color Smoothing Isolines and Isobands These options are defined in more detail below Color Smoothing Min Max Global in Time Min Max Global in Space Standard Scale Edit Scale and Colors Y solines Zs Colormap Isosurfaces y Color Points R sz 4 Color Edges 4 Velocity Vectors e nom Figure 154 The Color Scale Display Options menu Color Smoothing Min Max Global in Time Min Max Global in Space Standard Scale Custom Scale Edit Scale and Colors Isolines Colormap Isosurfaces Color Points Color Edges Velocity Vectors Colors are by default constant between isolines but change abruptly at the isoline Colors change gradually when this option is checked The minimum and maximum values for the color spectrum are selected based on minimum and maximum values of a certain variable during the entire simulation The minimum and maximum values for the color spectrum are selected based on minimum and maximum values of a certain variable in the entire transport domain even when only part of the domain is displayed e g one horizontal layer Users can select between a standard or user defined scale Users can select between a standard or user defined scale Calls the Edit Isoband Value and Color Spectra dialog window Fig 138 Displays a selected variable using isolines Displays a selected variable using isobands co
14. 114 whereas each horizontal vertical for some applications layer forms one additional section Sections ML_001 through ML_010 Mesh Layer in Fig 114 while the last section is made up by the vertical surface Section ML_000 Shell Fig 114 For example the bottom Mesh Layer can be displayed when the bottom boundary conditions are specified while the top Mesh Layer Section can be displayed when the surface boundary conditions are provided One can similarly display results at different depths using different horizontal sections Mesh Layers The Mesh Sections are generated automatically when the FE Mesh is generated or anytime using the menu command Edit gt Sections gt Generate FE Mesh Sections Automatically generated FE Mesh Sections in different HYDRUS versions are listed in Table 19 Mesh Sections can also be generated for each Geo Section see Section 8 1 8 Additional sections can be created using commands from the FE Mesh Sections part of the FE Mesh version of the Edit Bar One can display any existing section or set of sections and modify them using the Cut with Rectangle command and then create a new section using the New Section from View command This new section will then appear in the list of sections in the Section Tab of the Navigator Bar and can be recalled at any time Existing sections can be manipulated Display Hide Select Unselect Rename Delete Move Up and Move Down using the Edit Section command from the E
15. 5 44 Finite Element Mesh Refinement sie sissc ots 2a ihe aoas sols dade dideetade tetas eds Nidse Bleue 168 5 4 1 Finite Element Mesh Refinement for MeshGen2D n os 168 5 4 2 Finite Element Mesh Refinement for Genex T3D o cccccscccccceeeseceeeesteceeessteeees 171 5 5 Unstructured Finite Element Mesh Generator MeshGen2D ssc 174 5 6 Finite Element Mesh Statistics ss c0s 2 cottesive ciation caleilaect Uacadasi ca lanodiatsi eau recaasicn 178 5 7 Finite Element Mesh Sections vicovelvvaseaeovetiercets ete ae ae eae a 179 Domain Properties Initial and Boundary Conditions 0 cccccccececeseceesseeeesteeees 181 6 1 Default Domain Properties sta isos Se saiths Mtcnaetl Sceaese ts teceadd bona te Sidensaaacie taeda Geese ia 181 6 2 Initial Conditions yo diss octet ret ot acct tiered eae elms waged Dag ASE EAEn 182 6 3 B und ry Conditions ues ssa neg n aa a E a aaa 184 6 3 1 Time Variable Head Flux 1 BCS cicciiinncininknnadhnieukindduiaen 185 6 3 2 Special Boundary Conditions sssosossssseensseeeesseseessssessssereessereesseseesssseesssse 187 6 3 3 Triggered Irrigation oesseeesseeesssseesssseseessereesssseessssressssrresssereesseseesssseesssse 189 OA Domain Properties saian e a a a a E ea ese 191 6 5 Defining Properties on Geometric ODjeCHS ccccccccssccccscsscceceseessececssssececessuseeseeseaeseenes 193 6 5 1 Materials on Geometric Objects oonnneeonseensseeeesssseesssseresssereessoseesss
16. Code Mater Roots Axz Cancel 200 00 190 00 180 00 170 00 160 00 150 00 140 00 130 00 120 00 110 00 100 00 90 00 80 00 70 00 60 00 50 00 40 00 Io 7 Help MS Excel Import Export Copy Sel on nD on amp wm on nn Ae wh Copy All Edit in Resizeable Window ooocc 7c cF ccc co oO CoO COOoOloll 0 90 9 9 9 9 9 9 0 9 090 9 090 0 09 0o ooococcc Cc 7 CO CC CoO oO oO CoO oO OD lt ai 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 gt Fe cr ede areca afer and Heat Transport for changed Codes Linear Interpolation of Pressure Heads between the first and last layer Figure 115 The Default Domain Properties dialog window 6 2 Initial Conditions After selecting nodes graphically with the mouse for which the initial condition is to be specified and clicking on the command Set Values at the Edit Bar on the right side of the view window the Water Flow Initial Condition dialog window Fig 116 appears Using this command one can specify the initial conditions for water flow by defining the initial spatial distribution of the pressure head or water content over the flow domain The decision whether to use the pressure head or the water content initial distribution is made in the main module of the Iteration Criteria dialog window Fig 17 One can specify a the same value to all selected nodes Same value for all nodes b a distribution versus depth that is in hydrostatic equilibrium
17. Navigator Bar or Options gt Graph Type gt Isolines and or by animation using both contour and spectral maps The number of colors in the color spectrum as well as the numerical increment between isolines can be selected using the Edit Isoband Value and Color Spectra dialog window Fig 138 Contour and spectral maps may be drawn for the pressure head water content temperature solute concentration in the equilibrium or nonequilibrium phase and or velocity Animation of these four variables is also possible Flow Animation on the Results version of the Edit Bar or using Results gt Time Layer gt Animation Graphs of all variables along the boundaries Boundary Line Chart on the Results version of the Edit Bar or using Results gt Charts gt Boundary Line as well as those along any selected cross section Cross Section Chart on the Results version of the Edit Bar or Results gt Charts gt Cross Section can be readily obtained The entire finite element mesh the boundary nodes and the numbering of nodes elements and or edges can be displayed also using the Display Options dialog window Fig 137 or Options gt Display Options gt Edit together with isolines and spectral graphs Users may zoom into a certain part of the transport domain and can enlarge or reduce the transport domain among other features Flow animation is an alternative to displaying results at one particular time Distributions during flow animation are display
18. Number of Points on the Line Surfaces or Solids 2 Next users must assign the refinement to particular Points Lines or Surfaces so the program knows where the refinement should take place After double clicking on a particular point line arc circle or spline the corresponding dialog window will appear the Edit Point dialog window Fig 48 or the Edit Curve dialog window Fig 50 where users should select FE Mesh Refinement in the FE Mesh Tab The code will then create a list of nodes or lines or surfaces for a particular refinement that can be further edited by a user FE Mesh Refinement is graphically displayed using red dots in green circles for nodes green nodes for lines and a small square in the corner of a surface By clicking on these colored items the FE Refinement can be deleted or edited Editing of the FE mesh refinement will affect all objects to which a particular refinement was assigned 5 4 1 Finite Element Mesh Refinement for MeshGen2D Figure 106 below shows the New FE Mesh Refinement dialog windows that are used with the MeshGen module for four different types of refinements FE Mesh Refinements can be applied to a Point a Line and a Surface When the FE Mesh Refinement is assigned to a Point Figure 106 top left users only need to define the finite element size that is to be used at a given point This FE size will be used around a given point while sizes of neighboring FE will be gradually increased until
19. This selection is available only in the 3D Professional version of HYDRUS 4 4 1 3D Layered Hexahedral Solids x a Domain Geometry Set new Solid Brick a Numbers for new x Solid 4 Domain Geometn a Z Thickness 1 Set new Solid Extruded a Point 37 Numbers for new L Solid i Thickness Length Thickness 1 L 730 00 em Point 9 dl 10 00 cm Surface to extrude Thickness Direction Surface 2 Perpendicular to the Surface Autodetect O In X direction v Base Surfaces O In Y direction V Thick Vectors O InZdiection ti m Help a EE ad K Step 3 of 3 Ke Step 1 of 2 Set thickness of the new Select a Surface to extrude Solid Ke Press Esc or right mouse K Press Esc or right mouse button to end the tool button to end the tool Figure 73 The Edit Bar during the process of graphically defining a Hexahedral Solid Definition of a Base Surface on the left and a Thickness on the right A simple Hexahedral Solid can be created graphically using the menu command Insert gt Domain Geometry gt Solid gt Graphically or alternatively the command Solid Extruded on the Insert Object part of the Domain Geometry version of the Tool Bar Once a command for 130 defining a new Hexahedral Solid is selected a cursor in the View window will become a cross with a small empty circle in the middle The coordinates of the location of the cursor will be
20. and Boundary Conditions can be specified on Geometric Objects defining the transport domain rather than on the finite element mesh Import of initial conditions from existing HYDRUS projects even with slightly different geometry or FE mesh Import of various quantities e g domain properties initial and boundary conditions from another HYDRUS projects even with slightly different geometry or FE mesh Support of ParSWMS a parallelized version of SWMS_3D Support of UNSATCHEM a module simulating transport of and reactions between major ions The Mass Balance Inverse Information dialog window enables to display texts larger than the capacity of the Edit window Root distribution can be specified using GUI parallel with the slope for hillslopes Display of results using Isosurfaces 10 Support of anew CWM1 constructed wetland module Langergraber et al 2009 New features and changes in the HYDRUS in the computational modules 1 2 3 4 5 6 7 8 9 New initializations conditions for solute transport initial conditions can be specified in the total solute mass and nonequilibrium phases can be initially equilibrated Various new boundary conditions e g gradient surface drip subsurface drip and seepage face with a specified pressure head boundary conditions Triggered Irrigation irrigation is triggered by the program when the pressure head at a particular observation node drops below a specified value
21. project the initial conditions will be imported Import data from Hydrus project and offers quantities that can be imported as initial conditions Select quantities to import Select All or Unselect all commands can be used to make a selection Import data from Hydrus 3D project C ussl HYDRUS3D 2 0 Examples 2D_Tests Unsatchem h3d2 Select quantities to import C Domain Properties Material Distribution C Domain Properties Nodal Recharge C Domain Properties SF Pressure Head C Domain Properties SF Hydraulic Conductivity C Domain Properties SF Water Content C Domain Properties Anisotropy Angle C Domain Properties Anisotropy 1st Component C Domain Properties Anisotropy 2nd Component C Domain Properties Subregions _ Initial Conditions Pressure Head O Initial Conditions Solution Composition O Initial Conditions Exchanged Species O Initial Conditions Solid Species C Initial Conditions CO2 Concentration C Boundary Conditions Water Flow C Boundary Conditions Solute Transport Select Time Layer The Last Final Time Layer Time Layer No V Identical FE Meshes Figure 133 The Import Selected Quantities dialog window 203 Warning Import of selected quantities from another HYDRUS project can be done only from a project that has a similar geometry and FE Mesh discretization as the actual project Geometry cannot be significantly different Users ne
22. the Anchoring Point can be different than the Beginning Point which leads to the so called offset This option allows to define Domains that have both upper and lower surfaces deformed i e not a plane Vector Direction can be specified to be a Perpendicular to the Base Surface b in X direction c in Y direction or d in Z direction Thickness Vectors can be defined by clicking on individual Points selecting points with a rectangle rhomboid circle polygon clicking on a curve Thickness Vectors will be added to all points of a curve 139 a Domain Geometry Set new Thickness Numbers for new Thickness E Point 41 Definition by Point and Length Point and Coord O Two Points O Three Paints Vector Length L 100 00 fern C Reverse Paints Vector Direction Perpendicular to the Base Surface Oln ditection O In Y direction O In Z direction Help a Ke Set first point of the new Thickness Ke Press Esc or right mouse button to end the tool Ke Selection by rectangle or thomboid is enabled Figure 78 The Edit Bar during the process of graphically defining a Thickness Vector A definition of the Thickness Vector i e its Boundary Points is given and can be edited in the Thickness dialog window Fig 79 New thickness Thickness No 2 at Point No RE Boundary Points No 1 Thickness N1
23. 000 m E Set View Stretching Factors Automatically E Display Workspace Outline Sere Figure 6 The Domain Type and Units dialog window with 3D preview 33 l Domain Type Type of Geometry General 2D domain D 2D Simple Parametric sei Cancel 2D General Boundary Rep He z Help 3D Simple Parametric ee 3D Layered 3D General Boundary Rep 2D Domain Options 2D Horizontal Plane x D 2D Vertical Plane XZ Units Model Precision and Resolution Length m gt Epsilon 0 00019 m 7 Standard recommended Edit Properties on Geometric Objects T Edit domain properties initial and boundary conditions on geometric objects Initial Workspace x Y Z Min 5 000 0 000 5 000 m Max 30 000 10 000 15 000 m Set View Stretching Factors Automatically F Display Workspace Outline Previous Figure 7 The Domain Type and Units dialog window with 2D axisymmetrical preview There are two types of two dimensional transport domains Surfaces see also Section 4 2 depending upon the selection made in the Domain Type and Units dialog window Fig 6 and 7 e 2D Simple Parametric This type of solid has a Rectangular Shape and is defined by its basic dimensions Rectangular domains are defined by three straight lines one at the bottom of the domain and two at the sides whereas the upper boundary may or may not
24. 0080 Level to activate 3D Professional Network Licence No Time limited License No Request Code 1 316923815 Request Code 2 106300092 Licence Number 1001 Computer Description Home PC Customer PC Progress 4 Mi gt Figure 173 Email with the HYDRUS Activation Request in Outlook back the Activation Code Notes on Request Codes 1 Request Code 1 is a randomly generated number that can be used for a single activation After the activation either successful or unsuccessful this number is changed and therefore the same number cannot be used repeatedly even for the same computer Request Code 2 Computer ID is a number that uniquely characterizes the hardware of a computer or a computer network for the network license This number should be constant for a particular computer unless there is a change of hardware If this number changes the authorization system will evaluate the license as invalid It is thus necessary before the change of hardware e g a change of the motherboard or reinstallation of the operational system Windows to deactivate HYDRUS since HYDRUS will need to be reactivated after hardware changes are completed There are only three attempts available to activate HYDRUS with particular request and activation codes If wrong activation codes are inserted during the first three attempts 283 HYDRUS issues a warning After the third attempt with wrong activation codes the Reque
25. 1 d 0 18 DASRB rate constant for lysis 1 d 0 012 Koasrp saturation inhibition coefficient for So mg O L 0 0002 Ksasrp saturation inhibition coefficient for S mg CODs L 24 Kyoasrp saturation inhibition coefficient for Sno mg N L 0 0005 Kyuasrp saturation inhibition coefficient for Sny nutrient mg N L 0 01 Ksoasrp saturation inhibition coefficient for Sso4 mg S L 19 Kypsasrp saturation inhibition coefficient for Sms mg S L 140 91 Sulphide oxidising bacteria Hso maximum aerobic growth rate for Xsgop 1 d 5 28 7 SOB correction factor for anoxic growth of Xsos 0 8 Dsop rate constant for lysis 1 d 0 15 Kosos saturation inhibition coefficient for So mg O L 0 2 Kyosop saturation inhibition coefficient for Sno mg N L 0 5 Kyusop saturation inhibition coefficient for Syy nutrient mg N L 0 05 Kssop saturation inhibition coefficient for Spzs mg S L 0 24 Solute Transport Constructed Wetland Model No1 CWM1 Parameters Hydrolysis Hydrolysis Rate Constant 0 125 Sat Inh Coef Hydrolysis FB Correction Factor Heterotrophic Bacteria aerobic growth and denitrification Max Aerobic Growth Rate Anoxic Correction Factor Rate Constant for Lysis 0 25 0 0333333 0 4 Sat Inh Coef for SO Sat Inh Coef for SF Sat Inh Coef for SA Sat Inh Coef for SNO Sat Inh Coef for SNH Sat Inh C for SH2S Autotrophic
26. 100 0 095 0 089 0 100 0 070 0 068 LEAI 0 430 0 410 0 410 0 430 0 460 0 450 0 390 0 410 0 430 0 380 0 360 0 380 a cm 0 145 0 124 0 075 0 036 0 016 0 020 0 059 0 019 0 010 0 027 0 005 0 008 n 2 68 2 28 1 89 1 56 1 37 1 41 1 48 1 31 1 23 1 23 1 09 1 09 K cm a 712 8 350 2 106 1 24 96 6 00 10 80 31 44 6 24 1 68 2 88 0 48 4 80 Table 8 Soil hydraulic parameters for the analytical functions of van Genuchten 1980 for twelve textural classes of the USDA textural triangle as obtained with the Rosetta Lite program Schaap et al 2001 Textural class Sand Loamy Sand Sandy Loam Loam Silt Silty Loam Sandy Clay Loam Clay Loam Silty Clay Loam Sandy Clay Silty Clay Clay 6 LL 0 053 0 049 0 039 0 061 0 050 0 065 0 063 0 079 0 090 0 117 0 111 0 098 6 LL 0 375 0 390 0 387 0 399 0 489 0 439 0 384 0 442 0 482 0 385 0 481 0 459 57 0 035 0 035 0 027 0 011 0 007 0 005 0 021 0 016 0 008 0 033 0 016 0 015 3 18 1 75 1 45 1 47 1 68 1 66 1 33 1 41 1 52 1 21 1 32 1 25 643 105 38 2 12 0 43 7 18 3 13 2 8 18 11 1 11 4 9 61 14 8 Table 9 Soil hydraulic parameters for the analytical functions of Brooks and Corey 1964 for twelve textural classes of the USDA soil textural triangle according to Rawls et al 1982 Textural class O 0 a n K L L L L cm cm d Sand 0 020 0 417
27. 104 This dialog window has six and four Tabs for the MeshGen2D and T3D generators respectively in which various parameters of the unstructured finite element mesh can be specified The Main Tab The Targeted FE size i e the average size of the triangular elements in the generated finite element mesh is specified on the Main Tab Figs 98 The program selects by default a Targeted FE Size Users can change this value by deselecting the Automatic check box The finite element mesh with this Targeted FE size can be further modified using various tools such as Stretching in different directions on the Stretching Tab Fig 99 to make the mesh anisotropic specifying the Maximum Number of Nodes on Boundary Curve on the MG Options Tab Fig 103 and Minimum Number of Nodes on Boundary Curve on the Options Tab Fig 104 and using Finite Element Mesh Refinement Fig 106 While the Default command sets default values on a particular tab of the FE Mesh Parameters the All Default command sets default values on all four tabs For three dimensional applications only for 3D Layered geometries a user can specify on the Main Tab the No of Horizontal Layers which are layers parallel with the Base Surface to add the third dimension to the problem and if the finite elements used to discretize the three dimensional domain are to be Tetrahedrals or Triangular Prisms for 3D Layered geometries or Tetrahedrals or Mixed Elements multiple types of element
28. 2 x Destination Folder for HYDRUS Data Files Projects and User Settings C Users Public D ocuments PC Progress HYDRUS 2 x Install hardware key driver HASP Import information about your existing projects to the Project Manager Figure 182 The HYDRUS 2 xx Setup window with a choice to install the hardware key driver 290 Advantages of HASP Proven solutions by SafeNet verified by hundreds of installations and users No activation of the software e g HYDRUS is needed Activation of the program brings some disadvantages such as that the program can be activated only on the allowed number of computers and the activation is always time limited up to 1 year and needs to be repeatedly renewed Under certain circumstances the activation code may not be immediately available and users have to wait till they get it e g activation by e mail The hardware key dongle gives users assurance that the program can be easily installed and used for example on a new computer The program e g HYDRUS can be used on multiple computers e g desktop and laptop only by transferring a small USB key Easier and safer installation of a network version The network installation using a software key activation is somewhat more complicated and some network administrators have complained about its lack of flexibility The use of HASP eliminates these problems 291 9 3 Print Options Dialog Window The Print Options dialog window co
29. 22 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Figure 29 List of Figures The HYDRUS Graphical User Interface the main window cc eeseeeseeeseeeeeeeeees 24 The project Manager with the Project Groups tab ee eee eeeeeeceseeeeneecneeeeeeneeeeeneees 27 The Project Manager with the Projects tab eeesececesccecssececeseceeseeeeeseeeeeseeeeeaeeees 28 The Project Information dialog Window cessceceseeecseceeceeececeneeeceneceeseeeeseeeenaeeees 30 General description of the HYDRUS Project Groups eeceeeeeeeeseeeeeteeeesteeeeneeeenes 30 The Domain Type and Units dialog window with 3D preview eeeeeeeeeeeereees 33 Domain Type and Units dialog window with 2D axisymmetrical preview 34 Examples of rectangular top and general bottom two dimensional geometries 35 Example of a hexahedral three dimensional geometry cceeeeeceeeeeeeeeeeceeeeeeeteeeees 36 The Rectangular Domain Definition dialog window i ceeeeeeesecsneceeeeeeeeeeeeeseaeees 36 The Hexahedral Domain Definition dialog Window ceeceeeseeceeeeeeeeeeceeeeeeeteeeees 37 The Main Processes dialog Window ccessecesssecesscecesseeceencecesececeeneeceeeeeceeeeesteeeens 40 The Inverse Solution dialog window x cacesivevegiusseecteessvcesuasy satshedsteaeears cv crnsovseoensatvaee 42 The Data for Inverse Solution dialog window ccceeesseceenc
30. 3D_Tests Browse Figure 5 General description of the HYDRUS Project Group Projects created by the previous versions of HYDRUS e g HYDRUS 2D can be imported into the current version of HYDRUS using two ways 30 A Individual projects can be converted using the command File gt Import and Export gt Import HYDRUS 2D Project This is done by first creating a new Project and then selecting the above command and browsing for the location of a project created with a previous version of HYDRUS 2D The input data of the older project are then converted into the new HYDRUS format Results of the older project can then be viewed using the new version of HYDRUS while projects can be modified or recalculated as needed B Multiple HYDRUS 2D projects or HYDRUS projects created by earlier versions of HYDRUS can be converted simultaneously using the Convert command of the Project Manager One first creates a HYDRUS Project Group for a folder in which the HYDRUS 2D projects are located and selects the Show Old Projects option at the Project Tab of the Project Manager One then selects projects to be converted and clicks the Convert command HYDRUS in this way creates HYDRUS projects and stores all input and output files in the project_name h3d2 files Input data can be edited either using the HYDRUS graphical user interface this modifies directly the project_name h3d2 file or the input data can be modified manually In such c
31. 91 Temperature dependences stoichiometric parameters composition parameters and parameters describing oxygen transfer in the CW2D biokinetic model Langergraber ONG SUMUNEK ZOOD ci cee cece E OE E E Ten SE tS 94 Temperature dependences stoichiometric parameters composition parameters and parameters describing oxygen transfer in the CWM1 biokinetic model Langergraber CF GI ZOOD wives ca cesses ex ges ecn a eves ca easy siaseash oE aE a ESE AA E aAa 96 Definition of terms related to geometry design eeceeeccecssececeeeceeeeeeeeneeeenteeeenaees 102 Definition of terms related to boundary discretization ccceeeeeceesseceeeteeeesteeeenaees 175 Finite element mesh sections generated in different HYDRUS versions 179 Definition of commands used to manipulate Property Objects 0 00 eeeeeeeteeeeeeeee 194 Standard variables displayed in the View Window of the Results tab Results Graphical Display rererere a ate ee ea e aa hoes awn e SO geese 210 Alternative variables that can be displayed in the View Window of the Results tab 211 17 Table 23 Table 24 Table 25 Table 26 Table 27 Definition of various concentration modes for linear sorption model 06 212 Graph options in the HYDRUS interface syes c 2es2cesteed ogee ieee erast stages cette eade deteae 224 HY DRUS menu commands 4 6 20 Gee AGE GUAGE RG EU 248 Brief description of HYDRUS menu commands ee ese eesec
32. Authorization select the required HYDRUS Level to Activate i e 2D Lite 2D Standard 3D Lite 3D Standard or 3D Professional please note that this Level has to correspond with the purchased Level and the Type of License to activate e g Time Limited Authorization with the Expiration Date or the Network Installation with the Number of Clients If no checkbox is selected a Time Unlimited Single User License is authorized With regard to a possible loss of authorization due to failure of hardware it is recommended to choose a shorter period of validity default is 0 5 years 280 License Number Customer Enter your HYDRUS license number and or name and address of the institution that purchased the license WP Description Home PC Enter a text to identify this workplace or computer Required Authorization Select HYDRUS Levelto activate Time4imited Authorization C Network Installation Expiry Date ME 1 2011 Wr Number of Clients 0 Next Step Regenerate Request Codes Figure 171 The Activation by E mail dialog window Tab Step 1 After clicking on the Generate Request Codes button on Tab Step 1 of the Activation by E mail window Fig 184 user is prompted to confirm all entered information Fig 170 and then the Tab Step 2 Fig 172 appears 281 Activation by E mail Step 2 Step 3 Authorization Request Codes HYDRUS version 2 01 0080 Level to activate 3D Professional Network L
33. Circle a Parameters Numbers for new H 80 oo em Curve aP 10 00 fern Point 18 C Reverse Orient ETE Definition by R 130 00 cm Radius dR 10 00 em O Angle da 5 00 O Height Stop Stop n Joa 4 cee 2 of 2 Saati BARAT Set radius of the Circle Ke Press Esc or right mouse ina Preas fac or ds B button to end the tool Figure 51 The Edit Bar during the process of defining graphically a radius for a new arc left or a new circle right In addition to the General Tab Fig 52 left in the New Line dialog window the Edit Line dialog window has also the Arc Tab Fig 52 right A list of points defining the arc are given in the General Tab while coordinates of points defining the arc its center and other parameters are entered in the Arc Tab Double clicking on an existing line will recall the Edit Curve dialog window Fig 52 The Edit Curve dialog window Fig 52 has an additional FE Mesh Tab similarly as for a line in Fig 50 not shown here where a user can refine the FE Mesh along a given arc 109 New line i New line R General Arc General Arc Curve No Are No 5 Curve Type Definition Points List of Points gt i Adjustable Point New Pick When changing Are parameters adjust point Pick All Comment Are Center Arc Parameters x 50 00 fem r 50 25 em y 500 em s 50 25 em z ooo le
34. Density in Layers FE Mesh Density in Sub Layers __ FE Size RS RS Relative Size of Mesh Elements On Thick Vect gt n esness veror relative thickness of mesh layers No 1 Figure 76 The Edit Solid dialog window the FE Mesh Tab for a single and multiple layers 134 4 4 2 1 Division of a Solid into Columns Notice that the Base Surface must be defined using several Surfaces see Fig 63 Parts of the Solid above each Surface are called Columns and serve to geometrically divide the Solid in the vertical direction All Surfaces defining the Base Surface must lie in a single plane A list of these Surfaces can be defined manually using indexes or can be Autodetected by the program the Autodetect option A division of a Solid into Columns leads to an automatic creation of Mesh Sections that correspond with Columns after the generation of the FE Mesh These Mesh Sections can be used to define various properties e g materials distribution or initial and boundary conditions 4 4 2 2 Division of a Solid into Geo Layers Geo Layers alternative term Sublayers which was used in Version is used alternatively below are used to divide a Solid in the horizontal direction Fig 75 It is possible in the Edit Solid dialog to define number of Layers and their Thicknesses A Solid has always one Master Thickness Vector which is one of Thickness Vectors of a Solid that has a special meaning a
35. Exports information about the currently displayed quantity e g water content into a text file Export Isolines Exports spatial coordinates of isolines Export Data to ParSWMS ParSWMS is a parallelized version of SWMS 3D which can be run on clusters or supercomputers This commands creates input files for ParSWMS from the HYDRUS project Print Prints the content of the View window Print Preview Previews the content of the View window before printing 256 Print to the Clipboard Print Options Print Setup Project Information Project Manager Recent Files Exit Edit Undo Redo Copy Paste Select Select by Rhomboid Select by Circle Select by Polygon Add to Selection Remove from Selection Standard Selection Mode Properties Find Delete Delete All Domain Geometry Domain Type and Units Simple Domain 3D Layered Domain Delete 3D Layered Domain Points Lines Surfaces Openings Thickness Vectors Solids Copies the content of the View window to the clipboard for subsequent pasting into other software packages Select various print options such as print quality text size frame and text content Fig 183 Selects a printer and printer connection Displays information about the current project in the General Data dialog window Fig 4 Calls the Project Manager Figs 2 and 3 to manage data of existing projects helps to locate open copy delete or rename the desired projects and t
36. Figure 104 Figure 105 Figure 106 Figure 107 Figure 108 Consequence of missing an internal curve in the base surface on the FE Mesh of the top SU TAC Ciccone gate vibes Sune deze 2s ueacna E sumasa lay cesta N ca eeneas acne ta secon 142 The Edit Intersection dialog window for two Surfaces left and two Solids right 143 An example of an Intersection of two Surfaces and a resulting Partial Surface and Intersection Curves 2is i224 betes n lees ened ea aie aE NE AE ied Adee eee 144 Edit Bar during the process of graphically defining a Dimension Selection of two definition points the distance of which is to be labeled left and the dimension type OTST ese Naat va aca a aA aad Sed O OO estas cal Sarai EREE 145 The Edit Comment dialog Window cccssccssssscsensccsenencessccecssccecneccesneccesscecesneees 146 The Edit Bar during the process of graphically defining a Comment Selection of the Comment Position Comment Text Font and Color left and Offset right 147 The Edit Bitmap dialog Window ci ccsscciyectesessgexazavelcocersnecesestavedseassacsavechedansenseaservenanie 147 The Cross Section dialog windoW cscsicaivsscascsnatil scanned 148 The Mesh Line dialog WNdOW sidopossioisernn n e aa aa 149 The Fluxes across Mesh Line dialog windoW c ccssscesesseceeeseceeseeeeenteeeeseeeenaees 149 An example of the Background Layer nisccisccsssccssntsacesdecscasasosscccvenddeeds nncseatecessaceasssees 15
37. Ions in Soils Version 1 0 PC Progress Prague Czech Republic 52 pp 2012c im nek J M Th van Genuchten and M ejna The HYDRUS Software Package for Simulating Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated Porous Media Version 2 0 Technical Manual PC Progress Prague Czech Republic 258 pp 2012d im nek J M ejna and M Th van Genuchten The DualPerm Module for HYDRUS 2D 3D Simulating Two Dimensional Water Movement and Solute Transport in Dual Permeability Porous Media Version 1 0 PC Progress Prague Czech Republic 32 pp 2012e Skaggs T H P J Shouse and J A Poss Irrigating Forage Crops with Saline Waters 2 Modeling Root Uptake and Drainage Vadose Zone J 5 824 837 2006 Stumm W and J J Morgan Aquatic Chemistry An Introduction Emphasizing Chemical Equilibria in Natural Waters John Wiley amp Sons New York NY 1981 Taylor S A and G M Ashcroft Physical Edaphology Freeman and Co San Francisco California p 434 435 1972 Twarakavi N K C M Sakai and J im nek An objective analysis of the dynamic nature of field capacity Water Resources Research 45 W10410 doi 10 1029 2009WR007944 9 pp 2009 van Genuchten M Th A closed form equation for predicting the hydraulic conductivity of unsaturated soils Soil Sci Soc Am J 44 892 898 1980 304 van Genuchten M Th Convective dispersive transport of
38. L below which roots extract water at the maximum possible rate P2H Value of the limiting pressure head L below which roots cannot longer extract water at the maximum rate assuming a potential transpiration rate of r2H P2L As P2H but for a potential transpiration rate of r2L P3 Value of the pressure head L below which root water uptake ceases usually taken at the wilting point r2H Potential transpiration rate LT currently set at 0 5 cm day 79 r2L Potential transpiration rate LT currently set at 0 1 cm day The above input parameters permit one to make the variable P2 a function of the potential transpiration rate T P2 presumably decreases at higher transpiration rates HYDRUS currently implements the same linear interpolation scheme as used in several versions of the SWATRE code e g Wesseling and Brandyk 1985 The interpolation scheme is defined in the manual A database of suggested values for different plants for the Feddes et al 1978 model is provided in HYDRUS based on studies by Wesseling 1991 and Taylor and Ashcroft 1972 The Root Water Uptake Parameters for the S shaped water stress response function as suggested by van Genuchten 1985 Fig 34 right are as follows P50 The coefficient A50 in the root water uptake response function associated with water stress L Root water uptake at this pressure head is reduced by 50 P3 The exponent p3 in the root water uptake response function
39. OK TBound1 TBound2 TBound3 TBound4 TBound5 TWell Cancel 0 0 Help Heat Transport Parameters 1 Temperature Amplitude Set Default Volume ee s Heat Capacities Time interval for one temp cycle Thermal Conductivity Heat Transport Parameters 2 Solid bl b2 1 1 56728E 016 2 53474E 016 Previous Figure 32 The Heat Transport Parameters dialog window The following Heat Transport Parameters bottom part of the dialog window are specified for each soil material Solid Volume fraction of solid phase 8 Org M Volume fraction of organic matter 0 Disp L Longitudinal thermal dispersivity Az L Disp T Longitudinal thermal dispersivity Ar L bl Coefficient b in the expression for the thermal conductivity function W L K b2 Coefficient b2 in the expression for the thermal conductivity function W L K b3 Coefficient b in the expression for the thermal conductivity function W L K Cn Volumetric heat capacity of the solid phase Cn J L3 K Co Volumetric heat capacity of organic matter Co J L3 K 75 Cw Volumetric heat capacity of the liquid phase C J L K Boundary Conditions Temperatures for Boundary Conditions with time independent boundary conditions are also specified in this dialog window TBound1 Value of the temperature for the first time independent boundary condition K Set equal to zero if no time independent boundary condition is specified The same for
40. Scale see Figure 141 Edit Isoband Values and Color Spectra Scales Scales PH1 Default _ PH1 PH2 PH2 Standard Empty Standard Empty Fill n Eill Fill Max Min Fill Max Min 15 000 Save z Save 0 000 15 000 Palettes 30 000 Palettes 4000 60 000 75000 30 000 1 O E Format When drawing Isolines 0 When drawing Isolines Double click on the color When drawing Color Contours Double click on the color When drawing Color Contours panel to change colors panel to change colors Number of Intermediate Isolines Number of Intermediate Isolines J E Format Figure 141 Adjusting scale in the Edit Isoband Value and Color Spectra dialog window When using a Custom Scale the actual minimum or maximum of a displayed variable can be outside of the interval of the scale Values outside of the interval of the scale are not displayed in the View window resulting in empty spaces as shown in the upper part of see Figure 142 219 K HYDRUS Furrow HJO fie OR Yow jort Ciaiton Rens Took Qore Wire tb Sums els a alej4 E Furrow Results Pressure Head if 4 View Optors oO 4 Doman Geometry SE FE Meth Sochor OR Doms Propetes a OG ints Contin E Od bands Conditions M Rer WD Prornee Head OW Water Corrieri OW Terperstze Velocty Concentiaten 1 Concentuston 2 Corcentieter 3 COD fown Pace DE Ft Mew AG now AD Sutace
41. Sub Layers Thickness Profiles FE Mesh General Sub Layers Thickness Profiles FE Mesh Solid No Number of Sub Layers i ane nE C Sub Layers Constant Thickness Solid Type Layer Thickness T and Thickness Type Variable or Constant Layered Base Surfaces Autodetect j1 Thickness Vectors Autodetect 1 ET 500 cm Master Thickness Vector Variabl d ariable Comment _ No 1 M Thickness Length 500 cm Edit Solid General Sub Layers Thickness Profiles FE Mesh_ Thickness Profiles Profile Parameters E vo Name Default Profile This Profile is used on Thickness Vectors No Layer Thickness T Thickness Sum TS and Thickness Type Variable or Constant s 100 00 10 00 M 200 00 300 00 200 00 50000 M Figure 75 The Edit Solid dialog window the General Geo Layers and Thickness Profiles Tabs 133 Edit Solid General Sub Layers Thickness Profiles FE Mesh Number of Mesh Layers Generate non uniform distribution of Mesh Layers Update Set Relative Size of FE distance between mesh layers at the top and bottom of the domain RS1 1 RSZ 1 Generate Distribution F Edit Solid General Sub Layers Thickness Profiles FE Mesh FE Mesh Layers N 2q Set vertical Mesh
42. Surfaces User can change the default setting Program Default save it using the button Save as Default and then recall it using the button Set Default Note that different default setting can be saved for different types of domains Different FE Mesh Sections are generated depending on the type of Domain For the 3D Layered Domains FE Mesh Sections can be generated for the Boundary Shell for each Mesh Layer and for both automatically Generated and User Defined Geo Sections For the 3D General Domains FE Mesh Sections can be generated for the Boundary Shell and again for both automatically Generated and User Defined Geo Sections The Partial View is the status of the display in the View window when only part of the transport domain is displayed i e only one or few but not all Sections are displayed The parts that are not displayed are still visible in the background gray thin lines and or surfaces but are inactive and cannot be selected for various operations The Partial View can be cancelled and the entire domain displayed using the menu command Cancel Partial View or the popup menu command Display Whole Domain 234 8 2 Navigator Bars The Navigator Bar Fig 152 is by default located on the left side of the HYDRUS main window A user can however move the Navigator bar to other positions The Navigator Bar has three Tabs a A Data Tab to allow quick access to all input and output data Input data include Domain
43. Thickness should be used and d the position of numbers for various types of numberings fonts for the numbers and whether or not numbers are Transparent Display Options Category Parameters Geometry FE Mesh FE Mesh Nodes Surface Approx Mesh Refinement at Points Refinement on Lines Refinement on Surfaces Domain Properties Points Handles Line Type mail Nodes Solid Thickness Drains Flowing Particles O Dotted Boundary Conditions O Dashed 3 Results O Dash dotted Particle Trajectories Isolines Velocity Vectors Ls C Transparent Auxiliary Objects General OOO Colors Numbering Figure 137 The Display Options dialog window 215 7 1 3 Edit Isoband Value and Color Spectra The Edit Isoband Value and Color Spectra dialog window Fig 138 called by left clicking the color scale display options of the Results version of the Edit Bar allows users to define colors for display of isobands isosurfaces and color spectra and values of particular isolines The default scale has always 11 values which corresponds to 11 colors for color contours and 12 colors for isolines Values at the scale are calculated by evenly dividing the interval between the minimum and maximum of a particular variable Numbers are formatted depending on units used to display a particular variable When the number of displayed digits is insufficient it is possible to use a scientific format E fo
44. When the checkbox Synchronize selection in the Navigator and Views is checked clicking on any object on the Navigator Bar leads to its automatic selection in Views When this checkbox is not checked one can select an object by clicking on it with the right mouse button at the Navigator Bar and using the Select command from the popup menu Option Graphics Program FE Mesh Files and Directories User Interface Language English Visual Style Undo and Autosave Memory size for the Undo buffer Auto save input data to a temporary file enter 0 if you don t want to run auto save General Options J Reload last opened projects at startup Y Save automatically windows settings when dosing project V By default edit Domain Properties BDRC and INITC on Geometrical Objects Calculation and Results By default keep results in external directory for new projects Save FE Mesh in text format for calculation Save Domain Properties in text format for calculation V Use Parallel Calculation Module Figure 162 The Program Options dialog window the Program Options Tab In the Undo and Autosave part of the Program Options Tab Fig 162 one can a select a time interval for Auto save b specify Memory size for the Undo buffer and In the General Options part of the Program Options Tab one can a specify whether or not the program Reloads last opened projects at startup 272
45. actual water content and B is a solute dependent parameter usually 0 7 The reference water content 0 which may be different for different soil layers is calculated from the reference pressure head h which is considered to be constant for a particular compound The solute dependent exponent B and the reference pressure head h are entered in the Water Content Dependent Solute Reaction Parameters dialog window shown in Figure 29 Water Content Dependent Solute Reaction Parameters Parameter 1 B OK Sol SinkWaterl SinkSolid SinkGast Sinkwaterl SinkSoldl SinkGast er Sol Sink Water SinkSolid1 SinkGas1 SinkWaterl SinkSolid1 SinkGas1 Previous Figure 29 The Water Content Dependent Solute Reaction Parameters dialog window 12 3 15 Solution Compositions for the UNSATCHEM Module The set of solution adsorbed and precipitated concentration combinations for the UNSATCHEM module is specified in the Solution Compositions dialog window Fig 30 These solution adsorbed and precipitated concentration combinations can be used to specify the initial and boundary conditions The number of solution adsorbed and precipitated concentration combinations is specified in the General Solute Transport Information window Fig 24 Solution Concentrations need to be specified for all major ions Ca Mg Na K Alkalinity SO CT and an independent tracer Adsorbed Conc
46. amas 123 4 2 2 Steps to Define a Two Dimensional Domain 11 ccccccecceceeeesseeeteesteceensssesees 123 4 2 3 Several notes on rules for correct definition of the GeOMetry 11 ccccceceees 124 ADA dnternal OD CCIS tev sips secsales sirens uaarea a oeeash a a tundra dense eas 125 4 2 5 Check and Repair Geometry siciccicsesacsniiaacicthistsiasiestsceteasvsctiaeleneeneavaenns 127 Openin iSi ais Su E a El Bc a a a TRL Solan les aah ice Su Se vi 121 OMS iss shan cae shes choses acai ai ue tanec tat A a a ails ates stood se ctanien a tes sea T 130 4 4 1 3D Layered Hexahedral Solids ccccccsccccccssssccsssssscesssssececsssuececsssuseesessnaes 130 4 4 2 3D Layered General Solids veicsslsecte Stn cccsadsbahcsennticasaiegues tuts lacedeelgh Sevesticens 131 4 4 2 1 Division of a Solid into Columns cccccccccessececeesteceeeeesneeeeesneeeenees 135 4 4 2 2 Division of a Solid into Geo LayefS sessnnsseenseeeeesseseessesesssseee 135 4 4 2 3 Individual specification of different Thicknesses of Geo Layers at different Thickness Vectors i iioth Ze iin iwi vaduups voistessudsGeasedoaieitesiine 135 4 4 2 4 Steps to Define a 3D Layered DOMAIN 1scccccceeecceseenteeeteenteeeenees 136 AAS 3 D General Solids ira e a teeta aAa e AI ETE ATA aa eaS 136 Thickn ss VectotS urnie ioina ienna i a a a a a i E e a 139 Intersections of Surface and SOUS ssteitadscnionsatit eae Binsin aie 143 Auxiliary Objects irene TE E areas a te
47. and their visibility can be turned on and off using the View Tab at the Navigator Bar Auxiliary Objects gt Background Layers Background Layers are displayed in the View window using suppressed less intense colors so that they do not visually disturb when objects of the geometry are being defined The intensity of display and other parameters can be set intensity of their display can be set between 0 and 1 in the Display Options dialog window the Menu command Options gt Display Options gt Edit Fig 137 If the location of the template background layer is not satisfactory it can be Moved Fig 56 Rotated Fig 57 left Mirrored Fig 57 right Stretched Fig 58 left and or Skewed Fig 58 right as needed 152 4 8 Other Notes on Objects Objects Mesh Refinement define a local density of the FE Mesh in the vicinity of a particular object Possible types of Mesh Refinement are e Mesh Refinement at Point e Mesh Refinement on Curve given by number of points e Mesh Refinement on Curve given by FE size e Mesh Refinement on Surface 4 8 1 Object Numbering Each object has its own number index that serves for unique identification of an object for operations such as Edit Delete or Find Object numbering is fully controlled by the user a user specifies the object index and does not have to be continuous indexes do not have to sequentially increase 4 8 2 Relations among Objects More complex objects are defin
48. are transferred to the rest of the program only when the Apply command is clicked or after the window is closed using the OK button The command Renumber All can be used to renumber the Property Objects This is useful when some previously defined Properties were deleted and the numbering is no longer sequential 7 Sort Property Objects Property Objects EIB 1 Loam Top OO 2 Sand Cll 3 Silt modified Up Down Other Commands Renumber All F Auto apply Figure 127 The Sort Property Objects dialog window A single click on any Surface will select this surface A double click on any Surface will open a dialog for a Property assigned to a particular surface that is currently displayed e g the Edit Materials dialog window Fig 128 In this dialog one can change the Name of the material its Color the Default check box indicates whether the Color has been changed Assign it to different Surfaces indicated by their numbers and register brief Remarks characterizing a particular material 197 Color V Default Assigned to Surfaces No 2 Remark Default Material Apply Figure 128 The Edit Materials dialog window Once the FE Mesh exists assigned properties e g Materials can be transferred on the FE Nodes if it exist using the Edit Properties on FE Mesh when FEM exists and a particular Property has not been yet edi
49. b select Numbering turns on and off the display of numbering for objects selected under Numbering Options on the Navigator Bar c go quickly to various Numbering Options this command will bring the Navigator Bar to the View Tab on Numbering d switch Full Rendering Wire Rendering see 8 1 4 e start the Autorotate function that will rotate the transport domain in the View window f call the Show Work Plane i e to show the axis and the origin of the Work Plane g call the Set Grid and Work Plane dialog window Fig 147 Set Grid and Work Plane h select the Coordinate System call the List of Available Coordinate Systems dialog window and i call the Display Options dialog window Fig 137 231 View Isometric In x direction In direction 8 In Z direction S Reverse x direction Numbering Numbering Options Full Rendering P Autorotate oes g Reverse Y direction Show Work Plane Reverse Z direction 2 Set Grid and Work Plane PDE Tijl Perspective S Coordinate System A Display Options Figure 150 The Pop up Menu from the View window 8 1 7 Drag and Drop By clicking and holding the left mouse button on selected objects in the View window the Drag and Drop operation is started This operation allows selected objects to be moved to a new location Simultaneous holding the Ctrl keyboard button leads to the creation of a copy of the selected object The copy can be moved into a differe
50. condition for problems that involve slopes an option is provided to have pressure heads decrease in the x and y the latter only for three dimensional problems directions Slope in X direction and Slope in Y direction The right top part of the dialog window Values in selected nodes in Figure 116 provides information about the selected nodes i e the number of selected nodes and the minimum and maximum values of the pressure head or water content If a certain node is selected that is not located on the boundary this node can be declared an Internal Pressure Head Sink Source The pressure head at that node can then be kept constant or be time variable during the simulation When the option Set to Field Capacity is selected the initial pressure heads or water contents depending on the selection made in the Iteration Criteria window Fig 17 is assigned to selected nodes as follows Twarakavi et al 2009 183 _ Or 0 77 0 60 2 log19 K ae where Ox and Sp are the water content and saturation at field capacity and 6 0 n and K are the soil hydraulic parameters for the van Genuchten 1980 model Note that the water content at field capacity corresponds to the hydraulic conductivity of about 0 01 cm d Twarakavi et al 2009 The initial pressure head at field capacity is calculated from the water content at field capacity using the the van Genuchten 1980 retention curve model Similar but simpler dialog win
51. dauaees Gace gn deeeaetoeaedesiazal 79 3 20 Root Distribution Parameters secctosi ute teaedatevissete Ahead eae de 82 3 21 Time Variable Boundary Conditions cclaseuutucniawesueacavssntasadigoaneubacinusMubedhunstasoieasias 84 3 22 Constructed Wetlands ssrin asia an a aa T E A ERE 87 3 23 The Slope Stability Module te cituwieichcoslioveri caidas tan oteciadalcsn deticeidion Jar Wtetiaabanteketasins 97 4 Geometry of the Transport Domainn 0 cc cece cceccccesscecesececsseeeceececsseeeeseeeeseeeesaees 101 4 1 4 2 4 3 4 4 4 5 4 6 4 7 B o ndar Obje eean a AN NN a SI a ae 101 AWT Pomi Sanan nea a E a Reset eel eg aad ea ence 104 4 1 2 Einesand Polynesien a O60 aA epa e saan 107 4 1 3 Aresand Circles sc2 isceceesak ice esa deh ha Gessdde inaia i eels iais 108 4 1 4 Curves AN SINGS tiie Rie sda sata iia Silla aids eal Dain alae Bulletin 111 4 1 5 Common Information for a Graphical Input Of Objects cccccccccecccceeseteeeeeeees 113 4 1 6 Translate Copy Rotate Mirror Stretch and Skew Operations 114 4 1 7 Additional ODOT GONG peptic cts Ses deal eda danasbepalsVeiantacss hcles bute beaadatg iss eumetigadsidlatades 117 SUr OC OS cis to n Croce a cucelads ioesa a E Sadienes eecokneutetida 118 42 1 General TCI ONS ncssa A E Cheats tis 118 BD NL 5 gt Planar Surfaces ianen a i a eiia aai 119 42 12 Curved Surfaces otiuhsihand no nun aaa a a a aN 121 4 2 1 3 Partal SIATOCES noei an e a a a
52. displayed as being the same For example a hexahedral of any dimensions will be displayed as a cube b Mild Stretching which adjust view stretching only when large differences in dimensions in different directions exist By default there will be no view stretching when the larges dimension is 5 times larger than the smallest dimension A user should first select the Method for Calculation of Stretching Factors either Strict or Mild then click the command Calculate Factors which will calculate stretching factors based on the method of stretching selected and finally click the Apply command to update the View Window 229 8 1 4 Rendering Model Rendering serves to rapidly switching between displays of surfaces and solids One can select the Wire and Full Rendering options An advantage of Wire Rendering is mainly the speed of the display while Full Rendering provides a more realistic display of three dimensional objects 2 pE wie O Full S E Surfaces Outline O Transparent Filled S E Solids O Outline Transparent Filled H E44 Graph Type H E E gt Lighting a mA Color Scale a Data Go View amp Sections Figure 149 The Rendering part of the View Tab of the Navigator Bar 8 1 5 Selection and Edit Commands The selection of graphical objects is based on standards used in MS Office An object is selected by clicking the left mouse button a multiple selection is made
53. displayed next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 73 left The Edit Bar will also show which point curve and surface their numbers are being defined and what reference coordinate system the current coordinate system the grid origin or the last inserted point is used After two points defining a surface are specified both the cursor and the Edit Bar change Fig 73 right for the definition of the Thickness Vector The selection can be made on the Edit Bar that also displays the height of the Thickness Vector L and a step dL in which it can be increased The Thickness Vector can be created a Perpendicular to the Base Surface b in X direction c in Y direction or d in Z direction The process of defining a new Hexahedral solid is ended after the Thickness Vector is defined 4 4 2 3D Layered General Solids xi Aa Domain Geometry Set new Solid Extruded Numbers for new Tz oT Solid E i a Domain Geometry 7 s Thickness 1 Set new Solid Extruded a i Numbers for new peas 3 Solid L_ Thickness Length Thickness 1 L 590 00 fem Point 3 dL 10 oo cm Surface to extrude Thickness Direction Surface 2 Perpendicular to the Surface Autodetect O In x direction V Base Surfaces O In Y direction V Thick Vectors O InZ direction sm Stop Help Hel a bn Ke Step 2 of 2 Ke Step 1
54. edited using the following operations delete copy Fig 56 move Fig 56 rotate Fig 57 left and mirror Fig 57 right Note that in 101 addition to objects particular nodes of an object can belong to a selected set as well in which case the edit operations are carried out also for these points Editing of selected objects e g moving objects also depends on the currently selected input style The objects are moved with the cursor when the graphical mode is selected while in numerical mode a vector of translation X Y and Z must be specified It is possible to directly edit nodes of objects with the commands insert point Fig 48 delete point and or move point Before saving the data an option is always displayed whether or not to verify the consistency of the geometry We strongly recommend to regularly perform this test in order to prevent errors in subsequent calculations e g during mesh generation Table 17 Definition of terms related to geometry design Objects Objects are basic elements for building a geometric model of the computational domain and for defining other properties of the computational problem Objects are divided into several categories e g Geometry FE mesh or Auxiliary with each category containing several fields of objects of the same type The shape boundary of the computational domain is defined using Geometric objects Basic types of geometric objects are points curves poly
55. file called Level_01 dir that needs to be located in the same folder as the computational module This file can be written using any text editor such as Notepad This file must have one line which provides the path to the folder in which the input and output files are located Example of the Level_01 dir file c program files pc progress hydrus3d mydirect run1 For the input files to be available in the Working Folder the Working Folder needs to be either Permanent see the Project Information dialog or the HYDRUS GUI needs to be opened when the Working Folder is Temporary In each case the text input files need to be created using the menu command File gt Import and Export gt Export Data for HYDRUS Solver in Text Format HYDRUS 2D 3D allows users to select multiple projects and run them simultaneously using the Calculate All Open Projects or Select Projects to Calculate To run several projects sequentially is more complex One needs to prepare a batch file e g run bat and files describing paths e g pathl path2 etc to project folders to be run in advance One needs to copy these files into the program folder e g c program files ussl hydrus3d Additionally the check box Hit Enter at the End in the Output Information window has to be unchecked for all projects to be run sequentially Example of the run bat file copy path level_O1 dir h2d_calc copy path level_01 dir h2d_calc Exam
56. flux boundary 2 seepage face 3 variable pressure head or flux boundary 1 4 atmospheric boundary 5 drains 6 free or deep drainage boundary 7 8 and 9 variable pressure head or flux boundaries 2 3 or 4 respectively 45 3 3 Time Information The Time Information dialog window Fig 15 contains information associated with the Time Discretization the Time Units and the implementation of Boundary Conditions Seconds Initial Time day 90 Cancel _ gt Minutes Final Time day 270 Hours Initial Time Step day 0 05 Time Units Time Discretization Days Minimum Time Step day 1e 006 Years Maximum Time Step day 0 5 Boundary Conditions 7 Time Variable Boundary Conditions Number of Time Variable Boundary Records Number of times to repeat the same set of BC records Previous Previous Figure 15 The Time Information dialog window Boundary Conditions Time Variable Boundary Condition The Number of Time Variable Boundary Records and time dependent boundary conditions must be specified when this box is checked The boundary conditions otherwise are assumed to be constant in time The same set of boundary records can be repeated number of times Number of times to repeat the same set of BC records periodically with a time period tPeriod tAtmLast tInit where tInit is the Initial Time and tAtmLast is the time of the last specified time boun
57. had a box for possible comments or a description A surface must be created before one can do finite element discretization A Surface can also be created automatically by using the menu command Tools gt Generate Domain Surfaces or the Edit Bar command Planar Surfaces Generate After this command is clicked on the program analyses existing boundary curves and attempts to generate planar surfaces automatically i e without the user being required to define its boundaries This operation is usually successful when there is a single uninterrupted boundary curve The operation may fail when there are some ambiguities such as when there are multiple curves or when boundary curves are not closed If this operation fails the following warning is displayed Fig 61 and the user needs to define Surfaces manually 118 i The program was not able to create surface s automatically Possible reasons 1 Boundary curves are not closed 2 The boundary contains a point connecting three or more curves The program is not able to resolve this ambiguity i e it is not able to select a curve that should be used as the surface boundary Solution Please use the tool Surface via Boundaries to define boundary curves of the surface manually Figure 61 The warning issued when Surfaces cannot be created automatically and must be defined manually Edit Surface General Integrated Surface No Surface Type Number for new Planar Surface
58. head precision tolerances 50 Max Number of Iterations Maximum number of iterations allowed during any time step while solving the nonlinear Richards equation using a modified Picard method The recommended and default value is 10 It is usually not helpful to use a larger value than 10 If HYDRUS does not converge in 10 iterations then there is a relatively small probability that it will do so during more iteration Even if it does it is much more efficient to reduce the time step and attempt to find the solution with a smaller time step which is done automatically by the program when Iter is reached Water Content Tolerance Absolute water content tolerance for nodes in the unsaturated part of the flow region When the water contents between two successive iterations during a particular time step change less than this parameter the iterative process stops and the numerical solution proceeds to the new time step Its recommended and default value is 0 001 Pressure Head Tolerance Absolute pressure head tolerance for nodes in the saturated part of the flow region L When the pressure heads between two successive iterations during a particular time step change less than this parameter the iterative process stops and the numerical solution proceeds to the new time step Its recommended and default value is 1 cm Information specified in the Time Step Control part of the dialog window is related to the automatic adjustment of the time s
59. information is to be printed at a regular Time Interval 48 Screen Output Check box to decide whether or not information about the simulation run is to be printed to the screen during execution of the HYDRUS computational code We recommend to check this box for direct problems but not for inverse problems In the Print Times part of the dialog window one specifies the number of Print Times Count at which detailed information about the pressure heads water contents concentrations temperatures fluxes and the soil water and solute balances will be printed Clicking on the Default command button will cause the print times to be distributed evenly between the initial and final time Clicking on the Default log command button will cause the print times to be distributed evenly between the initial and final time on the log scale This option is enabled only for larger times Finally in the Subregions part one selects the number of regions for which a mass balance will be evaluated and printed to the Balance out output file 49 3 5 Iteration Criteria The Iteration Criteria dialog window Fig 17 contains information related to the iterative process that is used to solve the Richards equation Because of the nonlinear nature of the Richards equation an iterative process must be used to obtain solutions of the global matrix equation at each new time step For each iteration a system of linearized algebraic equations is first derived a
60. of the upper limit L of the pressure head interval for tension interval which a table of hydraulic properties will be generated internally for each material Finally in the Initial Conditions part of the dialog window a user specifies whether the initial conditions for the water flow calculations are to be specified in terms of the pressure head or water content 52 3 6 Soil Hydraulic Model In the Soil Hydraulic Model dialog window Fig 18 users select the Hydraulic Model to be used to describe the soil hydraulic properties and specify whether or not Hysteresis is to be considered during the calculations Hydraulic Model Single Porosity Models E With Air Entry Value of 2 cm Modified van Genuchten Brooks Corey Kosugi log normal Dual Porosity Dual Permeability Models Dual porosity Durner dual van Genuchten Mualem Dual porosity mobileimmobile water c mass transfer Dual porosity mobile immobile head mass transfer Dual permeability Add on Module Other options Look up Tables Hysteresis No Hysteresis Hysteresis in Retention Curve Hysteresis in Retention Curve and Conductivity Hysteresis in retention curve no pumping Bob Lenhard Initially Drying Curve Initially Wetting Curve Figure 18 The Soil Hydraulic Model dialog window Hydraulic Model The code allows users to select six types of models for the soil hydraulic properties a the van Genuc
61. on acetate SA 12 Lysis of XAMB Acetotrophic sulphate reducing bacteria 13 Growth of XASRB Anaerobic growth of acetotrophic sulphate reducing bacteria 14 Lysis of XASRB Sulphide oxidizing bacteria 15 Aerobic growth of XSOB on SH2S The opposite process to process 13 the oxidation of SH2S to SSO4 16 Anoxic growth of XSOB on SH2S Similar to process 15 but under anoxic conditions 17 Lysis of XSOB 88 Solute Transport Constructed Wetland Model CW2D Parameters Hydrolysis Hydrolysis Rate Constant oo O Sat Inh Coeff for Hydrolysis Heterotrophic Organisms Mineralization Max Aerobic Growth Rate Rate Constant for Lysis Sat Inh Coeff for 02 Heterotrophic Organisms Denitrification Max Denitrification Rate Sat Inh Coeff for 02 Sat Inh Coeff for NO3 Sat Inh Coeff for P Autotrophic Bacteria Nitrosonomas Max Aerobic Growth Rate Rate Constant for Lysis Sat Inh Coeff for 02 Autotrophic Bacteria Nitrobacter Max Aerobic Growth Rate Rate Constant for Lysis Sat Inh Coeff for 02 0 0167 0 0015 0 1 Sat Inh Coeff for Substr Sat Inh Coeff for NH4 Sat Inh Coeff for P Sat Inh Coeff for NO2 Sat Inh Coeff for Substr Sat Inh Coeff for NH4 Sat Inh Coeff for NH4 Sat Inh Coeff for P Sat Inh Coeff for NO2 Sat Inh Coeff for NH4 Sat Inh Co
62. or right mouse K Press Esc or right mouse button to end the tool button to end the tool Figure 86 The Edit Bar during the process of graphically defining a Dimension Selection of two definition points the distance of which is to be labeled left and the dimension type right 145 4 7 2 Labels Labels can add any desired text to the computational domain in the View window using the Insert gt Auxiliary Objects gt Dimensions command or the Comments command from the Insert Object part of the Domain Geometry version of the Edit Bar One then clicks simply anywhere in the View window and write the desired text The text itself its color frame and its offset can be specified in the Edit Comment dialog window Fig 87 Figure 107 shows an example of how the Furrow Label is used Edit Comment No Text This is a well Options Offset ay a inet C Frame dy pixels Figure 87 The Edit Comment dialog window After a command for defining a Comment is selected a user needs to first select a location to which the comment will point using a cursor The Edit Bar lists during this operation the coordinates of a cursor Position the color to be used for a comment and the comment text Text Fig 88 left A user can also select the Font to be used for the comment text After the position is selected a user defines an Offset of the Comment text The comment text the comment font
63. resolves problems with fonts for the Chinese Japanese and other similar Windows systems Version 2 04 additionally supports two add on modules such as the HyPar module see Section 9 1 and the Slope Stability module While the HyPar module is a parallelized version of the standard two dimensional and three dimensional HYDRUS computational modules h2d_calc exe and h3d_calc exe the Slope Stability module is intended to be used mainly for stability checks of embankments dams earth cuts and anchored sheeting structures This report serves as a User Manual and reference document of the Graphical User Interface of the HYDRUS software package Technical aspects such as governing equations and details about the invoked numerical techniques are documented in a separate Technical Manual 21 22 Introduction to the HYDRUS Graphical User Interface The past several decades or so has seen an explosion of increasingly sophisticated numerical models for simulating water flow and contaminant transport in the subsurface including models dealing with one and multi dimensional flow and transport processes in the unsaturated or vadose zone between the soil surface and the ground water table Even with an abundance of well documented models now available one major problem often preventing their optimal use is the extensive work required for data preparation numerical grid design and graphical presentation of the output results Hence the more widespr
64. saved as a series of lines i e SURFACE_LINES f The THICKNESS _ARR3Z_NLAYERS command allows importing multiple Thickness Vectors to define variable thickness of a Solid On each Thickness Vector one can define multiple z coordinates that are used to divide a Solid automatically into Layers with variable thicknesses The number of Layers is arbitrary min 1 max 100 and their number is given by the number of columns in the file KEY_WORD for Import Export POINTS LINES POLYLINE SPLINE CIRCLE ARC SURFACE_LINES SURFACE _POLYLINE SURFACE_SPLINE SURFACE _CIRCLE OPENING_LINES OPENING_POLYLINE OPENING_SPLINE OPENING_CIRCLE THICKNESS THICKNESS_ARR3Z THICKNESS_ARR3Z_NLAYERS Notes on the THICKNESS_ARR3Z_NLAYERS command the THICKNESS_ARR3Z command has only the first five columns Particular columns in the input file have the following meaning 154 Di ON en X coordinate m Y coordinate m Z coordinate m of the Definition Point of the Thickness Vector Anchor Point see Figure 79 of the User Manual with the Edit Thickness Vector dialog and the point denoted P The Definition Anchor Point must lie in the plane of the Base surface The Z coordinate in the third column will thus likely be constant for all Thickness Vectors unless the Base Surface is
65. solutes involved in sequential first order decay reactions Computers amp Geosci 11 2 129 147 1985 Vrugt J A J W Hopmans and J im nek Calibration of a two dimensional root water uptake model Soil Sci Soc Am J 65 4 1027 1037 2001 Vrugt J A M T van Wijk J W Hopmans and J im nek One two and three dimensional root water uptake functions for transient modeling Water Resour Res 37 10 2457 2470 2002 Vogel T and M Cislerova On the reliability of unsaturated hydraulic conductivity calculated from the moisture retention curve Transport in Porous Media 3 1 15 1988 Walker A A simulation model for prediction of herbicide persistence J Environ Quality 3 4 396 401 1974 Wesseling J G J A Elbers P Kabat and B J van den Broek SWATRE instructions for input Internal Note Winand Staring Centre Wageningen the Netherlands 1991 Yeh G T and V S Tripathi HY DROGEOCHEM A coupled model of HYDROlogic transport and GEOCHEMical equilibria in reactive multicomponent systems Environs Sci Div Publ No 3170 Oak Ridge National Lab Oak Ridge TN 1990 305
66. the Targeted FE Size is reached further away in the computational domain Notice that the dialog window also displays the Global Targeted FE Size The same FE Mesh Refinement i e the same refined FE size can be assigned to multiple Points in the transport domain There are two ways how the FE Mesh Refinement can be assigned to a Line Figure 106 top right and bottom left Users can either specify the FE Size Line FE Size Figure 106 top right or the Number of Points Line Number of Points Figure 106 bottom left to be used on the entire line Similarly as for points the FE Size either given directly or calculated from the number of points will be used on the Line while sizes of FE away from the Line will gradually increased until the Targeted FE Size is reached further away in the computational domain Again the same FE Mesh Line Refinement i e the same refined FE size can be assigned to multiple Lines in the computational domain The size of FEs specified by the Number of Points on the Line does not affect the sizes of FEs on neighboring lines The FE Mesh Refinement can also be assigned to a selected Surface Figure 106 bottom right In this case users need to define FE Size for a selected Surface Note that this option is useful only when multiple Surfaces are used in the computational domain The refined FE Size is then used on the entire surface including boundaries with other Surfaces and the Targeted FE Size is reach
67. the lowest z coordinate is found for all selected surfaces 2 The default solute and heat transport boundary conditions are the Third Type BCs which are listed right after the No Flux BC This BC is by default assigned to all boundaries to which the water flow BCs have been defined Note that if you redefine this BC e g change the Third Type BC into the First Type BC the newly defined BC will be used as a default BC for solute and or heat transport 200 No Name Boundary Condition Type 4 O0 No Flux i BOE Constant Head Boundary Condition Parameters OM Constant Flux OM Variable Head 1 Pressure Head Value 1 000 m Of Variable Head 2 OD variable Head 3 7 Equilibrium from the lowest located nodal OD Variable Head 4 point OW Variable Flux 1 OB Variable Flux 2 OD Variable Flux 3 OD Variable Flux 4 Assigned to Surfaces No Free Drainage OM Deep Drainage 6 24 OM Seepage Face OM Atmospheric Boundary Remark Color Ground Water 7 Default ico OK Cancel Figure 131 The Edit Water Flow Boundary Condition dialog window 6 5 5 Additional Notes on Properties at Geometric Objects a b c d e When the same pressure head initial or boundary condition involving either Equilibrium from the lowest located point or A linear distribution is chosen for multiple surfaces or curves then this condition is app
68. the numbering of objects All possible options related to the Content of the Scene are located on the Navigator Bar of the View Tab Section 8 2 c Displaying and or hiding parts of complicated objects One often needs to display only some part of a complicated object while hiding the rest For this purpose one can use commands related to Sections i e parts of the computational domain or FE Mesh Detailed information is given in Chapter 8 1 8 on Sections d Colors fonts and type of lines 227 One can define colors the style and thickness of lines fonts for numbering and other displaying options for almost all displayed used objects Separate default sets exist for the display for the screen and the printer Users can create and save additional combinations of display options Detailed information is provided in Chapter 7 1 1 on Display Options 8 1 2 Grid and Work Plane The Grid and Work Plane dialog window Fig 147 allows users to a select a Work Plane i e a plane in which users can specify various boundary objects initial and boundary conditions or other information b define the Origin of the coordinate system and c define the Alignment Grid The Grid is defined by its Origin the type Grid Type of coordinate system involved either Cartesian or Polar and the Grid Spacing The Grid can also be rotated to facilitate work for example when defining the domain for a hill slope problem Grid and Work Plane W
69. the point to which the Thickness vector is assigned This method is suitable especially in case when points located at the upper surface of the domain already exist see Tutorial 2 07 In this case we need to specify Thickness Vectors whose upper points were read in from a GIS file and we need to create the lower beginning points that would be located in the plane of the Base Surface Note in the Tutorial that the Reverse Points option was automatically checked on the Edit Bar This is because the thickness Vectors have to originate from the Base Surface and not from the upper surface If the Reverse Points option was not checked Thickness Vectors would originate from the upper surface and end at the Base Surface Two Points A user selects graphically two existing Points to form the Thickness Vector In this case an Anchoring beginning Point of a Thickness Vector is the first selected point It is therefore important to select points defining a Thickness Vector in the right order i e to first select a point at the Base Surface and only then a point at the upper surface of the domain Three Points A Thickness Vector is in general defined by three points an Anchoring Point a Beginning Point and an End Point Fig 79 The Anchoring Point must be located in the Base Surface The Anchoring Point is usually the same as the Beginning Point i e both Point indices are the same and one does not have to pay attention to it However in general
70. time centered implicit scheme and 1 0 for a fully implicit scheme The structure of the final set of linear equations G c g obtained after the 61 spatial and temporal discretization of the governing advection dispersion equation depends upon the value of the temporal weighing factor e The explicit e 0 and fully implicit e 1 schemes require that the global matrix G and the vector g be evaluated at only one time level the previous or current time level The other two schemes require evaluation at both time levels Also the Crank Nicholson and implicit schemes lead to an asymmetric banded matrix G By contrast the explicit scheme s 0 leads to a diagonal matrix G which is much easier to solve but generally requires much smaller time steps The Crank Nicholson centered scheme is recommended in view of solution precision The fully implicit scheme also leads to numerical dispersion but is better in avoiding numerical instabilities The explicit scheme is most prone to numerical instabilities with undesired oscillations and is currently disabled b Space Weighting Scheme HYDRUS provides three options for the Space Weighting Scheme i e the regular Galerkin Finite Elements formulation the Upstream Weighting Finite Elements formulation and the Galerkin Finite Elements formulation with Artificial Dispersion While the Galerkin Finite Elements formulation is recommended in view of solution precision Upstream Weigh
71. two points specifying their beginning and end Several lines can be connected to form polylines by connecting the beginning and end of two neighboring lines Nodes can not coincide while lines can not intersect each other Arcs An arc can be defined either by a three points on its circumference b a center a radius two angles starting and final angle and its orientation and c two points a center and a radius Circles A circle can be defined either by a center and a radius or by three different points Surface A surface the computational domain of two dimensional applications is defined by a finite number of continuous disjunctive bounded two dimensional subdomains Fig 46 This means that the domain can be multicomponent but that each of its components must have only one outer boundary curve The domain can contain any finite number of internal holes or internal curves Surfaces can be either planar surfaces defined in a single plane or curved surfaces e g Quadrangle Rotary Pipe or B Spline The base surface is a two dimensional planar surface that can be extended into a three dimensional solid the computational domain of three dimensional applications using thickness vectors Thickness Vectors The term thickness vector is used for a vector perpendicular to the base surface that extends the Base Surface to form a solid three dimensional computational domain Solids The term solid represents a three dimensio
72. when double clicking on an observation node in the View window when working in the Properties on Geometric Objects mode or an Observation Node item in the Navigator Bar This window displays a the Name of the observation node note that the observation node can be renamed using a brief text such as drain tensiometer TDR etc b indication whether it is Defined at Geometric Node or FE Mesh Node and c a brief Remark note Observation Node 1 Defined at Defined at geomentrical node No 0 Defined at FE Mesh Node Remark Figure 129 The Observation Node dialog window 6 5 3 Initial Conditions at Geometric Objects Property Objects for Initial Conditions are defined or edited using the New or Edit Pressure Head Concentration Initial Condition dialog windows shown in Figure 130 Note that parameters and values that are entered in these dialogs are the same as those entered in Figure 116 when defining Initial Conditions directly at the FE Mesh Here one can additionally define the Name of the Initial Condition the Color which represents it either Default or selected register a brief Remark and select to which surfaces it is assigned to Assigned to Surfaces No 199 No Name Color oeut BE et Distribution No Name Color 5 Constant 1 Concentration IC 1 F Default HM se Linear distribution with depth Equilibrium from the lowest located nodal point
73. with prescribed Dirichlet boundary conditions see the Technical Manual Nodal fluxes are calculated from the finite element matrix equation that is obtained by discretization of the Richards equation and assembled for all elements on one side of the selected internal line The finite element matrix equation for internal fluxes is calculated at the last iteration after convergence for given time level had been achieved Fluxes calculated directly from the Richards equation are much more accurate than fluxes calculated using Darcy s law and have the same accuracy as the overall solution Convective Solute Fluxes are then calculated simply by multiplying water flux values with nodal concentrations Note that the reported solute fluxes across mesh lines do not include dispersive diffusive solute flux 4 7 6 Background Layers Background Layers are geometric objects that can serve as a template for defining the transport domain A Background Layer consists of nodes and curves that are not part of the transport domain but its components can be used to define the transport domain A Background Layer is usually read from the DXF file AutoCAD Figure 95 but may be also read from another HYDRUS project h3d or h3d2 or from STL stereolithography TIN Triangular Irregular Network or BMT bitmap formats Figure 94 An example of a very complex Background Layer unrelated to hydrology read from the DXF file is given in Figure 93 In the New Backgr
74. 0 1380 0 592 504 0 Loamy Sand 0 035 0 401 0 1150 0 474 146 6 Sandy Loam 0 041 0 412 0 0682 0 322 62 2 Loam 0 027 0 434 0 0897 0 220 31 7 Silt 0 015 0 486 0 0482 0 211 16 3 Silty Loam 0 015 0 486 0 0482 0 211 16 3 Sandy Clay Loam 0 068 0 330 0 0356 0 250 10 3 Clay Loam 0 075 0 390 0 0386 0 194 5 52 Silty Clay Loam 0 040 0 432 0 0307 0 151 3 60 Sandy Clay 0 109 0 321 0 0343 0 168 2 88 Silty Clay 0 056 0 423 0 0292 0 127 2 16 Clay 0 090 0 385 0 0268 0 131 1 44 Table 10 Soil hydraulic parameters for the analytical functions of Kosugi 1996 for twelve textural classes of the USDA soil textural triangle Textural class 0 O a n K L L L L em cm d Sand 0 045 0 430 303 7 0 383 712 8 Loamy Sand 0 057 0 410 12 47 0 950 350 2 Sandy Loam 0 065 0 410 27 42 1 26 106 1 Loam 0 078 0 430 101 8 1 80 24 96 Silt 0 034 0 460 510 6 2 48 6 00 Silty Loam 0 067 0 450 325 9 2 30 10 80 Sandy Clay Loam 0 100 0 390 80 89 2 04 31 44 Clay Loam 0 095 0 410 666 3 2 81 6 24 Silty Clay Loam 0 089 0 430 2853 3 26 1 68 Sandy Clay 0 100 0 380 1129 3 41 2 88 Silty Clay 0 070 0 360 140538 4 49 0 48 Clay 0 068 0 380 103815 4 67 4 80 Note that in Version 2 each material can have a name e g Material 1 Sand Clay When soil hydraulic parameters are assigned using the Soil Catalog the names of textural classes will appear in the Name column These names will then appear throughout the HYDRUS GUL e g at the Edit Bar or in the Sort Property Object wind
75. 000 2 100000e 000 3 200000e 000 Other notes 9 10 11 2 The minimum number of columns is 5 this corresponds to a single layer Z coordinates must be entered in the correct sequence i e from the bottom Base Surface up towards the end of the Thickness Vector If layers are to be defined in a different direction than Z e g when the Base Surface lie in the XZ plane one needs to first carry out the standard import in the Z direction and then to rotate the entire domain using the Rotate function When the THICKNESS_ARR3Z_NLAYERS is used i e the input file includes data of thickness vectors with multiple geo layers this key word can be processed fully only if the domain already contains a 3D Layered Solid If there is no Solid defined yet then HYDRUS is not able to create a Solid automatically from imported points because its Base Surface can have a very complex shape There are two ways how to proceed a Press OK to continue HYDRUS will import first only thickness vectors without geo layers Then define a 3D Layered Solid using imported points and import the same file again Geo layers will be added to the Solid during this second import b Press Cancel to cancel this import First define a 3D Layered Solid and then import this file again Thickness vectors with layers will be added to the Solid 155 4 10 Import Geometry from a DXF File It is possible to Import the definition of object
76. 1 The New Background Layer dialog window escesceeeceeeseeeeeeceseeeeeeesaeecsaeeneeesees 151 The Import Geometry from a DXF File dialog window eeeceeeeeeseeeseeeteeeeees 156 The Rectangular Domain Discretization dialog WiINdOW ceeeeeeeeeseeeneeeteeeeees 158 The Hexahedral Domain Discretization dialog WindOW ccsccceeseceeeteeeeeteeeennees 159 The FE Mesh Parameters dialog window the Main Tab for 3D Layered left and 3D General right SEOMENIES is veiieisct cesacavtysedvestcvaussseenseed quadeawel aesaaeeaned baosnsetana eats 160 The FE Mesh Parameters dialog window Tab Stretching cece eeeeeeeeeeeeeeeeee 161 The Mesh Stretching dialog window for a Local FE Mesh Stretching 0 162 Listing of FE Mesh Stretchings on the Navigator Bar eeeseseeeseceseeeeeeeeeees 162 An example of the FE Mesh with three FE Mesh Stretchings assigned to areas below the dotiiain SULACE scc2 se scleg arate tan ets te cece sansa cote atts aed sie 163 The FE Mesh Parameters dialog window Tab MG Options scceesseeeeeteeees 164 The FE Mesh Parameters dialog window Tab Options e cc eeeeseeeseeereeereees 166 The FE Mesh Parameters dialog window Mesh Section Tab seneese 167 The New FE Mesh Refinement dialog window for the MeshGen2D module with four different types of refinements applied to a Point a Line with a given FE size or the number of Points and to a Surface
77. 12b The HP2 module is the result of coupling Hydrus its two dimensional part with the PHREEQC geochemical code Parkhurst and Appelo 1999 and corresponds to a similar one dimensional module HP1 Jacques and im nek 2005 2010 Jacques et al 2006 2008 HP2 has apart from the dimensionality 2D the same capabilities as HP1 HP2 contains modules simulating 1 transient water flow 2 the transport of 39 multiple components 3 mixed equilibrium kinetic biogeochemical reactions and 4 heat transport in two dimensional variably saturated porous media soils Detailed description of the HP2 Module is given in the HP2 user manual im nek et al 2012a The program automatically considers transient water flow when the Water Flow option is selected Otherwise the code tries to calculate steady state flow from the specified initial and boundary conditions The success of such calculations depends on the complexity and or nonlinearity of the problem If unsuccessful then a model run with constant boundary conditions and long simulation time may be required The Dual Permeability Model can be selected as an alternative description for water flow If the solute transport heat transport or root water uptake options originally considered in an existing project are switched off by the user the program issues a warning that all data related to these processes will be lost If this loss is undesirable we recommend that users fir
78. 166 Warning issued when attempting to make changes to the Authorization Status while not running HYDRUS with administrator privileges F Authorization Method Software Key Select available authorization method Hardware Key automatically at startup History of Activations Module Name Status UNSATCHEM 2D WETLAND 2D Enabled DualPerm 2D Enabled C Ride 2D Enabled HP2 Enabled Module Description The geochemical UNSATCHEM module Simunek and Suarez 1994 simulates the transport of major ions in variably saturated porous media including major ion equilibrium and kinetic non equilibrium chemistry The resulting code is intended for prediction of major ion chemistry and water and solute fluxes in soils during transient water flow including root water uptake The major variables of the chemical system in UNSATCHEM are Ca Mg Na K S04 Cl NO3 H4Si04 alkalinity and C02 The model accounts for various equilibrium chemical reactions between these components such as complexation cation exchange and precipitation dissolution UNSATCHEM is intended for evaluating soil salinization sodification and non point source pollution and or proper irrigation fertilization and surface soil including evaluating reclamation of sodic soils and groundwater management ok __ _ Cancel _Hep Figure 167 The HYDRUS Authorization Status dialog window Tab Add on Modules 277 The s
79. 198 The Observation Node dialog Window c cccessceceeneeceeeeeecseeeeesneeeeeeeeeneeeenaeeees 199 The Edit Pressure Head left and Concentration right Initial Conditions dialog STO Wot is Soe anaes ca a eA cee A cnet a a a Socata or a 200 The Edit Water Flow Boundary Condition dialog window eeseeeeeeeeeeereees 201 The Import Initial Condition dialog Window cceeseeeseceeeeeeeeeeeeceaeeeseeeeeeeeaeees 202 The Import Selected Quantities dialog WINdOW c cceeseceeeseceesteeeeeteeeenteeeenaeeees 203 The Import of Values from Scattered Points dialog window eseeeeeeereeeeeees 206 13 Figure 135 Figure 136 Figure 137 Figure 138 Figure 139 Figure 140 Figure 141 Figure 142 Figure 143 Figure 144 Figure 145 Figure 146 Figure 147 Figure 148 Figure 149 Figure 150 Figure 151 Figure 152 Figure 153 Figure 154 Figure 155 Figure 156 Figure 157 Figure 158 Figure 159 Figure 160 Figure 161 Figure 162 The Results Graphical Display part of Data Tab of the Navigator Bar for the standard left Unsatchem centre and Wetland right modules eee 213 The Results part of the View Tab of the Navigator Bar with the display of various alterat ve Vanavles 03d so ae ee OR RG Se ed eG 214 The Display Options dialog Window ceescceceeeeecseececseeeecseeceeseeeseeeeenaeeeenaeeees 215 The Edit Isoband Value and Color Spectra dialog W
80. 3 1996 Langergraber G and J im nek Modeling variably saturated water flow and multi component reactive transport in constructed wetlands Vadose Zone Journal 4 924 938 2005 Langergraber G and J im nek The Multi component Reactive Transport Module CW2D for Constructed Wetlands for the HYDRUS Software Package Manual Version 1 0 HYDRUS Software Series 2 Department of Environmental Sciences University of California Riverside Riverside CA 72 pp 2006 Langergraber G D Rousseau J Garcia and J Mean CWM1 A general model to describe biokinetic processes in subsurface flow constructed wetlands Water Science Technology 59 9 1687 1697 2009 Langergraber G and J im nek The HYDRUS Wetlands Module Version 2 HYDRUS Software Series 4 Department of Environmental Sciences University of California Riverside Riverside CA 56 pp 2011 Lazarovitch N J im nek and U Shani System dependent boundary condition for water flow from subsurface source Soil Sci Soc Am J 69 1 46 50 2005 Lenhard R J J C Parker and J J Kaluarachchi Comparing simulated and experimental hysteretic two phase transient fluid flow phenomena Water Resour Res 27 8 2113 2124 1991 Lenhard R J and J C Parker Modeling multiphase fluid hysteresis and comparing results to laboratory investigations In M Th van Genuchten F J Leij and L J Lund eds Proc Intl Workshop on Indirect Methods f
81. 8 36 s 6 12s 0 73 2DWater1s 2D WF ST 20 k 13 83 s 8 08 s 0 58 2DWater2 2D WF 200 k 310 24 s 169 45 s 0 55 2DWater2s 2D WF ST 200 k 508 79 s 262 87 s 0 52 2DWater3 2D WF 1 000 k 3134 9 s 1666 2 s 0 53 2DWater3s 2D WF ST 1 000 k 7296 0 s 3549 2 s 0 49 WF Water Flow ST Solute Transport 3D Tests Project Name Processes Number of Elements Standard Module HyPar Module Ratio 3DWater1 3D WF 20 k 15 88 s 5 78 s 0 36 3DWater1s 3D WF ST 20 k 32 24 s 12 19 s 0 38 3DWater2 3D WF 200 k 211 415 87 07 s 0 41 3DWater2s 3D WF ST 200 k 502 0 s 194 33 s 0 39 3DWater3 3D WF 1 000 k 1554 3 s 689 71 s 0 44 3DWater3s 3D WF ST 1 000 k 7078 0 s 2427 4 S 0 34 297 9 9 Video Files Users can save the flow animation using the Create Video File command Tools gt Create Video File This command calls the Create Video File dialog window Fig 186 in which a user needs to specify where the Video File should be saved and under what name type of the video file a Cinepac Codec by Radius b Microsoft Video 1 c Intel Indeo Video 4 5 d Intel Indeo Video 5 10 e Microsoft MPEG 4 Video Codec V1 and f Microsoft MPEG 4 Video Codec V2 and its Quality and finally whether recording is carried out at Real Time i e video will run at the same speed as HYDRUS animation or only when frames in the View Window change only changes in View Window are recorded Additional options such as Smoothness Data Rate i e kilobits per second are available for each part
82. 9 The New Line Arc dialog Window cccssccssscecsseceessececsscceessccessseceessceeeseeeeseees 110 The New Line Circle dialog window cccssscccssececesececssececsseceesseeeeneeeesecessaees 111 Edit Bar during the process of defining graphically a spline eee eeeeeeeteeeeeeeee 112 Snap to a point left and snap to a curve Tight 0 eee eee esneceseeeeeeeeseessaeenseeneees 113 The Translate Copy dialog windows eccessceesseceseeeseeeeseecaeceseeeseeesneecaaecnseensees 114 The Rotate left and Mirror right dialog windows cescceceseceeeseceeeteeeesteeeenaees 115 10 Figure 58 Figure 59 Figure 60 Figure 61 Figure 62 Figure 63 Figure 64 Figure 65 Figure 66 Figure 67 Figure 68 Figure 69 Figure 70 Figure 71 Figure 72 Figure 73 Figure 74 Figure 75 Figure 76 Figure 77 Figure 78 Figure 79 Figure 80 Figure 81 Figure 82 The Stretch left and Skew right dialog WiINdOWS ccescceeeseceeeteeeeeteeeenteeeeaees 115 The Manipulation Options dialog window The bitmaps indicate connecting lines between points surfaces between lines and solids between surfaces ccccssccccessseceeeesseeeeesenes 116 The Insert Point on Curve dialog WindOw ccccseseseeseseteseeeeeceenenseeeseseseneseeneneeenanees 117 The warning issued when Surfaces cannot be created automatically and must be d fined mantal y naetiri ie e
83. Bacteria Max Growth Rate XA Rate Constant for Lysis 0 0416667 0 00625 Sat Inh Coef for SO Sat Inh Coef for SNH Fermenting Bacteria Sat Inh Coef for SH2S Max Growth Rate XFB Rate Constant for Lysis Sat Inh Coef for SO 0 125 0 000833333 0 2 Sat Inh Coef for SF Sat Inh Coef for SNO Sat Inh Coef for SNH Sat Inh Coef for SH25 Acetotrophic Methanogenic Bacteria Max Growth Rate X4MB Rate Constant for Lysis Sat Inh Coeff for SO 0 00354167 0 000333333 0 0002 Sat Inh Coef for SA Sat Inh Coef for SNO Sat Inh Coef for SNH Sat Inh Coef for SH25 Acetotrophic Sulfate Reducing Bacteria Max Growth Rate X4SRB Rate Constant for Lysis Sat Inh Coeff for SO 0 0075 0 0005 0 0002 Sat Inh Coef for SA Sat Inh Coef for SNO Sat Inh Coef for SNH4 Sat Inh Coef for 5504 Sat Inh Coef for SH2S Sulphide Oxidising Bacteria Max Aerobic Growth Rate Anoxic Correction Factor Rate Constant for Lysis 0 00625 Sat Inh Coef for SO Sat Inh Coef for SNO Sat Inh Coef for SNH Sat Inh Coef for SH25 Previous Figure 39 The Constructed Wetland Model CWM1 Parameter I dialog window Solute Transport Const
84. Bitmap Background Layer Calculation FE Mesh Parameters Generate FE Mesh Delete FE Mesh FE Mesh Statistics Advanced FE Mesh Generation Fundamental Triangulation Mesh Refinement Retriangulation Check of Convexity Mesh Smoothing Calculate Current Project Calculate Current Project Select Projects to Calculate Results Display Quantity Pressure Head Water Content Velocity Concentration Nonequilibrium Concentration Temperature Boundary Information Pressure Heads Boundary Fluxes Cumulative Fluxes Solute Fluxes Observation Points Soil Hydraulic Properties Inserts auxiliary object dimensions Inserts auxiliary object comment Inserts auxiliary object bitmap Inserts auxiliary object background layer Specifies either parameters of the Unstructured Finite Element Mesh Generator the FE Mesh Parameters dialog window Figs 98 through 104 or parameters of the structured mesh the Rectangular Domain Discretization dialog window Fig 96 or the Hexahedral Domain Discretization dialog window Fig 97 Generates the unstructured finite element mesh Deletes the unstructured finite element mesh Provides information about the finite element mesh the FE Mesh Information dialog window Fig 113 Performs triangulation of boundary nodes based on the Delaunay criterion Inserts a new point in the center of all triangles that do not fulfill the smoothness criterion Retriangulates mesh accordi
85. Brakensiek and K E Saxton Estimating soil water properties ASAE Transactions 25 5 1316 1320 and 1328 1982 Schaap M G Leij F J and van Genuchten M Th Rosetta a computer program for estimating soil hydraulic parameters with hierarchical pedotransfer functions J of Hydrol 251 163 176 2001 Scott P S G J Farquhar and N Kouwen Hysteresis effects on net infiltration Advances in Infiltration Publ 11 83 pp 163 170 Am Soc Agri Eng St Joseph MI 1983 im nek J and D L Suarez Two dimensional transport model for variably saturated porous media with major ion chemistry Water Resour Res 30 4 1115 1133 1994 im nek J and J W Hopmans Parameter Optimization and Nonlinear Fitting In Methods of Soil Analysis Part 1 Physical Methods Chapter 1 7 Eds J H Dane and G C Topp Third edition SSSA Madison WI 139 157 2002 im nek J D J acques J W Hopmans M Inoue M Flury and M Th van Genuchten Solute Transport During Variably Saturated Flow Inverse Methods In Methods of Soil Analysis Part 1 Physical Methods Chapter 6 6 Eds J H Dane and G C Topp Third edition SSSA Madison WI 1435 1449 2002 im nek J N J Jarvis M Th van Genuchten and A G rden s Review and comparison of models for describing non equilibrium and preferential flow and transport in the vadose zone Journal of Hydrology 212 14 35 2003 im nek J M ejna H Sait
86. Color Points Color Edges Velocity Vectors Display Options Edit Default Read Save As Program Options Slope Stability Input Parameters Open Slope Stability Module Printout Report and Results Settings New Window Arrange Symbols Main and Secondary Tile Horizontally Tile Vertically Cascade Close All Context Sensitive Help Help Contents and Index Hydrus User Manual Hydrus Technical Manual 254 Hydrus Online Troubleshooting Hydrus License and Authorization About Hydrus 255 Table 26 Brief description of HY DRUS menu commands Group Command Brief description of the command A File New Creates a new project after user provides required information name and description in the New Project dialog window Fig 4 Project will be located in the current Project Group Open Opens an existing project represented by the project_name h3d2 file using the Open dialog window which a user uses to browse for the HYDRUS project Close Closes an open project Save Saves the input data of an actual project specified in the main program module if the data were either newly created or changed during an application run Save As Saves data of a particular project under a new project name using Save As dialog window Save All Saves data of all projects Import Import Hydrus 2D Project Imports Hydrus 2D projects from Version 2 0 Import Input Data from another HYDRUS Project Imports data from another project and interpol
87. CumDrain Cumulative flux across the boundary having a time variable flux or pressure head CumRootUp Cumulative actual root water uptake CumCh0 Cumulative zero order production in domain solute transport CumCh1 Cumulative first order degradation in domain solute transport CumChS Cumulative solute flux across the boundary having a time variable flux or pressure head hAtm The average pressure head at the atmospheric boundary hConst The average pressure head at the boundary having a constant flux or pressure head hDrain The average pressure head at the boundary having a time variable flux or pressure head hRoot The average pressure head in the root zone hSeep The average pressure head at the boundary with the seepage face vConstBC Flux across the boundary having a constant flux or pressure head vSeep Flux across the boundary having a seepage face 295 9 7 Running Computational Modules Outside of GUI or in a Batch Computational modules e g h2d_calc exe h2d_clci exe h3d_calc exe can be run either directly from GUI or by clicking on any of them in the folder in which HYDRUS is installed When these modules are run from GUI GUI will send them as a parameter the path to the folder in which the input and output files are located the working folder the path to which is displayed in the project manager h1d or in the project information dialog h3d When the program does not receive a path as a parameter it will look for the text
88. E Bondar EANES List of Boundary Curves 1 4 1 4 for example 1 9 3 7 Comment Help z K Pick a boundary curve of the new Surface K Press Esc or right mouse Cancel Ap p y button to end the tool Set new Surface Figure 62 The Edit Bar during the process of defining graphically a surface left and the General tab of the Edit Surface dialog window right 4 2 1 1 Planar Surfaces 119 A base surface is formed by a planar surface of arbitrary shape The base surface can contain openings internal curves and internal points Fig 63 In the current version of HYDRUS a base surface can be formed by a single surface Future versions will permit multiple surfaces to form one single base surface Figure 63 A solid showing the base surface If the solid needs to be divided into vertical columns then these columns must be defined using internal curves in the base surface The FE mesh then follows exactly the specified shape of these internal curves Fig 64 Figure 64 Solid showing separate vertical columns 120 A base surface can be defined by a plane other than the horizontal plane while thickness vectors can be defined in other than the vertical direction Figures 65 and 66 show an example of a solid that has a base surface in the XZ plane and thickness vectors in the Y direction Figure 65 A solid with its base surface in the
89. Edit Bar is by default located on the right side of the HYDRUS main window A user can however move the Edit Bar to other positions The Edit Bar is very dynamic since it changes depending upon the process being carried out Figure 153 shows the Edit Bars for different processes i e for the Material Distribution in the Domain Properties the Water Flow Boundary Conditions the Pressure Head Initial Conditions and the Water Content Results ax Material Distribution a WE Material 1 D Material 2 E Material 3 Commands a Z Edit Materials C Values by Pointer Help A Ke How to set Domain Pr gt Next Initial Conditions Back FE Mesh 3 Tools Water Flow C No Flux E Constant Head E Constant Flux WB Variable Head 1 Variable Head 2 WE Variable Head 3 WB Variable Head 4 OS Variable Flux 1 OS Variable Flux 2 E Variable Flux 3 B Variable Flux 4 I Free Drainage WS Deep Drainage WB Seepage Face OS Atmospheric Boundary Numbering z C Display Codes C Codes by Pointer Numbering Options Help a Ke How to set Boundary gt Next Calculation Res Back Initial Conditions Pressure Head h cm 1 000 10 000 19 000 28 000 37 000 46 000 55 000 64 000 73 000 82 000 31 000 100 000 1 000 Min 100 000 pt x Edit Commands Set Values C Values by Pointer Chart Tools Cross Section Chart Boundary Line Chart Help x Ke Right click on the Color Scale d
90. Edy COG Vin Edges aed Suface Facet C Asda Obyect CO Rendeng Model pyg 20000R 8 WO Rents Presse Head h om Custom Seale 00 E Boundary Line Chart y Daplay Vakses af Nodes Hee amp Pig cick on the Color Scale daplays options O7 Giph Type amp ODY Ltrs CBE Coke Scale G Back Bourclery Corcitore For Help press FI System Octad Prez X MBo Figure 142 The use of the Custom Scale A right mouse button click on the Color Scale at the Edit Bar displays the menu for a fast change of various options related to scale e Color Smoothing colors will change smoothly between particular iso spectra corresponding to changes of the displayed variable upper View at Figure 143 e Min Max global in Time the scale of a certain variable is defined by the minimum and maximum of all values from all time levels e Min Max global in Space the scale of a certain variable is defined by the minimum and maximum of all values over the entire transport domain e Standard Scale uses the Standard Scale while the Custom Scale for a given variable if it exists is remembered e Custom Scale uses the Custom Scale if it exists If it does not exist default this button is disabled If one wants to use the Custom Scale he she needs to first create it in the Edit Scale and Colors dialog e Edit Scale and Colors 220 hd HYDRUS Furrow H3O Fie Eat Vew Insert Caniston Ress Took Options Window Hep CICE aaa
91. Geometry Flow Parameters FE Mesh Domain Properties Initial and Boundary Conditions and Auxiliary Objects Output data include various Results Data are organized in a tree like structure Figure 152 shows Data with expanded Domain Properties on the left and Results in the middle b A View Tab on the right of Figure 152 to specify what and how information will be displayed in the View window and c A Sections Tab to show various Sections not shown here and defined elsewhere View Options on the View Tab of the Navigator Bar at first mirror more or less the Project Data i e View Options exists for Domain Geometry FE Mesh Domain Properties Initial and Boundary Conditions and Results Users can then select which objects Domain Geometry objects Domain Properties objects FE Mesh objects such as nodes edges triangles and tetrahedrals are to be numbered Numbering display Auxiliary Objects and initiate Rendering Outline transparent filled Users can also select the Graph Type CIsolines Isosurfaces Contours with or without Separation Lines and Color Edges Color Points and Velocity Vectors and Color Scale either with or without Min Max glob in time or Min Max glob in space Finally Lighting can be turned on or off the location of light sources can be shown Show Light Sources and the location of lights can be selected Light Switches 235 xxi xxi
92. Graphical Display 000 Pressure Head 000 L1 Dissolved Oxygen 000 L2 Fermentable Biodegr COD 000 L3 Fermentation Products QQ L4 Inert Soluble COD 000 L5 Ammonia NH4 N 000 L6 Nitrate and Nitrite NO2 NO3 000 L7 Sulphate Sulphur 504 00 Ls Dihydrogensulphide Sulphur H25 QQ L9 Slowly Biodegr COD 000 L10 Inert Particulate COD A L17 Tracer 000 52 Fermentable Biodegr COD 000 S3 Fermentation Products 000 S4 Inert Soluble COD 000 55 Ammonia NH4 N 000 S9 Slowly Biodegr COD 000 S10 Inert Particulate COD 000 S11 Heterotrophic Bacteria 000 S12 Autotrophic Bacteria 000 S13 Fermenting Bacteria 000 S14 Acet Methan Bact 000 S15 Acet Sulphate Red Bact 000 S16 Sulphide Oxidising Bacteria 000 S17 Tracer Figure 135 The Results Graphical Display part of Data Tab of the Navigator Bar for the standard left Unsatchem centre and Wetland right modules 213 Figure 136 The Results part of the View Tab of the Navigator Bar with the display of various alternative variables 214 7 1 2 Display Options The Display Options dialog window Fig 137 allows users to select a how different objects from the Category list are to be displayed b what colors are to be used colors can be redefined by clicking on the Edit Color command button c whether lines are displayed as solid dotted dashed or dash dotted Line Type and what
93. Hiickel equation is used to calculate ion activity coefficients Pitzer virial type equations are used above this value The Maximum Number of Iterations allowed during any time step between the solute transport and chemical modules When the maximum number of iterations is reached then the code proceeds to the new time level The recommended value if the iterative approach is to be used from our experience is 5 Set equal to one if no iteration we recommend this non iterative approach is required this in general leads to significantly lower computational time without significantly altering the results in most cases Whether the hydraulic conductivity is to be modified depending on the solution chemistry using the McNeal 1968 semi empirical approach the Conductivity Reduction due to Chemistry check box Chemical Parameters Chemical Parameters C Silica in Solution pH dependency fo 5 Critical lonic Strength Debye Huckel Pitzer equations 1 Maximum Number of Iterations Conductivity Reduction due to Chemistry Previous Figure 31 The Chemical Parameters dialog window for the UNSATCHEM module 74 3 17 Heat Transport Parameters Information needed for defining heat transport problem is entered in the Heat Transport dialog window Fig 32 In this window users specify Heat Transport Parameters and temperatures for the Boundary Conditions Heat Transport Parameters 2 Boundary Conditions
94. L Solute mass in the solid pK c PK p fen fCim p f Kpc s p s T s phase S M L Solute mass in the gas K ca Kca K ca K ca phase S M_L Total Concentration S S Ss Sg Si Ss S Si S S Si Ss S M L a air content LL c liquid phase concentration M L Cm liquid phase concentration in the mobile phase M L is PV OD water content L L liquid phase concentration in the immobile phase M L water content in the mobile phase L L Om water content in the immobile phase L E Henry s law constant distribution sorption coefficient L M S solute mass in the liquid phase M L Ss solute mass in the solid phase M L Sg solute mass in the gas phase M L 212 total concentration solute mass S S S S M L solid phase concentration M M solid phase concentration on kinetic sorption sites M M 000 Velocity 000 Velocity Vectors 000 Temperature QQ Concentration 1 Results Graphical Display a QQ Water Content 000 Velocity 000 Velocity Vectors 000 Calcium 000 Magnesium s 00 Sodium 000 Potassium 000 Alkalinity QQ Sulfate 000 Chloride QQ Tracer QQ Sorbed Calcium 000 Sorbed Magnesium 000 Sorbed Sodium a QQ Sorbed Potassium QQ Calcite 000 Gypsum 000 Dolomite 000 Nesquohonite QQ Hydromagnesite 000 Sepiolite solid phase concentration on first kinetic sorption sites M M en Results
95. Mesh Nodes Alternatively to linear interpolation values can be Transferred to FE Mesh nodes from nearest points without interpolation extrapolation Note that when the Linear interpolation of values option is selected linear interpolation 205 is done only between locations with imported values and a Transfer of values form nearest points is done in the rest of the domain outside of the area space with imported values but within the transport domain c Users can also select the Minimum and Maximum Values that cannot be exceeded by interpolation Value Limited d Finally users can define the so called Clipping Box This is a part of the transport domain defined by minimum and maximum x y and z coordinates X min X max Y min Y max Z min Z max for which a transfer of values from Scattered Points to FE Mesh Nodes is done There is no transfer of values outside of this box The actual transfer of values from Scattered Points to the FE Mesh Nodes is done only after the button OK is clicked Imported values Number of imported points 304 Minimum value 2 000000e 000 Maximum value 1 000000e 004 Bounding box m Xmin 1 991110e 002 Xmax 4 667620e 002 Ymin 2 634350e 002 Ymax 6 401870e 002 Zmin 8 amp 750000e 000 Zmax 3 325000e 001 Options for transfer of values to FE mesh nodes Transfer of values from nearest points without interpolation extrapolation Linear interpolation extrapolation of values V Val
96. Options Modules Slope Stability Input Parameters Open Slope Stability Module Printout Report and Results Settings Windows New Window Stretches a selected object Skews a selected object Finds the intercept of two lines and insert an interception point on the lines Finds the curve that is created by the intercept of two surfaces Splits lines Inserts points on a line Checks geometry for consistency Repairs geometry if inconsistent Attempts to generate Domain Surface if they were not specified Allows users to save flow animation in a video file Displays the transport domain as a solid object Displays the transport domain as a transparent object Displays the transport domain as a wired object Displays the spatial distribution of a particular variable by means of isolines Displays the spatial distribution of a particular variable by means of isobands Displays the spatial distribution of a particular variable by means of isosurface Color Points Displays the spatial distribution of a particular variable by means of color points Displays the spatial distribution of a particular variable by means of color edges Displays Darcy velocity vectors Edits display options in the Display Options dialog window Fig 137 Sets display options to their default values Reads display options from a file Saves display options to a file Displays program options information the Program Options dialog window
97. Options dialog window the Files and Directories Tab 274 The HYDRUS Authorization Status dialog window Tab Status eee 276 Warning issued when attempting to make changes to the Authorization Status while not running HYDRUS with administrator privileges ceeeeeseceesseeeenteeeeneeees 277 The HYDRUS Authorization Status dialog window Tab Add on Modules 277 The HYDRUS License and Activation dialog window Tab History of Activation hig ale i a cs AE Sls edge ig Jeli Date seeded te ig da isin iene nN 278 The Online Activation dialog WiIndOW esccecssscecssececeeececsteeeeseeeesteeeeneeeenaeeees 279 Window requesting confirmation of entered parameters esseeeeeeeeereereeseeereereese 280 The Activation by E mail dialog window Tab Step 1 eeeeeeeseeeeeserereeresrreren 293 The Activation by E mail dialog window Tab Step 2 eeeeseeeseceseeeeeeeeneees 282 Email with the HYDRUS Activation Request in Outlook eee eeeceeeseeeeeteeees 283 Window inquiring if the user wants to enter the Activation Code cece 284 The Activation by E mail dialog window Tab Step 3 eecceeeseeeesteeeesteeeeeteeees 285 Window confirming successful HYDRUS authorization 0 00 ee eee eeteeeeeeeeeee 285 Window reporting a failure of HYDRUS authorization 0 0 eee eeneeeteeeeeee 286 The Online Deactivation dialog window csscceceeeceeeseeeceteeeeeeeeeseeeeneeeeaeeees 287 Window confi
98. PC PROGRESS N Engineering software developer HYDRUS User Manual Version 2 The HYDRUS Software Package for Simulating the Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated Porous Media User Manual Version 2 04 M Sejna J im nek and M Th van Genuchten July 2014 PC Progress Prague Czech Republic University of California Riverside Riverside CA Department of Mechanical Engineering Federal University of Rio de Janeiro Brazil 2014 J Siminek and M ejna All rights reserved Table of Contents ES 0 Sr Contents yL nee gr ve PP PF ere nee Pee ee Pee rere rere reer eee rere eee 3 Fist of BUG CS eesin ania arin a eE AEON AEON cies ON EE ANA AE ANa Aa AA 9 List of Tables einn enera ranir n nR RRR ERR RRR Lo Vey RER RRR RE ER RRR n 17 Apstract oeron Fane ects Sac E ERNEUT a a A Ni 19 Introduction to the HYDRUS Graphical User Interface 0 0 0 0 ccc cccccceseeseeeeeeeeeeeseeseeeeees 23 1 Project Manager and Data Management ccccccscesseseeeseeseeeseeseeseeseesseeseesseeseeeseeseeens 27 2 Projects Geometry Information cccccccccssscecsssseessscecsssceessscessssceensecesseneesnseeesnecessaes 33 3 SLO Wye ParametetS oenar heoa a ane sahd ska T E tesa a atoms meagan aa 39 Delis Main PROCESSES Sind oat GGG sila ila aoa acl T eda eG EEI i 39 3 2 TRVCESE Solution cates h ese eas ee Bitte e ee iti vy Baa ote c
99. RUS Menus III Tools Options Windows and Help 247 Group A File B Edit Table 25 HYDRUS menu commands Menu New Open Close Save Save As Save All Import Export Print Print Preview Print to the Clipboard Print Options Print Setup Project Information Project Manager Recent Files Exit Undo Redo Copy Paste Select Properties Find Delete Submenu Sub Submenu Import Hydrus 2D Project Import Input Data from another HYDRUS Project Import Input Data from IN Files Import Quantity defined by values at Scattered Points Import Points from Text File Import Geometry from Text File Import Geometry from DXF File Import Geometry from ESRI File Import Background Layer Import Data to ParSWMS Export Data for Hydrus Solver in Text Format Export Geometry to Text File Export Selected Geometrical Objects Export FE Mesh Export Current Quantity Export Isolines Export Data from ParSWMS Select by Rhomboid Select by Circle Select by Polygon Add to Selection Remove from Selection Standard Selection Mode 248 Delete All Domain Geometry Flow Parameters FE Mesh Domain Properties Domain Type and Units Simple Domain 3D Layered Domain Delete 3D Layered Domain Points Lines Surfaces Openings Thickness Vectors Solids Main Processes Inverse Solution Time Information Output Information HP2 Print Information Water Flow Parameters Iteration Criteria Hydra
100. Rep 3D Layered and 3D General Boundary Rep While the unstructured mesh generator MeshGen2D is used to generate FE meshes for two dimensional domains 2D General Boundary Rep and for the Base Surface of three dimensional layered domains 3D Layered the mesh generator Genex T3D is used to generate three dimensional FE meshes for the 3D General Boundary Rep geometry 5 2 Structured Finite Element Mesh Generator As discussed in Section 2 two dimensional transport domains can be defined using modified rectangles Simple rectangular domains are defined by three straight lines one at the bottom of the domain and two at the sides while the upper boundary may or may not be straight see examples in Fig 8 Nodes along the upper boundary may in that case have variable x and z coordinates but the lower boundary line must be straight horizontal or with a specified slope whereas the left and right boundary lines must be vertical The flow region can then be discretized into either a structured or an unstructured triangular finite element mesh When the structured mesh is used one then needs to specify in the Rectangular Domain Discretization dialog window the number of nodes Count on the horizontal Horizontal Discretization in X Direction and vertical Vertical Discretization in Z Direction sides of the rectangular region including their nodal coordinates Fig 96 The relative size of finite elements on the vertical side can be
101. Run Time Information Mass Balance Information Bitmap Background Layer Fundamental Triangulation Mesh Refinement Homogeneous Retriangulation Check of Convexity Mesh Smoothing Pressure Heads Water Content Concentration Nonequilibrium Concentration Temperature Velocity Pressure Heads Boundary Fluxes Cumulative Fluxes Solute Fluxes Chemical Mass Balance Information Convert Output to ASCII Inverse Solution Results Fluxes across Mesh Lines HP2 Text Output Time Layer Charts Flowing Particles Delete Results Show Grid Snap to Grid Grid and Work Plane Define Work Plane Coordinate System Color Scale First Last Previous Next Animation Cross Section Boundary Line Mesh Line Draw Particles Positions Draw Particles Trajectories Set Origin Define XY Define YZ Define XZ Color Smoothing 253 H Options I Modules J Windows K Help Min Max Values Global in Time Min Max Values Global in Space Standard Scale Custom Scale Edit Scale and Colors Translate Rotate Mirror Stretch Skew Intersect Lines Intersect Surfaces Split Lines Graphically n Points Distance Insert Points on Line Graphically n Points Distance Generate Boundary Lines from Points Generate Surfaces from Curves Check Data Consistency Repair Geometry Create Video File Rendering Mode Solid Model Transparent Model Wire Frame Model Use Material Colors Graph Type Isolines Colormaps Isosurfaces
102. Systems dialog window Fig 185 top called by the Tools gt Coordinate System command Cartesian Cylindrical and Spherical systems are available The Cartesian coordinate system is selected by default A New Coordinate System can be defined using the dialog window of the same name Fig 185 bottom List of available Coordinate Systems Existing Coordinate Systems ane Description O Cartesian Default Absolute coordinate system OX Cylindric Ov Cylindric OZCylindric Spherical Polar New System New Coordinate System Name Description Definition of the Coordinate System x em Y erm 2 cm CS Origin 0 00 ooo 0o00 Point on x Axis 00 0 00 0 00 Point in XZ Plane 00 0 00 0 00 Pick All 3 Points Figure 185 The Coordinate Systems dialog windows 294 9 6 DOS Window During Calculations During the calculations different type of information can be written to the screen The following information may be written to the screen depending upon the problem Time Time T Level Time level ItW Number of iterations to solve the water flow problem at a certain time step ItC Number of iterations to solve the solute transport problem at a certain time step ItCum Cumulative number of iterations CumAtmBC Cumulative flux across the atmospheric boundary CumConst Cumulative flux across the boundary having a constant flux or pressure head
103. T Water Material Properties for Water Flow Number of Materials 3 Model van Genuchten 1980 Mualem Mat Name Or Qs Alpha 1 cm n Ks cm day If a Help 1 Loam 0 078 0 43 0 036 1 56 24 96 O 5 2 Sand 0 045 0 43 0 145 2 68 712 8 0 5 3 Silt modified 0 034 0 46 0 016 1 37 6 2 0 5 Soil Catalog Loam x Neural Network Prediction E Temperature Dependence Water Flow Parameters Inverse Solution Material 1 Material Properties for Water Flow Number of Materials 1 Model van Genuchten 1980 Mualem arf Initial Estimate 0 034 Minimum Value 0 Maximum Value Fitted Qs 0 46 Soil Catalog Silt v Neural Network Prediction Mit OK Cancel Previous Figure 19 The Water Flow Parameters dialog window for direct top and inverse bottom problems 55 Durner s 1994 model has three additional parameters w2 w2 Alpha2 L and m n2 where w2 is the weighting factor for the second overlapping region and and m are empirical parameters for the second region The hysteretic model has also three additional parameters w QsW the saturated water content of the main wetting branch w AlphaW L the shape parameter of the main wetting branch and Ky KsW Bib bal the saturated hydraulic conductivity associated with the main wetting branch in case hysteresis also occurs in the conductivity function Temperature Dependence Check this b
104. TBound2 through TBound4 TWell Value of the temperature for the sixth time independent boundary condition K If internal sources are specified then TWell is automatically used for the temperature of water injected into the flow region from sources in the transport domain Set equal to zero if no sixth time independent boundary condition and no internal sources are specified The boundary condition at the soil surface may be approximated using a sinus wave with the maximum one hour after noon and the minimum one hour after midnight as follows 1 T T Acos 23 24 where To is the average temperature at the soil surface K A is the Temperature Amplitude at the soil surface K and p is the Time Interval for completion of one sine wave temperature usually 1 day the default value The second part of the sine term is included to set the maximum temperature at 1 p m Default values for the parameters in the Thermal Conductivities of three textural classes sand loam and clay are provided by HYDRUS Chung and Horton 1987 Default volumetric heat capacities for the solid phase organic matter and liquid phase are also given Set Default Volumetric Heat Capacities When the parameter estimation option is selected then users must provide initial estimates of the optimized heat transport parameters specify which parameters are to be optimized check appropriate checkboxes and provide parameter constraints for the optimization Zero va
105. W Results Pressure Head zz 5g lt gt C Flow Animation Chart Tools rosaire Fes F Cross Section Chart 00 water Content E Boundary Line Chart 000 velocity y Display Values at Nodes 00 velocity Vectors Help w Temperature KA Right click on the Color 000 Concentration 1 Scale displays options sial Concentration 2 Back Boundary Conditions Concentration 3 3 Gj Results Other Information W Dike it Fi Data Gu Viel Sections A Geometry AFE Mesh Domain Proper Gad Initial Conditions Boundary Condi For Help press F1 Figure 1 The HYDRUS Graphical User Interface the main window Figure 1 shows the main window of the HYDRUS graphical user interface including its main components such as the Menu Toolbars the View Window the Navigator Bar Tabs and the Edit Bar These terms will be used throughout this user manual The text below provides a detailed description of all major components of the graphical user interface At the end of this user manual a list is given of all commands accessible through the menu Table 25 as well as a brief discussion of the action taken with particular commands Table 26 More detailed descriptions are available through the on line help Work for a new project should begin by opening the Project Manager see Chapter 1 and giving a name and brief description to the new project Next the Domain Type and Units dia
106. WORD followed by coordinates of points defining given object Two or three coordinates for two and three dimensional problems units must be always in meters of a single point are given on a single line Numbers can be delimited using a space a semicolon or a tabulator 153 b Points associated with higher objects i e lines openings or surfaces are listed as part of this object Similarly lines associated with higher objects i e openings or surfaces are listed as part of this object Only points that are not part of any higher object should thus be listed under the object POINTS and only lines that are not part of any higher object e g that do not form boundaries of surfaces should thus be listed under the object LINES c Lines with a semicolon at the beginning are ignored as Comments Note that comment lines can appear only between blocks but not inside of any particular block d It is possible that exported Geometry once imported back into HYDRUS can have different numbering i e the project may not be identical e Below is a list KEY_WORD of all possible objects POLYLINE is a single line defined by multiple nodes while LINES is a series of lines multiple objects Surfaces or Openings must be defined by a single closed curve the type of which is given in the name of the object e g SURFACE CIRCLE When this rule is not fulfilled e g for a surface with complex boundary this complex boundary will be
107. XZ plane and thickness vectors in the Y direction Figure 66 FE Mesh for a solid with its base surface in the XZ plane and thickness vectors in the Y direction 4 2 1 2 Curved Surfaces There are currently four types of Curved Surfaces Fig 67 available in the 3D Professional version Quadrangle Rotary Pipe and B Spline While the boundary of a Planar Surface must be formed by multiple different Curves the boundary of a Curved Surface can contain one curve two times An example is a Pipe Surface Fig 67 in which the curve along a pipe occurs twice each time with a different orientation Note that the list of curves defining Pipe and Rotary Surfaces is generated automatically and cannot be edited contrary to the list of curves defining Quadrangle or B Spline for which curves are selected by a user Quadrangle is a Surface defined by its boundary curves of an arbitrary type except a circle Curves do not have to be placed in a single plane that is in general a Quadrangle can be a curved surface This type of surface corresponds to a general surface with four corners i e it is 121 typically defined by four boundary curves although this is not a necessary condition If there is another number of boundary curves than four it is necessary to define corner nodes of a Quadrangle A B Spline Surface is a Surface defined using Boundary Curves similarly as a Quadrangle However for this type of Surface one needs to also def
108. YDRUS application 268 8 6 Input Tables in HYDRUS Tables e g in the Water Flow Parameters Fig 19 or the Time Variable Boundary Conditions Fig 37 windows are compatible with various standard spreadsheet software e g MS Excel Input data can be prepared in such software e g MS Excel and then copied into various input tables of HYDRUS One can use keyboard keys Ctrl C to Copy a content selected cells in Excel into the clipboard and Ctrl V to Paste it into the HYDRUS table 269 270 9 Miscellaneous Information 9 1 Program Options The Program Options dialog window has four tabs one related to Graphics Fig 161 one to Program Options Fig 162 one to FE Mesh Fig 163 and one to Files and Directories Fig 164 Graphics Program FE Mesh Files and Directories OpenGL V OpenGL Hardware Acceleration Options Fmin 5S E Gradient Background Flow Animation Minimum Time for one Frame l Maximize Speed set Off if problems with graphic occur 7 Simplified display in Dynamic View mode Move Zoom Rotate a The simplified display will be activated when there are less than Fmin refreshments per second V Invert direction of mouse scroll wheel when zooming Pre selection mark object while hovering above it with cursor 4 Display values properties at pre selected objects Synchronize selection in View with selection in Navigator Data Tree 500 m
109. Z direction Sets the view of the transport domain in the reverse X direction Sets the view of the transport domain in the reverse Y direction Sets the view of the transport domain in the reverse Z direction 262 List Boxes for Inverse Data Insert Domain Geometry Points Graphically Dialog Lines Line Polyline Arc Circle Spline Surfaces Planar Surface Quadrangle Surface Rotary Surface Pipe Surface B Spline Surface Openings Thicknesses Solids 3D Layered Domain General Solid FE Mesh Refinement Graphically Dialog Domain Properties Material Distribution Root Distribution Nodal Recharge Scaling Factor Hydraulic Conductivity Pressure Head Water Content Local Anisotropy Angle First Component Second Component Index Shows text information in the inverse data list the Data for Inverse Solution dialog window Fig 14 Inserts single points graphically Inserts single points numerically the Edit Point dialog window without the FE Mesh tab Fig 48 Inserts a line either graphically or numerically the Edit Curve dialog window without the FE Mesh tab Fig 50 Inserts a polyline either graphically or numerically the Edit Curve dialog window without the FE Mesh tab Fig 50 Inserts an arc either graphically or numerically Inserts a circle either graphically or numerically Inserts a spline either graphically or numerically the Edit Curve dialog window without the FE Mesh tab F
110. a st production of S in hydrolysis 0 0 J BMSE fraction of Sp generated in biomass lysis 0 05 femx fraction of X generated in biomass lysis 0 1 Yu yield coefficient for XH 0 63 Ya yield coefficient for XA 0 24 Yep yield coefficient for XFB 0 053 YAMB yield coefficient for XAMB 0 032 Yasrp yield coefficient for XASRB 0 05 Ysop yield coefficient for XSOB 0 12 Composition parameters in sr N content of Sp g N g CODsr 0 03 in st N content of S g N g CODs 0 01 inxs N content of Xs g N g CODxs 0 04 N xI N content of X g N g CODx l 0 03 N BM N content of biomass g N g CODgmy 0 07 Oxygen cO2_sat_20 saturation concentration of oxygen g m 9 18 Tdep_cO2_sat activation energy for saturation concentration of oxygen J mol 15000 rate_O2 re aeration rate 1 d 240 96 3 23 The Slope Stability Module The add on Slope Stability module Fig 42 can be activated in the Main Processes window Fig 12 and is available only for projects with the domain type 2D General see Section 2 Once the module is active related commands can be found in the main menu Modules gt Slope Stability or in the Navigator data tree item Slope Stability Detailed description of the module is available in the separate help and or User s manual of the Slope Stability module The Slope Stability module Fig 42 is intended to be used mainly for stability checks of embankments dams earth cuts and anchored sheeting structures The influence of wat
111. ace to assign it c Click on the command Set Material in the Commands section of the Edit Bar from the list box of the Set Materials window Fig 125 Select Material to set click Assign to close the window and click on a particular Surface to assign the selected material Available Materials Select Material to set 2 Loam A PE Silt modified Figure 125 The Set Materials dialog window Note that nodes that are at the curve shared by two surfaces will be assigned a material with a higher number Color squares at nodes defining the Geometry Fig 126 indicate which material will be assigned to curves shared by two Surfaces E 500 Figure 126 The transport domain with materials specified on geometric objects The sequence of materials as well as other objects such as Initial Conditions can be reordered or sorted using the Sort Materials command on the Edit Bar and the Sort Property Objects dialog window Fig 127 In this dialog the order of materials can be sorted using the Top Up Down and Bottom command While the sequence of materials can be sorted colors representing the first second and other materials will remain the same 196 Sorting can be done in two modes When the Auto apply check box is checked any change done in the Sort Property Object window is immediately transferred to the transport domain and to the rest of the program When this checkbox is unchecked changes made in this dialog
112. ace and Time Weighting Schemes the Iteration Criteria for nonlinear problems and additional Solute Information such as mass units pulse duration if applicable and number of solutes Time Weighting Scheme Space Weighting Scheme Explicit Sct Galerkin Finite Elements Crank Nicholson Scheme Upstream Weighting FE C Implicit Scheme C GFE with Artificial Dispersion Solute Information Number of Solutes 1 Mass Units Pulse Duration day 0 25 Stability Criterion F Temperature Dependence of Parameters Water Content Dependence of Parameters Use Tortuosity Millington amp Quirk Moldrup Attachment Detachment Concept virus bacteria transport Filtration Theory Furnigant Module Additional Fumigant Application at a GivenT ime Iteration Criteria for Nonlinear Adsorption only Absolute Concentration Tolerance Relative Concentration Tolerance Maximum Number of Iterations Initial Conditions In Liquid Phase Concentrations Mass_solute Volume_water In Total Concentrations Mass_solute Volume_soil Nonequilibrium phase is initially at equilibrium with equilibrium phase E Figure 23 The Solute Transport dialog window a Time Weighting Scheme The Time Weighting Scheme defines the temporal weighing coefficient used in the numerical solution of the transport equation The temporal weighting coefficient is equal to 0 0 for an explicit scheme 0 5 for a Crank Nicholson
113. ag Time days Figure 120 The Triggered Irrigation tab of the Boundary Condition Options dialog window 190 6 4 Domain Properties Other parameters characterizing the flow domain initial condition material distribution are defined in a similar way Users must first select that part of the transport domain to which he she wants to assign a particular value of the selected variable It is possible to select the entire transport domain part of it or only individual nodes or elements A particular part of the transport domain can be selected as follows first move the mouse to a selected position The beginning and end of the selection operation is framed by clicking the left mouse button The selected area is the rectangle defined by the two mouse positions when the left mouse button was clicked Selection can alternatively instead of using the rectangular selection be made using a rhomboid with the Edit gt Select gt Select by Rhomboid command circle Edit gt Select gt Select by Circle or polygon Edit gt Select gt Select by Polygon When the selection is completed users must click the Set values button and specify the value of a particular variable The given value will then be assigned to the selected area When material numbers are to be specified users can do this directly by clicking on the color representing a particular material at the Edit Bar All variables are assigned to nodal points except for those
114. ailable at the end of the tool bar za next to the Results button and at the Edit Bar However to be able to use this option to specify properties on Geo Sections the Transport Domain must be defined using or divided into a set of Geometric Objects on which various properties can then be specified An example of the transport domain divided onto three components or Surfaces S2 S2 or S3 is shown in Figure 123 rc s3 a s2 L 500 L 350 t _ L 2000 Figure 123 An example of the transport domain defined using three components S1 S2 and S3 While for two dimensional problems the Geo Sections displayed at the Navigator Bar at the Section Tab need to be defined manually for three dimensional problems they can also be generated automatically see Section 8 1 8 what and how are these Sections generated At the same time when HYDRUS generates 3D objects it also generates Surfaces belonging to each of 193 these objects Some of these Surfaces are Horizontal and some are Vertical although these terms are only approximate Surfaces can then be used to specify Boundary Conditions Vertical Surfaces are always created over the entire curve which forms the boundary of the Base Surface When the boundary of the Base Surface consists of several curves then an independent Vertical Surface is created above each curve Since the curves of the Base Surface can be arbitrarily divided Vertical Surfaces can be created rela
115. al distribution of the second component of local anisotropy for two dimensional applications Specifies the spatial distribution of anisotropy tensors for three dimensional applications 263 Subregions Observation Nodes Drains Flowing Particles Initial Conditions Pressure Head Water Content Concentration Nonequilibrium Concentration Temperature Import Boundary Conditions Water Flow No Flux Constant Head Constant Flux Seepage Face Variable Head 1 4 Variable Flux 1 4 Free Drainage Deep Drainage Atmospheric Boundary Solute Transport First Type Third Type Volatile Type Heat Transport First Type Third Type Cross Sections Graphically Dialog Mesh Line Graphically Dialog Auxiliary Objects Specifies the spatial distribution of subregions for mass balance calculations Specifies observation nodes for output of the pressure head water content temperature and concentration at each time step Specifies nodal points representing tile drains Specifies nodal points representing flowing particles Specifies the initial condition for water flow Specifies the initial condition for solute transport Specifies the initial condition for nonequilibrium solute transport Specifies the initial condition for heat transport Imports initial conditions for water flow solute transport and or heat transport Specifies a no flux boundary condition along a selected part of the boundary Spec
116. alee Bel reas ase i Bae ebsites 71 The Water Content Dependent Solute Reaction Parameters dialog window 12 Figure 30 Figure 31 Figure 32 Figure 33 Figure 34 Figure 35 Figure 36 Figure 37 Figure 38 Figure 39 Figure 40 Figure 41 Figure 42 Figure 43 Figure 44 Figure 45 Figure 46 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figure 52 Figure 53 Figure 54 Figure 55 Figure 56 Figure 57 The Solution Compositions dialog window for the UNSATCHEM module 13 The Chemical Parameters dialog window for the UNSATCHEM module 74 The Heat Transport Parameters dialog WiIndOW cccsscceceseeeceeeeeceeeceeeneeeeneeeenaeeees 75 The Root Water Uptake Model dialog Window ccesscecesececeeeceseeeceeseeeeeneeeenaeeees 77 The Root Water Uptake Parameters dialog window for the stress response function of Feddes et al 1978 left and van Genuchten 1985 right ce eeeeeeeeeeeeeeeeeeeeeeees 79 The Root Water Uptake Parameters dialog window for the solute stress response function based on the threshold model left and S shape model of van Genuchten LLIS Sht 5 aa hs ocd Socata cans cae E A cin ech E T EE E pa 80 The Root Distribution Parameters dialog WiIndOW c cccescceeeseceeeeeceeseeeeenteeeenaeeees 83 The Time Variable Boundary Conditions dialog Window ssssssssessssssesssesssesessees 84 The Constructed Wetlan
117. all triangles that do not fulfill the smoothness criterion Retriangulates mesh according to Delaunay criterion Corrects possible errors which may appear during smoothing and retriangulating Smoothes the mesh by solving a set of coupled elliptic equations using a recursive algorithm Specifies the spatial distribution of soil materials Specifies the spatial distribution of root water uptake Specifies the spatial distribution of nodal recharge 259 Scaling Factor Hydraulic Conductivity Pressure Head Water Content Local Anisotropy Angle First Component Second Component Index Subregions Observation Nodes Edit Delete Clear All Drains Edit Delete Clear All Drain Parameters Flowing Particles Edit Delete Clear All Stochastic Distribution of S F Subregions Material Distribution Nonequilibrium Conc a Equil Conc Parameters for Root Distribution Delete All Domain Properties Default Domain Parameters Initial Conditions Pressure Head Water Content Concentration Nonequilibrium Concentration Temperature Import Delete All Initial Conditions Specifies the spatial distribution of hydraulic conductivity scaling factors Specifies the spatial distribution of pressure head scaling factors Specifies the spatial distribution of water content scaling factors Specifies the spatial distribution of the angle of local anisotropy Specifies the spatial distribution of the first componen
118. als and that this value is used only in the Depth dependent blocking function iPsi 4 developed by Bradford et al 2002 which was developed for homogeneous laboratory column It is less clear have is should be used in multi layered systems for other than the first layer Also note that this blocking function depends on a vertical spatial coordinate This means that one needs to specify the origin of the function i e the inflow and inter material interfaces HYDRUS allows doing this for up to 2 materials using the cBnd vector as described in the help Type of blocking on the second sorption sites 0 No blocking 1 Langmuirian dynamics 2 Ripening 3 random sequential adsorption model 4 depth dependent blocking coefficient Same for the first sorption sites Parameter in the blocking function for the second sorption sites Smax for blocking options 1 2 and 3 and b for 4 First order deposition attachment coefficient ka Fe for the second sorption sites First order entrainment detachment coefficient ka is bal for the second sorption sites Parameter in the blocking function for the first sorption sites First order deposition attachment coefficient ka T for the first sorption sites First order entrainment detachment coefficient ka T for the first sorption sites When Filtration Theory Fig 23 is used to calculate the attachment coefficient then the following parameters must b
119. ameters are specified for each soil material Kd Adsorption isotherm coefficient ks M L Nu Adsorption isotherm coefficient 7 ML Beta Adsorption isotherm exponent Henry Equilibrium distribution constant between liquid and gaseous phases k SinkL1 First order rate constant for dissolved phase 4w TH SinkS1 First order rate constant for solid phase 4s T SinkG1 First order rate constant for gas phase 4g TH SinkL1 First order rate constant for dissolved phase 44 T as part of a solute decay chain SinkS1 First order rate constant for solid phase 44 T as part of a solute decay chain SinkG1 First order rate constant for gas phase 4g T as part of a solute decay chain Sink W0 Zero order rate constant for dissolved phase ML T SinkS0 Zero order rate constant for solid phase y T SinkGO Zero order rate constant for gas phase y ML T 67 Alpha First order rate coefficient for one site or two site nonequilibrium adsorption mass transfer coefficient for solute exchange between mobile and immobile liquid regions o T When the Attachment Detachment Model Fig 23 is used then some parameters listed above are replaced with different parameters needed for the attachment detachment model D_Soil iPsi2 iPsil SMax2 AttachSolid2 DetachSolid2 SMax1 AttachSolid1 DetachSolid1 Diameter of the sand grains de L Note that HYDRUS allow only one value for all materi
120. ance D lt Eps1 Remove curves with length L lt Eps1 and incorrectly defined curves Create intersections of lines Remove incorrectly defined openings Check All Clear All Apply Figure 71 The Repair Domain Definition dialog window HYDRUS automatically analyzes defined Geometry and if it is not consistently defined it displays a warning at the Edit Bar in its Help section Errors in Domain Definition After double clicking on this warning HYDRUS displays a message informing what is wrong incorrect similarly as when using the Check Data Consistency command 128 4 3 Opening An opening is an internal hole defined by a boundary curve having the following properties the curve is closed positively oriented in a counter clockwise direction does not intersect any other curve or itself and has the computational domain located on its right hand side in the sense of positive orientation while the left side is not part of a computational domain An opening is not part of the computational domain or surface An opening is created graphically as follows One first defines boundary objects that create a closed boundary curve One then uses the command IJnsert gt Domain Geometry gt Opening gt Graphically from the menu or alternatively the command Opening via Boundaries on the Insert Object part of the Domain Geometry version of the Tool Bar A user creates an opening by clicking on the closed curve one o
121. and Z axis or in the direction perpendicular to an extruded Surface When a Surface is not in a plane e g is curved and perpendicular extruding is selected extruding is done in directions of local perpendicular lines to an extruded Surface During extruding one can select on the Edit Bar the length step dL or enter numerically desired length of extruding L Note that the command Extrude can be used only for Planar Quad and B Spline Surfaces and it cannot be used for Partial Surfaces and for Surfaces containing a zero Curve i e a curve with a zero length from point P to point P 138 4 5 Thickness Vectors The term Thickness Vector is used for a vector usually but not always perpendicular to the Base Surface that extends the Base Surface to form a solid the three dimensional computational domain A new Thickness Vector can be defined either graphically or numerically Fig 79 There are several ways in which a Thickness Vector can be specified graphically and these are displayed at the Edit Bar Fig 78 which appears once a command for defining a Thickness Vector is selected a b c d Point and Length A user specifies the length of the Thickness Vector on the Edit Bar Vector Length and with the mouse selects the point to which the Thickness vector is assigned Point and Coordinate A user specifies the End Coordinate of the Thickness vVctor on the Edit Bar End Coordinate and with the mouse selects
122. and color and offset are displayed at the Edit Bar Fig 88 right 4 7 3 Bitmaps Textures Bitmaps Textures serve to use scanned figures maps as means to define the computational domain in the View window Bitmaps can be added using the Insert gt Auxiliary Objects gt Textures command Corners of the Bitmap must be anchored at 4 points coordinates of which must be selected such that the scale of the Bitmap corresponds with the scale of the View window Anchor points can be selected one at a time using either a Listbox containing list of all defined nodes or using a command Pick and selecting nodes using a cursor All anchor points can be also selected simultaneously using a command Pick ABCD The Edit Bitmap dialog window then provide information about the selected Bitmap such as its Size in pixels and kB One can then simply trace the bitmap to specify the computational domain 146 a Domain Geometry Set new Comment a Set new Comment 2 Number for new Number for new Comment Comment Text Text Test D Text E me Frame C Frame Position Offset x 862 63 cm di a pix kc dy 130 pix z 173 88 cm Step 10 pix Help x Help a Ke Step 1 of 2 Ke Step 2 of 2 Set position of the new Set offset of the new Comment Comment Ke Press Esc or right mouse Ke Press Esc or right mouse button to end the tool button to end the tool Figure 88 T
123. anic phosphorus are 16 XSOB Sulphide oxidizing bacteria modeled as part of the COD Nitrification is modeled as to step process Organic nitrogen and organic phosphorus are modeled Bacteria are assumed to be immobile as part of the COD 87 Table 12 Comparison of CW2D and CWM processes CW2D CWM1 Langergraber and Simunek 2005 Langergraber et al 2009 Heterotrophic bacteria 1 2 3 4 5 Hydrolysis conversion of CS into CR Aerobic growth of XH on CR mineralization of organic matter Anoxic growth of XH on CR denitrification on NO2N Anoxic growth of XH on CR denitrification on NO3N Lysis of XH Autotrophic bacteria 6 T 8 Aerobic growth of XANs on SNH ammonium oxidation Lysis of XANs Aerobic growth of XANb on SNH nitrite oxidation Lysis of XAND Heterotrophic bacteria 1 Hydrolysis conversion of XS into SF 2 Aerobic growth of XH on SF mineralization of organic matter 3 Aerobic growth of XH on SA mineralization of organic matter 4 Anoxic growth of XH on SF denitrification 5 Anoxic growth of XH on SA denitrification 6 Lysis of XH Autotrophic bacteria 7 Aerobic growth of XA on SNH nitrification 8 Lysis of XA Fermenting bacteria 9 Growth of XFB fermentation 10 Lysis of XFB Acetotrophic methanogenic bacteria 11 Growth of XAMB Anaerobic growth of acetotrophic methanogenic bacteria XAMB
124. approximate size of the transport domain Type of Geometry This section allows a user to choose between simple geometries having a structured finite element mesh i e 2D Simple Parametric and 3D Simple Parametric or more general geometries having an unstructured finite element mesh i e 2D General Boundary Rep 3D Layered and 3D General Boundary Rep Available options depend on the level of authorization purchased License Only simple geometries 2D Simple Parametric and 3D Simple Parametric are available for HYDRUS Levels 2D Lite and 3D Lite respectively 2D General Boundary Rep is available for the 2D Standard Level 3D Layered for the 3D Standard Level and 3D General Boundary Rep for the 3D Professional Level r Domain Type a Type of Geometry General 3D domain Ol A defined by boundary surfaces 2D Simple Parametric 2D General Boundary Rep on Help D 3D Simple Parametric D 3D Layered 3D General Boundary Rep 2D Domain Options f i 2D Horizontal Plane XY 2D ttical Plane XZ 2D Axisymmetrical Vertical Flow Units Model Precision and Resolution Length m v Epsilon 0 00019 m 7 Standard recommended Edit Properties on Geometric Objects Edit domain properties initial and boundary conditions on geometric objects Initial Workspace x Y zZ Min 5 000 0 000 5 000 m Max 30 000 10 000 15
125. arger than F the FE mesh is automatically refined 165 The Options Tab Minimum Number of Points Boundary Curves is set by default equal to 15 This number can be changed in the FE Mesh Parameters dialog window of the Options Tab Fig 104 This parameter is important when such objects as openings representing wells or drains are included in the transport domain These objects may be very small compared to the global finite element mesh i e smaller than the targeted finite element size Having a minimum number of nodes on boundary curves will then lead to local refinement of the finite element mesh around these objects thereby ensuring that relatively small objects are accurately represented in the numerical solution FE Mesh Parameters Main Stretching Options 1 Options 2 Mesh Sections _ Minimum number of points on boundary curves Check number of points on each boundary curve and increase the number if it is less than Option Off Option On Previous Apply All Default Figure 104 The FE Mesh Parameters dialog window Tab Options The Export Tab In the Export Tab not shown users can select options for export of the FE Mesh to a text file One can for example choose which points to export including or excluding the intermediate points on boundary curves and whether or not to include in the export also internal curves 166 The Mesh Section Tab The program can generate defa
126. ary Working Directory option Fig 4 is used It contains only the input data when the Permanent Working Directory option is selected HYDRUS input files used by the computational modules are extracted from the project_name h3d2 file into a working subdirectory output data created by the calculation module are sent into the same folder When saving a project output files created by the computational modules are also included into the project_name h3d2 file when the Temporary Working Directory option is used The input and output files can be either permanently kept in the external working directory or are stored in this folder only during calculations Fig 4 the radio buttons Temporary is deleted after closing the project and Permanent result files are kept in this directory The location of the external working directory is specified in the Project Description Fig 4 and the Program Options dialog window Fig 162 E Project Manager Project Groups Projects Current Project Group Name 3D_Tests Description Directory C USSL HYDRUS3D 3D_Tests Name Description Path 2D_Tests Two Dimensional Examples C ussl Hydrus3D Projects 2D_Tests 2D_tests C ussl Hydrus3D 2D_Tests 3D_Tests Three Dimensional Examples C ussl Hydrus3D Projects 3D_Tests 3D_Tests C USSL HYDRUS3D 3D_Tests Demos C USSL HYDRUS3D Demos Direct C USSL HYDRUS3D Projects Direct1 Tutorials C ussl Hydrus3D Tutorials Edit Remove Set Current
127. ase HYDRUS input files need to be stored in the working external directory sent there by the command File gt Import and Export gt Export Data for HYDRUS Solver and then can be imported back into the HYDRUS project_name h3d2 file using the command File gt Import and Export gt Import Input Data from JIn Files The Working Directory is a folder into which the program stores temporary data Each open project has its own Working Directory where the program stores for example input files for computational modules and where computational modules write the output files When saving a project data from the Working Directory are copied into the main project file project_name h3d2 When the project is closed the Working Directory is deleted Only when a user selects the option Permanent result files are kept in this directory Fig 4 is the Working Directory not deleted after closing the project in which case the temporary data are not copied into the main project file 31 32 2 Projects Geometry Information In the first dialog window that a user encounters after creating a new project he she needs to specify whether the flow and transport problem occurs in two or three dimensional transport domains Geometry type is selected in the Domain Type and Units dialog Window Fig 6 and 7 In this dialog window users specify the Type of Geometry the 2D Domain Options the Length Units and the size of the Initial Project Group the
128. associated with water stress its recommended and default value is 3 We have additionally included a parameter PW i e pressure head at the wilting point L below which transpiration stops Root Water Uptake Parameters Root Water Uptake Parameters Threshold Model S Shape Parameters Threshold Slope f 5 Conversion to pressure osmotic head Conversion to pressure osmotic head Osm Coeff Osm Coeff Database eee Figure 35 The Root Water Uptake Parameters dialog window for the solute stress response function based on the threshold model left and S shaped model of van Genuchten 1985 right The Root Water Uptake Parameters for the Threshold Model Maas 1990 of the salinity stress response function multiplicative Fig 35 left are as follows Threshold Value of the minimum osmotic head L the salinity threshold above which root water uptake occurs without a reduction 80 Slope Slope of the curve determining the fractional root water uptake decline per unit increase in salinity below the threshold The Root Water Uptake Parameters for the S Shaped Model van Genuchten 1985 of the salinity stress response function multiplicative Fig 35 right are as follows P3 The exponent p in the root water uptake response function associated with salinity stress The recommended value is 3 c50 The coefficient A50 in the root water uptake resp
129. ate HYDRUS and after clicking Yes the confirmation that HYDRUS has been successfully deactivated on your computer Fig 181 The Deactivation Code will then appear in the HYDRUS Deactivation window Fig 180 This code can be copied to the clipboard using the Copy to Clipboard button and then sent by email to the HYDRUS support or other HYDRUS distributors The command Send Deactivation Code by E mail will attempt to start emailing program e g Microsoft Outlook directly and copy there automatically an email address of the HYDRUS support support pc progress cz and all required information see an example of such email displayed in Outlook in Fig 173 HYDRUS Deactivation Deactivate HYDRUS This action will deactivate HYDRUS Deactivation will create a special code that can be later used for verification that HYDRUS has been deactivated on this computer Please save this code and send it to your HYDRUS reseller and or to supportpe progress cz WARNING After deactivation HYDRUS will run as a demo version i Deactivate HYDRUS Now Deactivation code Deactivation code is not available Copy to Clipboard Send Deactivation Code by e mail r Close Help Figure 180 The HYDRUS Deactivation dialog window 288 ho A This action will deactivate Hydrus Deactivation will create a special key deactivation code that should be sent to hydrus pc progress cz as a proof that HYDRUS was rea
130. ates properties when FE Mesh grids are different Import Input Data from IN Files Imports input data from in files that may have been modified manually outside of the HYDRUS GUI Import Quantity defined by values at Scattered Points Imports various quantities such as initial conditions from a text file with values given for a series of locations Import Points from Text File Reads single point coordinates from a text file Import Geometry from Text File Reads definition of the entire geometry from a text file Import Geometry from DXF File Reads definition of the entire geometry from a DXF file Import Geometry from ESRI File Reads definition of the entire geometry from a ESRI file Export Isolines Exports spatial coordinates of isolines Import Background Layer Imports background layer as a template for defining the transport domain Imports Data from ParSWMS Imports output data created by ParSWMS on a supercomputer or cluster of computers and display them in HYDRUS GUI Export Export Data for Hydrus Solver in Text Format Exports data for the HYDRUS solver into the working directory from which the computational module reads inputs and into which it writes outputs Export Geometry to Text File Writes definition of the entire geometry to a text file Export Selected Geometrical Objects Writes definition of the selected objects to a text file Export FE Mesh Exports information about the FE Mesh to a text file Export Current Quantity
131. ation dialog window for a two dimensional problem top and a three dimensional problem bottom Figure 113 shows dialog windows that provide information about the finite element mesh for two and three dimensional applications For two dimensional grids the window shows the number of finite element Nodes the number of boundary D Elements boundary edges between boundary nodes and the number of 2D Elements triangles For three dimensional grids the window shows again the number of finite element Nodes in the entire 3D domain the number of boundary D Elements boundary edges between boundary nodes on the bottom plane i e the 2D base surface of the transport domain the number of 2D Elements the number of triangles on the bottom plane of the domain and the number of 3D Elements tetrahedrals in the entire transport domain 178 5 7 Finite Element Mesh Sections FE Mesh Sections allow users to split the computational transport area into arbitrarily complicated shapes that are defined by external 3D points These FE Mesh Sections can then be used for example to define the material distribution or other properties FE Mesh Sections are parts of the FE Mesh used to specify input variables and to display results of calculations By default two dimensional problems have only one section consisting of the entire transport domain For three dimensional problems one section by default is formed by the Whole FE Mesh Section DO_000 in Fig
132. ation domain can be formed using several surfaces that can touch each other but can not overlap Fig 46 It is possible to create an opening in the base surface and then enter another surface into it Division of the transport domain into individual surfaces enables easier work with it since the program creates for each surface its own section and users can then specify different domain properties and initial and boundary conditions on these sections Internal Point Surfacel Surface2 Internal Curve Figure 46 A base surface showing several basic geometric objects 4 1 1 Points Points can be either used to define Boundary Objects or can be located inside of the Surface computational domain and not be associated with any boundary object Single Points Points 104 can be entered either graphically using a cursor most common or using the New Point dialog window identical to the General Tab of the New Point dialog Fig 48 To enter a new point graphically select the command Insert gt Domain Geometry gt Point gt Graphically from the menu or Points from the Insert Object part of the Domain Geometry version of the Tool Bar at the right side of the View Window and then enter the points using a cursor Once a command for defining a new point graphically is selected a cursor in the View window will become a cross with a small empty circle in the middle The coordinates of the location of the cursor will be displayed
133. ats sh ote lad eto cei lane 119 Edit Bar during the process of defining graphically a surface left and the General tab of the Edit Surface dialog window right eecceeeseeceeececeseeeecseeeecsneeeeneeeeneeeeaees 119 A solid showing the base surface ac cosa vescies orcas ts eeen ee eave eee ne 120 Solid showing separate vertical columns ce ceeceeseeeescecseecsaeceeeeeeeeeaeecsaeenseensees 120 A solid with its base surface in the XZ plane and thickness vectors in the Y direction E EE dp S E E eens dn E blesses cyst on ana ab E E wuse abu dy E 121 FE Mesh for a solid with its base surface in the XZ plane and thickness vectors in the X directions mere Sede eed ote ee eee Sia cand ajdt A a easel hee 121 Examples of Curved Surfaces Rotary Pipe B Spline and Quadrangle Surfaces 122 The Integrated Tab of the Edit Surface dialog Window cei eeeeeeeeeeneeenteeeteeeeees 125 An example of internal objects cniienni ne utente dele eadeeare antet nai 126 An example of an Upper Surface definition using Internal Curves and Thickness MW CLOTS iss nde tailpipes Bu G AER EERE R inch dune vip A N E R ARRETE 127 The Repair Domain Definition dialog window eeeeceessecsteceseeeeeeesseeenaeeneeesees 128 The New Opening dialog Window cccccesscecssececssececesceecssececeeeeeseeeeneceesaeeeesaees 129 The Edit Bar during the process of graphically defining a Hexahedral Solid Definition of a Base Surface on the lef
134. ature is below 2 C all precipitation is in the form of snow When the air temperature is above 2 C all precipitation is in the form of liquid while a linear transition is used between the two limiting temperatures 2 2 The code further assumes that when the air temperature is above zero the existing snow layer if it exists melts proportionally to the air temperature Boundary condition options a through g can be used only with the first time variable head condition Time Variable Head Flux 1BCs Special Boundary Conditions Triggered Irrigation Basic Options Switch the boundary condition from Time Variable Pressure Head to No Flux BC when Var H 1 gt 999999 F No Flux BC when the specified nodal pressure head is negative E Atmospheric BC when the specified nodal pressure head is negative Seepage Face BC when the specified nodal pressure head is negative E Treat the Time Variable Flux boundary condition as the Atmospheric BC q e with limited pressure heads E Apply Atmospheric boundary condition to nonactive Seepage Face Other Boundary Conditions Options Consider snow accumulation at the soil surface when temperatures are negative E Consider only horizontal projections of boundary elements for Time Variable Flux BCs ioe lene Goals Figure 118 The Time Variable Head Flux 1 BCs tab of the Boundary Condition Options dialog window 186 6 3 2 Special B
135. atures Since the Standard Palette can not be changed once any color is changed the program will request to save a new scale under a new name The changed colors will be used for all displayed variables not only the actual one aa EESTE mE i f Ere E E mE f ieee EE FF 4 EEE EEE g EEE H Custom colors Hue 40 Red IB BEES Engg gg oe Sat 240 Green 252 ColorlSolid in 119 Blue 0 Figure 140 The Color dialog window Define Cu Custom Scale A user can define his her own scale that is then remembered by the software and used for a particular variable in a given project When one wants to use a certain scale also in other projects he she needs to save it using the Save command Other commands e Default Sets the number of intervals to 11 and automatically fills values for the default scale 218 e Empty Deletes all values used with commands Fill and Fill Max Min e Fill Fills empty spaces between specified upper and lower values using linear interpolation e Fill Max Min Similar to Default except that this command does not set the number of values to 11 it uses the number of values selected by a user Save Saves the Scale for use with other projects e Delete Deletes a selected Custom Scale The number of values at the Scale can not be increased it can only be lowered from 11 using a slider By drawing a slider one can also generate values at a
136. b specify whether or not the program should Save automatically windows settings on close project c select whether Domain properties and boundary and initial conditions are edited by default on Geometrical objects or finite element mesh In the Calculation and Results part of the Program Options Tab one can a specify whether the results are to be kept in an external directory By default keep results in external directory b select whether the FE Mesh is to be saved in text format Save FE Mesh in text format c select whether or not Domain Properties are to be saved in text format Save Domain Properties in text format d Select whether the parallelized version i e the HyPar module see Section 9 8 of the standard computational module h2d_calc exe and h3d_calc exe is to be used Use Parallel Calculation Module Graphics Program FE Mesh Files and Directories Mesh Limits Recommended max number of finite elements for 2D Projects Recommended max number of finite elements for 3D Projects 500000 Export Options F Export intermediate points on boundary curves E Indude internal curves in the BOUNDARY INFORMATION table REMARK These two options are only intended for new projects Old projects can be changed individually in FE Mesh Parameters Write Description of Tables Preferred Generator for 2D Meshes Structured Mesh Meshgen C Genex Figure 163 The Program O
137. be straight Nodes along the upper boundary line may in that case have variable x and z coordinates However the lower boundary line must always be horizontal or have a specified slope while the left and right boundary lines must be vertical The flow region is then discretized into a structured triangular mesh Examples of simple rectangular geometries are shown in Figure 8 top e 2D General Boundary Rep This type of Surface is defined by a set of Boundary Curves see Section 4 2 Examples of general two dimensional geometries are shown in Figure 8 bottom and Figure 46 There are three types of three dimensional transport domains Solids see also Section 4 4 depending upon the selection made in the Domain Type and Units dialog window Fig 6 and 7 34 dimensional objects are formed by boundary This type of solid is defined using a set of surfaces that This type of geometries is available only in the 3D This type of solid has a Hexahedral Shape and is defined by type of solid is defined by the Base Surface see Section 4 2 and one boundaries This its basic dimensions The base can have a certain slope in the X and Y dimensions Fig 9 Hexahedral domains must have similar properties as rectangular domains i e vertical planes at the sides a horizontal or with a specified slope plane at the bottom boundary and with only the upper boundary not needing to be a plane An example of a
138. bjects for details rather than only on FE Mesh as available in Version 1 0 of HYDRUS This option will be by default On for new projects and it is Off for projects converted from Version 1 0 Users can turn this option Off and continue defining various properties on FE Mesh as they have been used to Users can turn this option On for projects converted from Version 1 0 of HYDRUS However they will then lose their original definitions and will have to specify them again on Geometric Objects 37 38 3 Flow Parameters 3 1 Main Processes In the Main Processes dialog window Fig 12 users specify the processes to be simulated 1 e Water Flow Solute Transport Heat Transport and or Root Water Uptake When Solute Transport is selected users can choose from multiple modules of different complexity The Standard Solute Transport module is described in detail in the HYDRUS Technical Manual Siminek et al 2012d This module allows consideration of individual solutes one or several that are either independent or subject to sequential or consecutive first order decay reactions Other solute transport modules briefly described below can consider multiple solute components that can mutually interact Wetland Module Unsatchem Module C Ride Module HP2 Module Check this box if the Wetland module is to be used The Wetland Module for two dimensional problems only was developed to model biochemical transformation a
139. ble errors which may appear during smoothing of the finite element mesh Convexity Check Operations 2 through 5 are repeated until a prescribed smoothness of the mesh has been achieved An unstructured triangular mesh for a given boundary nodal distribution can be generated in two different ways a step by step approach Calculation gt Advanced FE Mesh Generation gt Fundamental Triangulation and subsequent commands or by clicking on the Fundamental Triangulation command of the FE Mesh Advanced part of the FE Mesh version of the Tool Sidebar or by using automatic mesh generation Calculation gt Generate FE Mesh or the Generate FE Mesh command on the Edit FE Mesh part of the FE Mesh version of the Tool Sidebar The step by step approach should be used only for special cases and then only by experienced users Automatic generation recommended is a much faster and easier approach The mesh generation parameters must be specified before the mesh generation process is started By modifying the mesh generation parameters users can influence the smoothness of the mesh Smoothing Factor Fig 103 its anisotropy Figs 99 and 112 computational time and the possible display of intermediate results among other features The most important mesh generation parameter is the smoothing factor which can significantly affect the final number of elements The smoothing factor is defined as the ratio of the minimum and maximum dimensions of a triangle Wh
140. by simultaneously holding the Shift button A selection can be made using a rectangle by clicking with the left mouse button outside of objects and holding the left mouse button while moving the mouse rhomboid see Chapter 8 4 on Toolbars and Tools with the Edit gt Select gt Select by Rhomboid command circle Edit gt Select gt Select by Circle or polygon Edit gt Select gt Select by Polygon In the Standard Selection Mode Edit gt Select gt Standard Selection Mode the status of the selected object is changed selected or unselected after its selection i e the selection is toggled If we want to only add or remove objects to or from existing selection i e we want to prevent switching the status of selected objects toggling respectively it is possible to choose two special selection modes Add to Selection Edit gt Select gt Add to Selection or Remove from Selection Edit gt Select gt Remove from Selection Both commands are accessible from the submenu Edit gt Select or from the toolbar under the button Tools for Selection Two special Selection Modes can also be activated by holding the Left Ctrl Add to Selection or Right Ctrl Remove from Selection keyboard buttons When the cursor mouse is moved above an object information about that object appears on the status bar and the object is temporarily highlighted this process is referred to as pre selection 230 Apart from selectin
141. cal user interface GUI By holding the F1 button or clicking on the Help button while working in any window the user obtains information about the window content In addition context sensitive help is available in every module using the SHIFT F1 help button In this mode the mouse cursor changes to a help cursor a combination arrow question mark which a user can use to select a particular object for which help is needed e g a menu item toolbar button or other features At that point a help file will be displayed giving information about the item on which the user clicked Except for the computational modules that are written in FORTRAN the entire GUI is written in C The HYDRUS Graphical User Interface Fig 1 is the main program unit defining the overall computational environment of the system This main module controls execution of the program and determines which other optional modules are necessary for a particular application The module contains a project manager and both the pre processing and post processing units The pre processing unit includes specification of all necessary parameters to successfully run the HYDRUS FORTRAN codes modules H2D_CALC H2D_CLCI H2D_WETL H2D_UNSC and or H3D_CALC grid generators for relatively simple rectangular and hexahedral transport domains a grid generator for unstructured finite element meshes appropriate for more complex two dimensional domains a small catalog of soil hydraulic pro
142. ce there is currently no technical manual describing the two dimensional version of the UNSATCHEM module users are referred to the HYDRUS 1D manual Simiinek et al 2008 which provides all relevant information about this module Solute Transport Time Weighting Scheme Space Weighting Scheme Explicit Scheme Galerkin Finite Elements Crank Nicholson Scheme Upstream Weighting FE Implicit Scheme GFE with Artificial Dispersion Units and Stability Mass Units mmol Stability Criterion 2 Use Tortuosity Factor Composition Number of Solution Concentration Combinations Number of Adsorbed Concentration Combinations Number of Precipitated Concentration Combinations Previous Figure 24 The Solute Transport dialog window for the UNSATCHEM module 65 3 11 Solute Transport Parameters Soil and Solute Specific Transport Parameters are specified in the Solute Transport Parameters dialog window Fig 25 Solute Transport Parameters Soil Specific Parameters Solute Specific Parameters Bulk D Disp L Disp T Fract Thimob Sol Difus W Difus G 1 5 0 5 0 1 1 0 0 1 5 0 5 0 1 Next Figure 25 The Solute Transport Parameters dialog window The following Soil Specific Parameters left part of the dialog window are specified for each soil material Bulk d Disp L Disp T Frac ThImob Bulk density ML Longitudinal
143. centration Nonequilibrium Concentration Temperature Import Delete All Initial Conditions Water Flow Solute Transport Heat Transport Boundary Conditions Options Delete All Boundary Conditions Edit Properties and Conditions on FE Mesh Edit Properties and Conditions on Geometric Objects Transfer all Properties to FE Mesh Sections Cross Sections Edit Sections Generate Sections New Section from Selection New Section from View Display Whole Domain Display Previous Hide Selection Display only Selection Display Reverse Cut with Rectangle Cut with Indexes Import FE Mesh Sections Edit Delete Selected Delete All Auto Adjust Work Plane 250 Auxiliary Objects Dimensions Delete Selected Delete All Comments Edit Delete Selected Delete All Background Layers Edit Move Rotate Mirror Stretch Skew Delete All C View Geometry FE Mesh Domain Properties Initial Conditions Boundary Conditions Results Navigator Edit Bar Tabs in View Status Bar Toolbars Reset Toolbars Customize Toolbars Standard View Zoom by Rectangle View All Previous View Dynamic View Scroll Zoom Rotate View Stretching Perspective Auto Rotate Display Whole Domain View in Direction Isometric In X direction In Y direction In Z direction Reverse X direction Reverse Y direction Reverse Z direction List Boxes for Inverse Data D Insert Domain Geometry Points Graphically Dialog Import Points from Text File Curves Line Polyline A
144. cm Z 0 00 cm Figure 49 Different ways of adding Parametric Points on a curve 4 1 2 Lines and Polylines Lines and Polylines are the most commonly used objects for describing the boundaries of a two dimensional domain and its internal curves Similarly as above for Points Lines and Polylines can be entered either graphically using a cursor most common or using the New Line dialog window identical to the General Tab of the Edit Line dialog Fig 50 When entering a new line graphically users can select the command Insert gt Domain Geometry gt Line Polyline gt Graphically from the menu or Line Abscissa or Line Polyline from the Insert Object part of the Domain Geometry version of the Tool Bar at the right side of the View Window and then enter the lines using a cursor Once a command for defining a New Line a single abscissa or a New Polyline is selected a cursor in the View window will become a cross with a small empty circle in the middle The 107 coordinates of the location of the cursor will be displayed next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 47 right The Edit Bar will also show which point and curve their numbers are being defined and what reference coordinate system the current coordinate system the grid origin or the last inserted point is used Once a single Line is specified for a new line one can immediately continue in specifying the
145. cted mesh line Draws positions of flowing particles Draws trajectories of flowing particles Deletes all output results Shows or hides the grid Specifies whether or not the mouse should move in steps defined by the grid Calls the Grid and Work Plane dialog window Fig 147 Redefines origin of the grid Sets Work Plane to the XY plane Sets Work Plane to the YZ plane Sets Work Plane to the XZ plane Selects coordinate system Changes color from abrupt to gradual at isolines Selects minimal and maximal values for the color scale either for the entire time duration or only for a selected time layer Selects minimal and maximal values for the color scale either for the entire transport domain or only for displayed part of the domain Selects a standard color scale for the display of a particular variable Selects a custom color scale for the display of a particular variable Calls the Edit Isoband Value and Color Spectra dialog window Fig 138 Moves or copies a selected object Rotates a selected object Mirrors a selected object 266 Stretch Skew Intersect Lines Intersect Surfaces Split Lines Insert Points on Line Check Geometry Repair Geometry Generate Domain Surfaces Create Video File Options Rendering Mode Solid Model Transparent Model Wire Frame Model Graph Type Isolines Colormaps Isolines Color Edges Velocity Vectors Display Options Edit Default Read Save As Program
146. ction is displayed in the View the values are transferred only to FE nodes of this Section Format of a text file with spatial coordinates and property values a The input text file must have the following format depending on the type of the transport domain of a project to which data are imported For 3D Domains Columnl x coordinate m Column2 y coordinate m Column3 z coordinate m Column4 value unit of the quantity displayed in the active view Example 0 000000e 000 0 000000e 000 8 000000e 001 3 000000e 001 0 000000e 000 0 000000e 000 0 000000e 000 5 000000e 001 3 000000e 000 0 000000e 000 0 000000e 000 5 000000e 001 For 2D XY Domains Columnl x coordinate m 204 Column2 Column3 y coordinate m value unit of the quantity displayed in the active view Example 0 000000e 000 8 000000e 001 3 000000e 001 0 000000e 000 0 000000e 000 5 000000e 001 3 000000e 000 0 000000e 000 5 000000e 001 For 2D XZ Domains Expected format Columnl x coordinate m Column2 z coordinate m Column3 value unit of the quantity displayed in the active view Example 0 000000e 000 8 000000e 001 3 000000e 001 0 000000e 000 0 000000e 000 5 000000e 001 3 000000e 000 0 000000e 000 5 000000e 001 Other Formats In addition to formats described above one can also import values from a file generated using the function File gt Export gt Export Current Quantity Although this file has a s
147. ction 2 what Processes are involved W water flow S solute transport T heat transport R root water uptake Inv Inverse problem the size of the project MB when the project was created Date and whether or not the Results exist Fig 3 The Project Manager can also display a preview of the Project s geometry see the check box Show Project Preview in Fig 3 Commands of the Project Manager are listed in Table 1 Table 1 Commands in the Project Manager Group Command Description Project Group New Registers a new Project Group in the Project Manager Edit Renames the selected Project Group and changes its description and or location Remove Removes registration of a selected Project Group from the Project Manager Set As Current Sets a selected Project Group as the active Project Group Close Closes the Project Manager Project New Creates a new project in the current Project Group Copy Copies a selected project within the current Project Group Rename Renames a selected project Delete Deletes a selected project Open Opens a selected project Close Closes the Project Manager Convert Converts projects created by earlier HYDRUS versions i e either HYDRUS 2D or version 1 0 of HYDRUS 2D 3D Calculate Calculates selected HYDRUS projects This command allows users to calculate multiple selected projects simultaneously Options Description Show Project Preview Provides a preview of the geometry of a particular
148. ctivation you can deactivate HYDRUS either by email the command Deactivate by E mail or online the command Deactivate on line 9 2 3 1 On Line Deactivation After clicking on the command Deactivate on line in the HYDRUS Authorization Status dialog window Fig 165 in the Online Deactivation window Fig 178 enter the Activation Key and press the button Deactivate Now You should receive a warning that this action will deactivate HYDRUS and after clicking Yes the confirmation that HYDRUS has been successfully deactivated on your computer Fig 179 i Online Deactivation Current License License Number 1001 Workplace Name PEX Computer Description Home PC Enter Password Activation Key Enteri Activation Key here E is Figure 178 The Online Deactivation dialog window f HYDRUS 2 xx kem HYDRUS 2 xx i This action will deactivate Hydrus Warning After deactivation Hydrus will run as a demo version A Hydrus has been deactivated on this computer Do you want to continue Figure 179 Window confirming successful online deactivation of HYDRUS 287 9 2 3 2 Deactivation by Email After clicking on the command Deactivate by E mail in the HYDRUS Authorization Status dialog window Fig 165 in the HYDRUS Deactivation window Fig 180 press the button Deactivate HYDRUS Now You should receive a series of warnings that this action will deactiv
149. ctivation by TAMA ce Kista isto Joh ia atta ices edi vo Waa bandae 280 9 2 3 Reinstallation Moving to another Computer cccccccssecsceeeestecetsesteceeessseeees 286 9 2 3 1 On Line Deactivation seiiscectie ices tcdc neha eed ek 287 9 2 3 2 Deactivation by TMI chia bth da ita ie Bini wish ela ete dain toe Gases 288 9 2 4 Extending Activation 43 scc4 sts ccecsisiua ciasdanatessl stebsstamiaauasiaekeneattealecasaanameeiaans 289 92 5 Hardware Key merisier ET E RE AS aiia 290 93 Print OPUONS goaie ui t e a a ia a a i i 292 9 4 Print Preview and Copy to the Clipboard Commands ccccsscccceeseeeceeeteseeeeneseseenss 293 9 5 Coordinate Systems pinin ia a a E E E A E E i dina 294 9 6 DOS Window During Calculations ooooneoeenneeeensseseesssseessssesesssereesseseesssseesssseeess 295 9 7 Running Computational Modules Outside of GUI or in a Batchuu icecccccccccsccecerseeeees 296 9 8 The HyPar Module a parallelized Version iswsccicssceccseeesartaiinsdinsnivanats s attabndwnds heaves 297 99 Video PUBS n an EE GREE Sh CRG E A ia Fe 298 910 Abon VEDI Sete cost E E E E ea eden es dade E Peale dae eae 300 References mensan ria ane hs hia cane EE aa Ea a aa E aa AEA ae eeu ones 301 Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 Figure 15 Figure 16 Figure 17 Figure 18 Figure 19 Figure 20 Figure 21 Figure
150. ctors Edits solids 257 Flow Parameters Main Processes Inverse Solution Time Information Output Information HP2 Print Information Water Flow Parameters Iteration Criteria Hydraulic Properties Model Soil Hydraulic Parameters Anisotropy Tensors Solute Transport Parameters General Information HP2 Components HP2 Definitions Solute Transport Parameters Solution Composition Solute Reaction Parameters Constructed Wetlands Parameters I Constructed Wetlands Parameters II Temperature Dependence Water Content Dependence Chemical Parameters Fumigant Application Selects the processes to be simulated i e water flow multiple solute transport heat transport and or root water uptake the Main Processes dialog window Fig 12 Selects type of weighting of measured data and whether soil hydraulic parameters solute transport parameters and or heat transport parameters are to be fitted the Inverse Solution dialog window Fig 13 Selects time units and gives the time discretization information the Time Information dialog window Fig 15 Specifies print options The Output Information dialog window Fig 16 Specifies print options for the HP2 modules Specifies iteration criteria for the solution precision and parameters for the time step control The Iteration Criteria dialog window Fig 17 Selects the type of model used for the soil hydraulic properties and decides whether hyste
151. d Users select which parameters the soil hydraulic solute transport and reaction and or heat transport parameters are to be optimized Estimate from the specified experimental data One also selects the method of Weighting of Inversion Data in the objective function Users can choose between no weighting weighting by mean ratios or weighting by standard deviations When no weighting is selected one needs to supply weights for particular data points in the Data for Inverse Solution dialog window Fig 14 When weighting by mean ratio or weighting by standard deviation is selected then the code calculates either the means or the standard deviations of the different data sets e g water contents pressure heads concentrations and adjusts the weights proportionally These internal weights can still be multiplied by weights from the Data for Inverse Solution dialog window Fig 14 Inverse Solution Estimate Soil Hydraulic Parameters Solute Transport Parameters Help Concentration Type Resident Concentrations Log Resident Concentrations O Total Resident Concentration Weighting of Inversion Data No Internal Weighting Weighting by Mean Ratio Weighting by Standard Deviation Other Parameters Max Number of Iterations Number of Data Points in the Obiective Function Figure 13 The Inverse Solution dialog window 42 The objective function for the in
152. d Model CW2D Parameter I dialog window 0 89 The Constructed Wetland Model CWM1 Parameter I dialog window 92 The Constructed Wetland Model CW2D Parameter II dialog window 93 The Constructed Wetland Model CWM1 Parameter II dialog window 95 The main window of the Slope Stability Module 0 eee ee eeseeeeeeereeceaeeeeeeeeeeeeneees 97 The Slope Stability Parameters dialog Window eccesseesseceseceeeeesseeeaeceeeeseeeeneees 98 The Default Parameters for Slope Stability Module dialog window cesses 99 An example of the Print and Export document generated by the Slope Stability TINO OU Cia occa Gar sieietan aa E a on A E aden anette A N ee 100 A base surface showing several basic geometric ODjeCts ce eeeeceeeseeeeeteeeetteeeensees 104 The Edit Bar during the process of defining graphically a new point left and a new Jine ght eseri sca ak alata ea ai a Queenan ara a a e eaa aieeaa o aai Teams 105 The Edit Point dialog window iiisiccetasecescaavesaceeshicceentsacaacesonsactaavaccdaetsdentmeawavaccesndes 106 Different ways of adding Parametric Points on a curve essssseseseseerersrrererrerserereeees 107 The Edit Curve dialog windoW sessssseesseessesssessseeesseessseesseesseesseeessseesseesseesseesseee 108 The Edit Bar during the process of defining graphically a radius for a new arc left or ANEW Cll CLE TTL E E E E EE EE T 10
153. d Vz or Vx and Vy or Vx Vy and Vz or by selecting two points in the transport domain Pick Two Points Note that Local FE Mesh Stretchings are ignored when a Global FE Mesh Stretching is defined i e a Global FE Mesh Stretching has to be equal to 1 if one wants to consider Local FE Mesh Stretchings FE Mesh Stretching is available only for 2D General and 3D Layered domains Mesh Stretching No On Surface No Z E Cancel Surfaces No Help Fs ao i Mesh stretched in __SetNo Stretching x direction with factor i H J i Stretching direction Fs 3 0 direction Y direction Z direction General direction only 2D projects Y Parallel Perpendicular x N i V2 8 Comment Pick Two Points Figure 100 The Mesh Stretching dialog window for a Local FE Mesh Stretching In the example below a listing from the Navigator Bar the first FE Mesh Stretching has a Stretching Factor of 0 03 in the direction of the Z coordinates assigned to Surface 3 the second FE Mesh Stretching has a Stretching Factor of 0 01 in the direction of the general V2 vector assigned to Surface 2 etc 99 FE Mesh Stretchings lt i 1 Z 0 03 3 i 2 V2 0 01 4 3 V2 0 20 1 Figure 101 Listing of FE Mesh Stretchings on the Navigator Bar 162 Local FE Mesh Stretchings can be edited by clicking at them at the Navigator Bar Figure 102 below shows an example of the
154. d calculate actual and cumulative water and solute fluxes across this Mesh Line The fluxes across the Mesh Line are then displayed using the Fluxes across Mesh Lines dialog window Fig 92 after using the Results gt Fluxes across Mesh Lines command This dialog displays actual and cumulative water and solute only convective fluxes across individual Mesh Lines Fluxes across Mesh Lines Meshline Mesh Line No 1 Flux Type Water flux across the meshline Water flux across the meshline No 1 0 3 0 2 0 1 0 0 0 1 0 2 0 3 o mA 6 E D H 2 B 5 tS 5 0 4 0 5 150 200 Time days Figure 92 The Fluxes across Mesh Line dialog window 149 Information for this graph is read from the CrossSect out file that contains data organized into the following columns Variable Description Units Time Time T Flux i Water flux across the ith cross section LT or L T j CumFlux i Cumulative water flux across the ith cross section L7 or L SolFlux i Convective solute flux across the i th cross section M L L T M L T or M L L T M T CumSFlx i Cumulative convective solute flux across the i th M L L7 M L or cross section M L L M t for 2D and three dimensional axisymmetrical problems respectively Water Fluxes across internal lines mesh lines are calculated in HYDRUS similarly as fluxes through the boundary nodes
155. d number of nodes was reached during the mesh generation process and the user needs to decide whether or not so many nodes are needed for the envisioned FE mesh and either increase this number or adjust other parameters so that less nodes and FE elements are generated For 3D General geometries there is in the Mesh Consistency Check section an additional check box Detect Collisions This check box is important only for complex 3D General geometries consisting of multiple solids When this check box is on the program checks collisions of different objects The solids cannot intersect each other without having the intersections properly defined using boundary curves The program also detects if one Solid is entirely inside of another Solid i e its boundaries do not intersect The former Solid has to be in such case defined as an Opening Hole Cavity The check box Detect Collisions enables users to turn off this check in cases when they are absolutely sure that there are no such collisions and they still receive warning about a collision of solids The Stretching Tab Stretching of the finite element mesh i e the degree of mesh anisotropy in a certain direction is defined using the Stretching Factor and Stretching Direction Fig 99 The finite elements are made larger in the particular Stretching Direction if the Stretching Number is larger than one and smaller if smaller that one The result of this transformation is a mesh deformed
156. dary record Note that tMax lt tInit n tPeriod 46 Table 5 Time Information variables Time Units Time units T to be used throughout the application years days hours min sec When units are changed during or after data entry then all input variables are converted automatically into the new units Initial Time Starting time T of the calculation Final time T of the calculation Initial Time Step Initial time increment At T The recommended value for the initial time step depends on the type of simulation and boundary conditions used When simulating a process that starts with a large initial pressure head or concentration gradient at the boundary e g ponded infiltration or a sudden change of boundary concentration use a small value of the initial time step e g 1 s When simulating a long term process with variable boundary conditions e g seasonal or multiyear simulation start with a larger time step e g 15 min This is because this initial time step is used whenever time variable boundary conditions significantly change e g the water flux changes by 25 or more If needed if there is no convergence for Atini the program will still use a smaller time step than Atinin but starting with larger Atin leads to more efficient calculations In general smaller initial time steps must be used for soil with more nonlinear soil hydraulic properties e g course textured soils and larger initial time steps ca
157. defining anisotropy angles the first and second components of anisotropy and subregion numbers which are all assigned to elements Scaling Factors can be generated for two dimensional applications using a random generator by clicking on the command Edit gt Domain Properties gt Stochastic Distribution of S F that calls the Stochastic Distribution of Scaling Factors dialog window Fig 121 Each scaling factor can be generated either independently of the other scaling factors or by assuming Miller Miller similitude In that case the program generates hydraulic conductivity scaling factors and automatically calculates from their values the pressure head scaling factors Stochastic Distribution of Scaling Factors Stochastic Distribution of Scaling Factors K Hydraulic Conductivity Scaling Factor Cancel Pressure Head Scaling Factor Help C Water Content Scaling Factor Other Options Recalculate Parameters Figure 121 The Stochastic Distribution of Scaling Factors dialog window Parameters for random generation of the scaling factors are specified in the Stochastic Parameters dialog window Fig 122 In this dialog users need to specify whether the scaling 191 factors are normally or log normally distributed using the check box Log Normal Distribution and provide values for the standard deviation of a particular scaling factor and correlation lengths in the x and z directions if the scaling factors are spa
158. deling of rigid bodies e Earthquake effects e Geo reinforcement may be included e Analysis according to safety factor e Analyses methods Bishop Fellenius Petterson Spencer Morgenstern Price The basic input parameters of the Slope Stability module such as basic Soil Characteristics Water Influence and the Factor of Safety are specified in the Slope Stability Parameters window Fig 43 All additional parameters such as for Earthquake Anchors Reinforcements Surcharge and Analysis options are specified directly in the Slope Stability module B Slope Stability Parameters Soil Characteristics tweidht 17 5 n Pre Unit weight kN m 3 Cancel 3 Silt Loam Angle of internal friction 15 Help Cohesion of soil 7 kPa Saturated unit weight 18 5 kN m 3 Select from Catalogue Water Influence Analysis Type of water inlfuence Pore Pressure X Factor of safety 1 5 HYDRUS printout time Final Time T Remark This dialog contains just basic parameters for the Slope Stability Module All other parameters Next such as Earthquake Anchors Reinforcements Surcharge and Analysis options can be i specified in the Slope Stability Module window Figure 43 The Slope Stability Parameters dialog window Additional parameters Soil Characteristics needed for the calculations of slope stability slope are specified here for all materials used in HYDRUS Paramet
159. dispersivity Dz L Transverse dispersivity Dr L Dimensionless fraction of adsorption sites classified as type 1 sites i e sites with instantaneous sorption when the chemical nonequilibrium option is considered Set this parameter equal to 1 when equilibrium transport is considered Frac becomes the dimensionless fraction of adsorption sites in contact with mobile water when the physical nonequilibrium option is considered In that case Frac should be set equal to 1 when all sorption sites are in contact with mobile water The immobile water content Set equal to 0 when the physical nonequilibrium option is not considered The following Solute Specific Parameters right part of the dialog window are specified for each solute Diffus W Diffus G Molecular diffusion coefficient in free water D LTH Molecular diffusion coefficient in soil air Da LTH 66 3 12 Solute Reaction Parameters The Solute Reaction Parameters and concentrations for Boundary Conditions are specified in the Solute Reaction Parameters dialog window Fig 26 Each solute has its own Solute Reaction Parameters dialog window Reaction Parameters for Solute 1 Boundary Conditions OK cBnd i cBnd2 cBnd3 cBnd4 cRoot cwell cBnd c tm Cancel 1 0 0 0 0 0 0 0 Help Reaction Parameters Henry SinkL1 SinkS1 Previous Figure 26 The Solute Reaction Parameters dialog window The following Solute Reaction Par
160. dit Bar or using Edit gt Sections gt Edit Sections Table 19 Finite element mesh sections generated in different HYDRUS versions HYDRUS Version Generated FE Mesh Sections 2D Lite Nothing 2D Standard For each Surface of more than one and each Geo Section see Section 8 1 8 defined by user 3D Lite For each layer of the FE Mesh 3D Standard For each FE layer each geometric layer and for each Column 3D Professional For each Geo Section as defined in Section 8 1 8 179 The function Import FE Mesh Section allows importing FE Mesh Sections by reading their definition from a text file The text file has the following format The first three columns are the coordinates of the point and the fourth is an index of the FE Mesh Section this Section will be created after the text file is read into which the point belongs An example of the text file http www pc progress com Images Pgm_Hydrus3D Test3_Sections txt can be downloaded from the Tutorial 2 12 http www pc progress com en Default aspx h3d tutorials which Figure 114 The FE Mesh Sections dialog window FE Mesh Sections Sections Selected Sections DO_000 Whole FE Mesh ML_000 Shell ML_001 Mesh Layer ML_002 Mesh Layer ML_003 Mesh Layer ML_004 Mesh Layer ML_005 Mesh Layer ML_006 Mesh Layer ML_0O0 Mesh Layer ML_008 Mesh Layer ML_009 Mesh Layer ML_010 Mesh Layer Create New Section From Current View Default Sect
161. dows are used to specify initial values of the temperature and the liquid and adsorbed concentrations e g Temperature Distribution dialog window Fig 117 The dialog window will then again provide information about the selected nodes Values in selected nodes i e the number of selected nodes and their minimum and maximum temperatures concentrations One can specify either constant value for all selected nodes or have the values change linearly with depth When the box Use top value for the entire selected region is checked the value in the Top box is assigned to all selected nodes Temperature distribution Values in selected nodes Number of Selected Nodes 222 Minimum value 20 Maximum value 20 New values linear constant distribution Top 20 Use top value for the entire selected region i Cancel Figure 117 The Temperature distribution dialog window The initial conditions for the UNSATCHEM module are defined in terms of the Solution Composition numbers integer Exchange Species numbers Solid Species numbers and CO2 Concentrations real The composition numbers refer to different Solution Compositions Exchange Species and Solid Species defined in Figure 30 6 3 Boundary Conditions Specification of the boundary conditions is relatively straightforward Users must first select from the Navigator Bar particular Boundary Conditions i e water flow solute transport or heat transport and then cl
162. e actual water uptake rate Fig 34 Root water uptake with compensation can be simulated when the Critical Stress Index is smaller than one see the Technical Manual im nek et al 2010 b Solute Stress Model The effect of salinity stress on the root water uptake can be either neglected No Solute Stress or considered using the Additive or Multiplicative models i e salinity stress is either added to water stress or uptake reduction due to water stress and salinity stress are multiplied When the multiplicative model is used for salinity stress one can use either the Threshold Model Maas 1990 or an S Shaped Model van Genuchten 1985 Fig 35 77 c Active Solute Uptake Model Total root nutrient uptake is determined from the total of active and passive nutrient uptake The partitioning between passive and active uptake is controlled by the a priori defined concentration value cRoot Fig 26 Passive nutrient uptake is simulated by multiplying root water uptake with the dissolved nutrient concentration for soil solution concentration values below cRoot Passive nutrient uptake is thus zero when cRoot is equal to zero One must therefore specify the maximum allowed concentration cRoot in the passive root solute uptake term When zero is specified all solute is left behind in the soil there is no passive root solute uptake and only solute free solution is taken up When the concentration is lower than cRoot all solute is
163. e calculations 62 Stability Criterion Use Tortuosity Factor Temperature Dependence Concentration units in general should be given in ML where M is Mass Units specified in the Solute Transport dialog window Fig 22 and L is Length Units specified in the Domain Type and Units dialog window Fig 6 However since the concentration variable appears in each term of the governing solute transport equations Eq 3 1 and 3 2 of the Technical Manual it is possible to use different length units than those used to define geometry and fluxes e g geometry may be specified in meters while concentrations are given in mg cm In such case the solute fluxes cq will then be in units of ML L T where L is the length unit e g cm used to define concentrations and Lg the length unit defining geometry and fluxes e g m Similarly the solute mass c V obtained by integrating solute over the transport domain will be in units of ML Lg Similar adjustments of units need to be done for other variables that involve both concentration and length units Product of the dimensionless Peclet and Curant numbers Pe Cr This criterion is used either to add artificial dispersion in the Galerkin Finite Elements with Artificial Dispersion scheme or to limit the time step leading to lower Courant numbers for a given Peclet number for the Galerkin Finite Elements scheme Check this box when molecular diffusion coefficients in the water and
164. e catalog for the Kosugi s model were obtained by fitting retention curves generated using the Carsel and Parrish 1988 parameters for the van Genuchten s 1980 model using RETC The following soil textural classes are represented in the soil hydraulic catalog Sand Loamy Sand Sandy Loam Loam Silt Loam Sandy Clay Loam Clay Loam Silty Clay Loam Sandy Clay Silty Clay Clay Neural Network Prediction The program uses pedotransfer functions PTFs based on neural networks Schaap et al 2001 to predict van Genuchten s 1980 water retention parameters and the saturated hydraulic conductivity K based on textural information see Section 3 8 below 56 When the parameter estimation option is selected then users have to provide initial estimates of the optimized soil hydraulic parameters specify which parameters are to be optimized check appropriate checkboxes and provide parameter constraints for the optimization Entering zeros the default values for the minimum and maximum values signifies that the parameters are unconstrained Table 7 Soil hydraulic parameters for the analytical functions of van Genuchten 1980 for twelve textural classes of the USDA soil textural triangle according to Carsel and Parrish 1988 Textural class Sand Loamy Sand Sandy Loam Loam Silt Silty Loam Sandy Clay Loam Clay Loam Silty Clay Loam Sandy Clay Silty Clay Clay L L 0 045 0 057 0 065 0 078 0 034 0 067 0
165. e entered instead D_Soil D_Virus SMax2 Stick Eff2 DetachSolid2 Diameter of the sand grains de L Diameter of the particle d e g virus bacteria e g 0 95 um or 0 95e 6 m L Parameter in the blocking function for the second sorption sites Smax for model 2 Sticking efficiency a for the second sorption sites First order entrainment detachment coefficient ka TH for the second sorption sites 68 SMax1 Parameter in the blocking function for the first sorption sites Stick Eff1 Sticking efficiency a for the first sorption sites DetachSolid1 First order entrainment detachment coefficient ky T for the first sorption sites Boundary Conditions Concentrations for time independent Boundary Conditions are also specified in this dialog window cBnd1 Value of the concentration for the first time independent boundary condition ML gt Set equal to zero if no time independent boundary condition is specified The same for cBnd2 through cBnd4 cRoot Value of the concentration for the fifth time independent boundary condition ML 3 If water uptake is considered then cRoot is automatically used for the maximum concentration of water removed from the flow region by root water uptake When zero is specified then all solute is left behind in the soil and only a solute free solution is being taken up When the concentration is lower than cRoot all solute is taken up When the concentration
166. ead use of multi dimensional models requires ways which make it easier to create manipulate and display large data files and which facilitate interactive data management Introducing such techniques will free users from cumbersome manual data processing and should enhance the efficiency in which programs are being implemented for a particular example To avoid or simplify the preparation and management of relatively complex input data files for two and three dimensional applications and to graphically display the final simulation results we developed an interactive graphics based user friendly interface HYDRUS for the MS Windows 95 98 NT ME XP Vista and 7 environments The interface is connected directly to the computational codes The current version 2 0 of the HYDRUS graphical user interface represents a major upgrade of version 1 0 which itself was a complete rewrite of the version 2 0 of HYDRUS 2D that expanded capabilities of HYDRUS 2D to three dimensional problems Version 2 which includes the 3D Professional Level of HYDRUS includes many new features as compared to version 1 0 In particular it includes support for complex general three dimensional geometries and an option to specify various domain properties and initial and boundary conditions on geometric objects rather than directly on the finite element mesh In addition to information given in this user manual extensive context sensitive on line help is made part of the graphi
167. eceeeeeceeeeeceeeeeceteeeeeeeeees 43 The Time Information dialog Window ccecescsseeseeeseeseceseceeceseeeeceseceeeeaeceeeeeeeaeeeeeaes 46 The Output Information dialog windoW ccsccesseseeseeeecesececceseeeceeseeeeeeaeeeeeeeeeneeeeeaes 48 The Iteration Criteria dialog Wino we lt sc ccseciasiepcesacedsandestsesdates eeeecneieanaaessasaadaateosaacateke 50 The Soil Hydraulic Model dialog Window eeceeccesssecsseceeeeeeeeeeseecsaeceeeeseeeeaeessaeens 53 The Water Flow Parameters dialog window for direct top and inverse bottom PREC UTA EE E E es oad E EEE E E TE E i 55 The Rosetta Lite Neural Network Predictions dialog window cccceeesseeeeeeeees 59 The Edit Local Anisotropy dialog window for two dimensional applications 60 The Tensors of the Anisotropy dialog WiNdOW esssesceseeeceeneeeesecneeeeseeeeaeeesaeens 60 The Solute Transport dialog wind Wes ssscesscsiesissssgsscniqats ai deceasatsveads idesdoe soonest eecaaense 61 The Solute Transport dialog window for the UNSATCHEM module eee 65 The Solute Transport Parameters dialog Window c scceeseeceseeeceeeeeeeeeeeceteeeeteeeeees 66 The Solute Reaction Parameters dialog window ecsseceesceceeeeceeeeeceeeeeceteeeeneeeees 67 The Solute Reaction Parameters dialog window for the UNSATCHEM module 70 The Temperature Dependent Solute Transport and Reaction Parameters dialog VUNG Washi Si eed ae gel e dd aed ee
168. ecip Similar adjustments are not done for cVal2 and other concentration values CVal2 The second time dependent solute concentration ML that can be used for nodes with prescribed time variable boundary conditions atmospheric BC variable head flux BC not specified when solute transport is not considered CVal3 The third time dependent solute concentration ML that can be used for nodes with prescribed time variable boundary conditions atmospheric BC variable head flux BC not specified when solute transport is not considered The last three entries are entered for each solute The table in Figure 37 can be edited by manually adding or deleting lines The table has a capacity for about 32 000 records depends on the number of columns When a longer time record is to be simulated then one needs to directly edit the Atmosph in input file in the working directory using any standard software such as MS Excel The manually modified Atmosph in file then needs to be imported back into the HYDRUS project_name h32d file using the command File gt Import and Export gt Import Input Data from In Files Data for the Time Variable Boundary Conditions can be prepared in any spreadsheet software and then copied into the table using Windows paste hot keys i e Ctrl V The total number of atmospheric data records is given in the Main Time Information dialog window Fig 15 Surface Area Associated with Transpiration The total transpiration f
169. econd Tab of the HYDRUS Authorization Status window i e the Add in Modules Tab list additional HYDRUS modules e g Unsatchem Wetland DualPerm C Ride or HP2 that are currently available and activated At the top of the Tab there is an indication which Authorization Method either of Software Key or a Hardware Key is used The third Tab of the HYDRUS Authorization Status window i e the History of Activation Tab reports recent actions related to HYDRUS activation r Status History of Activations Server response F Online operation error 113 There is no Single user type of the requested produc lt lt lt Online Activation finished gt gt gt Generating of the Request Codes started at 2011 01 01 12 17 05 HYDRUS version 2 01 0080 Level to activate 3D Professional Network Licence No Timesimited License Yes Expiry Date 2011 07 01 Request Code 1 311157192 Request Code 2 106300092 Licence Number 1001 Computer Description Home PC Customer PC Progress lt lt lt Generating of the Request Codes finished at 2011 01 01 12 17 05 gt gt gt Activation attempt made at 2011 01 01 12 19 51 With Request Code 1 311157192 Request Code 2 106300092 Activation Code 1 218309801 Activation Code 2 0 Activation Code 3 0 Licence No 1001 Attempt No 1 Workplace Name PCX Expiry Date 2011 07 01 lt lt lt Activation attempt ended with status Successful activation
170. ect Time Layer The Last Final Time Layer Time Layer No 7 Identical FE Meshes ox cancel te Figure 132 The Import Initial Condition dialog window 202 Note While in the previous HYDRUS versions the import of results from previous calculations as initial conditions for the new simulation could be done only from a project that had an identical geometry and FE Mesh discretization as the actual project in newer HYDRUS versions version 2 02 and later the geometry may be slightly different should not differ too much and the FE Mesh discretization can be different as well Whether the FE Meshes of the two projects are identical can be identified by the user a check box Identical FE Meshes so that the code can simply transfer nodal values without the need to interpolate 6 6 2 Import Data from HYDRUS Projects Various other properties such as Domain Properties Initial Conditions and Boundary Conditions can be imported from an existing HYDRUS project using the Import command File gt Import gt Import Input Data from Another HYDRUS Project After clicking on this command an Open dialog window appears with Files of type preselected for HYDRUS applications i e h3d2 One then needs to browse for the HYDRUS project from which the initial condition is to be imported After selecting a particular project the Import Selected Quantities dialog window appears Fig 133 This window provides information from which
171. ed continuously at consecutive times thereby visualizing the flow and transport process Note however that display times are defined by the print time intervals specified in the input data file This means that the print times must be at constant intervals so that the time scale of the flow animation will not be distorted In other words undistorted flow animation requires that the print time intervals be constant The speed of the flow animation depends on the hardware being used i e the speed of the microprocessor and graphical card 209 7 1 1 Displayed Variables Multiple variables can be displayed in the View window A comprehensive list of standard and alternative variables that can be displayed in the View window are summarized in Tables 21 and 22 respectively Table 21 Standard variables displayed in the View Window of the Results tab Results Pressure Head Water Content Velocity Velocity Vectors Root Water Uptake Concentration i Sorbed Noneq Conc i Immobile Conc i Temperature Unsatchem Variables Wetland Variables Graphical Display Pressure head h L displayed always Water content or 8 when dual porosity model is used displayed always Values of the Darcy s flux q LT displayed always Darcy s flux vectors q LT displayed always Root water uptake S T displayed when root water uptake is considered Liquid phase concentration c M Lw J displayed when solute transport in t
172. ed only further away in the other Surfaces of the computational domain 168 The Point or Surface with an assigned FE Mesh Refinement are indicated using the following marks D and z respectively FE Mesh Refinement is marked on curves using green points visible in the edit mode site Contrary to other green points on the curves they can be selected New FE Mesh Refinement O Line FE Size O Line Number of Points O Surface Finite Element Size s 2 60 om Current Global Targeted Size of Finite Elements 7 90 cm Comment New FE Mesh Refinement Apply FE Mesh Refinement to O Point Oli O Surface Number of Points n 202 Current Global Targeted Size of Finite Elements 7 90 cm Comment New FE Mesh Refinement FE mesh Refinement S at Point S 2 cm i Global FE Size 5 cm FE mesh Refinement on Line given by N points K N 17 Global FE Size cm Apply FE Mesh Refinement to Ou z O Line Number of Points O Surface Finite Element Size 2 60 cm Current Global Targeted Size of Finite Elements 7 90 cm Comment FE mesh Refinement on Line given by FE Size S 2 cm gt Global FE Size 5 cm New FE Mesh Refinement No 1 Apply FE Mesh Refinement to O Point O Line FE Size Line Number of Points ET Fin
173. ed to carefully check results of the import if Geometries or FE mesh are different 6 6 3 Import Data from a Text File HYDRUS users often encounter a problem of defining a certain property for which they have only limited information from multiple locations such as the initial location of a contamination plume A new function File gt Import gt Import Quantity defined by values at Scattered Points was implemented in version 2 03 and later that allows users to import such information from a text file of a specified format This function reads values defined in generally spaced points for both 2D and 3D problems and transfers them to the current FE mesh using a linear interpolation of these values a Only input variables defined using real numbers scalars can be imported this way Integer values specified in points e g material numbers can be imported differently using FE mesh Sections see Tutorial 2 12 at http www pc progress com en Default aspx h3d tutorials It is not also possible to import output variables results b The variable to be imported has to be displayed in the active View before the import process can be started c The values are transferred onto the current FE mesh which implies additional restrictions on quantities that can be imported this way If the entire domain is displayed in the View the values are transferred to all FE nodes of the domain If only a certain part of the domain FE mesh Se
174. ed using simpler objects For example a surface is defined by indices of its boundary curves and a boundary curve is defined by indices of its points The curve however does not own its points since these points can also be used to define other curves This is especially true for points at the beginning and end of a curve since these points are usually used also by neighboring curves A relation Parent Descendent exists among objects In case of a curve points are Parent objects and a Surface is its Descendent 4 8 3 References among Objects and Convention for Writing a List of Indices Objects are referenced using a list of indices A list of indices is written using a text format where individual indices are separated by a comma and dash between two indices indicates a range from to e g 1 5 10 35 30 8 11 After inserting new indices the list is always reformatted to minimize the length of the text Depending on circumstances the list of indices respects does not respect sequence in which objects were defined 4 9 Import Geometry from a Text File It is possible to Import definition of objects defining the Geometry of the transport domain from a text file using a command Import Geometry from a Text File It is possible to import export points curves polylines circles arcs and splines surfaces openings and thickness vectors a Definition of each object starts with the word OBJECT KEY_
175. ee Stee Baebes 42 3 3 Time dnjorma tion sermien enne a sated a ina a amalaahadetiedauas 46 Z4 Output Inf rmation srsrseesan enaa AE R A A a e Eea 48 3 3 PICA Criteria ati ete ai i a A E E E RE E REE REE E E E A ade 50 Gs Soil Hydra lie Model ceseeninen a aa aa aai a ai a Eiai 53 31 Water Flow Parameters iiiciiiniiiiiiniininnininnn naaa 55 3 8 Neural Network Predictions oessssssseeseesessesseereeressereresresstssresressessrssressereresreeseeseee 59 3 9 Anisotropy in the Hydraulic Conductivity ccceccccecvsics csiasnaieasanaisdedassacecssasdeascasancceasesises 60 3 10 Solute Transpo soni asp cattoh tes alah eoe a a a a a 61 3 11 Solute Transport Parameters assssicticassice ted aude Rgasseedyueabintinadsasaghed ademas guano Beals alaean 66 3 12 Solute Reaction Parameters iccie tuscan eetacu didn ei adel ese dee nee 67 3 13 Temperature Dependence of Solute Transport PAVameters s 71 3 14 Water Content Dependence of Solute Transport Parameters cccsccccceesceeeeeteeeeteenes 12 3 15 Solution Compositions for the UNSATCHEM Module 0 ccccccccccceesteceeeenseceeessteeeeeeneaes 73 3 16 Chemical Parameters for the UNSATCHEM Module 1 ccccccccccccceessscetesnseceenssseeseeseuaes 74 3 17 Heat Transport Parameters ormieresi a a e 75 3 18 Root Water Uptake Model acre oii ohana sent de Siusclevsig Wes soda tuck Sisvora be ven eedsie sede Bunitahedisa te 77 3 19 Root Water Uptake Parameters cia Ssait stented ceecvigaa toes berated
176. eeeeecseeeeceeeeeenneeeeneeeees 180 The Default Domain Properties dialog window esceeeeeeeessseceeceeeeeeeeesaeeeaeens 182 The Water Flow Initial Condition dialog Window c cceeescecssneeeeeeeeeeeeeeeeteeeees 183 The Temperature distribution dialog WindOW cccceeeeceeeeeeceeeeeceeeeeesteeeeeeeeees 184 The Time Variable Head Flux 1 BCs tab of the Boundary Condition Options dialog RTM OW oegi eise at Seon nosed ahs ats Set tees tekoa deh SS Eea adit alah es sian ca Mea eall 186 The Triggered Irrigation tab of the Boundary Condition Options dialog window 190 The Stochastic Distribution of Scaling Factors dialog wWindow cccssceeeseees 191 The Stochastic Parameters dialog Window sessssseessesssseesseessesesseeesseesseesseessees 192 An example of the transport domain defined using three components S1 S2 and SO eee BGs ae Si E ee hl ae BN a et he 193 The upper part of the Edit Bar which displays defined materials and commands for various actions with materials 254 3 5cci4e ss ccsucec eal cd sect aecaunatel deen ca cens tastes cases tccinaics 195 The Set Materials dialog Window cscccesscecesceceeccecssceceeseceeseceeseeeesaeeeeaeeees 196 The transport domain with materials specified on geometric objects 0c 196 The Sort Property Objects dialog windoW eeceesessseceseceseeeeeeeeaeecnaeeeseeeeeeeeneees 197 The Edit Materials dialog windOW a 2c ic ieien as banding e eee
177. eeeeeeeeeseeenseeneeneees 256 A comparison of the HyPar module to standard computational modules 297 18 Abstract Sejna M J im nek and M Th van Genuchten The HYDRUS Software Package for Simulating Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated Porous Media User Manual Version 2 04 PC Progress Prague Czech Republic 305 pp 2014 This report documents version 2 0 of the Graphical User Interface of HYDRUS a software package for simulating water heat and solute movement in two and three dimensional variably saturated porous media The software package consists of the computational computer program and the interactive graphics based user interface The HYDRUS program numerically solves the Richards equation for variably saturated water flow and advection dispersion equations for both heat and solute transport The flow equation incorporates a sink term to account for water uptake by plant roots The heat transport equation considers transport due to conduction and convection with flowing water The solute transport equations consider advective dispersive transport in the liquid phase as well as diffusion in the gaseous phase The transport equations also include provisions for nonlinear nonequilibrium reactions between the solid and liquid phases linear equilibrium reactions between the liquid and gaseous phases zero order production and two first order degrada
178. eement h Authors a 2D 3D Version 2 x Dr M Sejna and Prof J Simunek Dr Rien Yan Genuchten Copyright 2006 2011 PC Progress s 1 0 Anglicka 28 Prague Czech Republic All Rights Reserved Support hydrus pe progress cz admin pc progress cz WEB site www hydrus3D com WWW pc progress com Figure 187 The About HYDRUS dialog window the Program tab top and the Authors tab bottom 300 References Bradford S A S R Yates M Bettehar and J im nek Physical factors affecting the transport and fate of colloids in saturated porous media Water Resour Res 38 12 1327 doi 10 1029 2002WR001340 63 1 63 12 2002 Brooks R H and A T Corey Properties of porous media affecting fluid flow J Irrig Drainage Div ASCE Proc 72 IR2 61 88 1966 Carsel R F and Parrish R S Developing joint probability distributions of soil water retention characteristics Water Resour Res 24 755 769 1988 Chung S O and R Horton Soil heat and water flow with a partial surface mulch Water Resour Res 23 12 2175 2186 1987 Durner W Hydraulic conductivity estimation for soils with heterogeneous pore structure Water Resour Res 32 9 211 223 1994 Feddes R A P J Kowalik and H Zaradny Simulation of Field Water Use and Crop Yield John Wiley amp Sons New York NY 1978 Hopmans J W J im nek N Romano and W Durner Inverse Modeling of Transient Wat
179. een Surfaces selected surfaces and their copies Rotation Options When rotating create between selected nodes and their copies Straight Lines Arc Lines Connect Lines if they contact Lines between Points Surfaces between Lines Solids between Surfaces Figure 59 The Manipulation Options dialog window The bitmaps indicate connecting lines between points surfaces between lines and solids between surfaces 116 4 1 7 Additional Operations Additional operations that can be used to manipulate boundary objects are Intersect Lines Insert Points on Line and Split Line All three commands again can be accessed either from the Tools menu or from the Transform Object part of the Domain Geometry version of the Tool Bar on the right side of the View Window The first command Intersect Lines finds the Intersect of two lines whereas the second command Inserts Points on a Line This can be done either graphically or numerically by specifying the number of nodes to be inserted on the line or distance of the point from the beginning of the line Fig 60 The third Split Line command can be used to split a line into two or more parts Insert Points on Curve Line No Number of Paints Number of New Points if Type of Points O Split Curve at Inserted Points Insert Parametric Points O Insert Intermediate Points Numbering starts with No Point Automatic Line
180. eff for P 89 Previous Figure 38 The Constructed Wetland Model CW2D Parameter I dialog window Table 13 Kinetic parameters in the CW2D biokinetic model Langergraber and im nek 2005 Description unit Value Hydrolysis for 20 C 10 C K hydrolysis rate constant 1 d 3 2 Ky saturation inhibition coefficient for hydrolysis g CODcs g CODgm 0 1 0 22 Heterotrophic bacteria aerobic growth Ly maximum aerobic growth rate on CR 1 d 6 3 by rate constant for lysis 1 d 0 4 0 2 Kyret 02 saturation inhibition coefficient for So mg O L 0 2 Kret cr saturation inhibition coefficient for substrate mg CODcp L 2 Khet NH4N saturation inhibition coefficient for NH4 nutrient mg N L 0 05 Khet p saturation inhibition coefficient for P mg N L 0 01 Heterotrophic bacteria denitrification HDN maximum aerobic growth rate on CR 1 d 4 8 2 4 Kret o2 saturation inhibition coefficient for So mg O L 0 2 Kret No3N saturation inhibition coefficient for NO3 mg N L 0 5 Kret No2N saturation inhibition coefficient for NO2 mg N L 0 5 Kbet crR saturation inhibition coefficient for substrate mg CODcpr L 4 Knet NHAN saturation inhibition coefficient for NH4 nutrient mg N L 0 05 Krete saturation inhibition coefficient for P mg N L 0 01 Ammonia oxidising bacteria Nitrosomonas spp LANs maximum aerobic grow
181. en a very smooth finite element mesh is required the smoothing factor should be decreased to about 1 1 when a coarser mesh is possible the smoothing factor can be increased The code saves mesh data by default in a binary format the file MESHTRIA 000 However users have the option to also save mesh data into a file MESHTRIA TXT in ASCII format the Program Option dialog window Fig 162 and then use possibly the data later for other calculations 176 When users do not have authorization to use the MeshGen2D module they can employ the internal mesh generator for relatively simple rectangular or hexahedral transport domains A TAKA AU Il iN Mt 7 A oth KEAN ane UNORA AAVA NA TIRANA oe YY Ny W ON i Wank i AN Wy l WA uh Y i NAA SAKA AVIAN A an TASHA ENN UIE Sue in di a NWN NX i Example of mesh stretching using a stretching factor of 3 in the x direction 177 Figure 112 5 6 Finite Element Mesh Statistics FE Mesh Information Number of Nodes 898 1D Elements 176 2D Elements 1618 3D Elements 0 FE Mesh Information Number of Program has created a default set of FE Mesh sections You Nodes can create your own sections to 1D Elements simplify graphical input of data 2D Elements 3D Elements Previous Figure 113 The FE Mesh Inform
182. eneral Picture and Legend tabs of the Print Options dialog window 292 9 4 Print Preview and Copy to the Clipboard Commands Result of commands Print Preview and Copy to the Clipboard is shown in Figure 184 The Print Preview command displays the content of the View Window on the screen as it would appear in printed formed while the Copy to the Clipboard command copies the same content to a metafile enhanced metafile EMF http en wikipedia org wiki Windows_Metafile in the Clipboard for subsequent pasting into other software packages such as Word PowerPoint etc Additional content of the metafile in addition to the content in the View Window such as the text of the legend is defined using the Print Options window The metafile contains the bitmap the resolution of this bitmap max 6000x6000 pixels can be specified in the Print Option window with the graphics displayed in the View Window and additional vector objects e g texts and or numbering 0 000 0 004 0 008 0 012 0 016 0 020 0 024 0 028 0 033 0 037 0 041 0 045 Concentration c mmol cm 3 Min 0 000 Max 0 045 Project 3DFumig6 3D Finite res Heat Tr Tarp Tarp removal part untarped Results Concentration Time 6 1 50 days Figure 184 Result of commands Print Preview or Copy to the Clipboard 293 9 5 Coordinate systems The Coordinate System to be used for the transport domain definition can be selected from the List of Available Coordinate
183. entrations for all cations Ca Mg Nat and K and Precipitated Concentrations for all solids that UNSATCHEM can consider calcite dolomite gypsum nesquohonite hydromagnesite and sepiolite Solution Concentrations need to be specified in meq L L liter and Adsorbed Concentrations and Precipitated Concentrations in meq kg meq mmol Solute Compositions Solution Concentrations meq L Sol Ca Ma Na K Alk 504 CI Tracer 1 2 63 1 05 2 55 0 06 2 33 2 03 1 94 1 2 12 2 9 66 37 5 0 27 6 5 22 1 31 1 0 Cancel Adsorption Concentrations meqg kg Ca 50 Precipitated Concentrations meq kg Prec Calcite Gypsum Dolomite HydroMg Nesqoh Sepiolite 1 500 200 0 0 0 0 Previous Figure 30 The Solution Compositions dialog window for the UNSATCHEM module 73 3 16 Chemical Parameters for the UNSATCHEM module The following chemical parameters and selections for the UNSATCHEM module are specified in the Chemical Parameters dialog window Fig 31 Whether the kinetic or equilibrium model for the precipitation and dissolution of calcite and dissolution of dolomite is to be used the Kinetic Precipitation Dissolution check box Whether the silica content in the solution is to be calculated based on the solution pH or whether the effect of pH is to be neglected the Silica in Solution pH Dependency check box The Critical Ionic Strength i e the ionic strength below which the extended Debye
184. epage Face Head Drainage Boundary Head Free and Deep Drainage Boundary Head Variable Boundary Head 2 Variable Boundary Head 3 Variable Boundary Head 4 All Boundaries Water Boundary Fluxes Time Potential Atmospheric Flux Potential Root Water Uptake Rate Actual Atmospheric Flux Actual Root Water Uptake Rate Variable Boundary Flux 1 Constant Boundary Flux Seepage Face Flux Drainage Boundary Flux Free and Deep Drainage Boundary Flux Variable Boundary Flux 2 Variable Boundary Flux 3 Variable Boundary Flux 4 All Atmospheric Fluxes All non Atmospheric Fluxes Surface Runoff Infiltration Evaporation Cumulative Water Boundary Fluxes Time Potential Atmospheric Flux Potential Root Water Uptake Rate Actual Atmospheric Flux Actual Root Water Uptake Rate Variable Boundary Flux 1 Constant Boundary Flux Seepage Face Flux Drainage Boundary Flux Free and Deep Drainage Boundary Flux Variable Boundary Flux 2 Variable Boundary Flux 3 Variable Boundary Flux 4 All Boundaries Fluxes Surface Runoff Infiltration Evaporation 224 Solute Fluxes Time Cumulative Zero Order Reaction Cumulative First Order Reaction Cumulative Root Solute Uptake Cumulative Non Equil Mass Transfer Cumulative Constant Boundary Solute Flux Cumulative Seepage Face Solute Flux Cumulative Variable Boundary 1 Solute Flux Cumulative Atmospheric Solute Flux Cumulative Drain Boundary Solute Flux Cum Free Deep Drainage Bound Solute Flux Cumulative Variable Boundary 2 Solute F
185. er Flow In Methods of Soil Analysis Part 1 Physical Methods Chapter 3 6 2 Eds J H Dane and G C Topp Third edition SSSA Madison WI 963 1008 2002 Jacques D and J im nek User Manual of the Multicomponent Variably Saturated Flow and Transport Model HP1 Description Verification and Examples Version 1 0 SCKeCEN BLG 998 Waste and Disposal SCK CEN Mol Belgium 79 pp 2005 Jacques D J im nek D Mallants and M Th van Genuchten Operator splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles J Contam Hydrology 88 197 218 2006 Jacques D J im nek D Mallants and M Th van Genuchten Modeling coupled hydrological and chemical processes Long term uranium transport following mineral phosphorus fertilization Vadose Zone Journal 7 2 698 711 2008 Jacques D and J im nek Notes on HP1 a software package for simulating variably saturated water flow heat transport solute transport and biogeochemistry in porous media HP1 Version 2 2 SCK CEN BLG 1068 Waste and Disposal SCK eCEN Mol Belgium 113 pp 2010 Kool J B and J C Parker Development and evaluation of closed form expressions for hysteretic soil hydraulic properties Water Resour Res 23 1 105 114 1987 301 Kosugi K Lognormal distribution model for unsaturated soil hydraulic properties Water Resour Res 32 9 2697 270
186. er is modeled using the distribution of pore pressure which is imported automatically from the HYDRUS results for specified times Each time step of water distribution can be analyzed separately The slip surface is considered as circular and is evaluated using the Bishop Fellenius Petterson Janbu Morgenstern Price or the Spencer method Hydrus installation program contains several examples for the calculation of slope stability which are located in the Slope Stability Project Group see Project Manager r Slope stability HYDRUS 2xx Soy File Edit Input Pictures Settings Help ors B amp Q QQ AGA A Breusizen Detailed results Circular slip surface Analysis Center Method i Slope stability verification Bishop Modfy wesc Sum of active forces Fa 11 01 N m 4381 m Analyss type Optimization Sum of passive forces Fp 26 77 KN m z 1 636 m Angles 7 Assume anchors as infinite Siding moment Ma 16 72 kNm m a Resisting moment Mp 40 66 KNm m as 16 04 1 Factor of safety 2 43 gt 1 50 R 1 519 m 81 41 4 jo a Slope stabilty ACCEPTABLE Figure 42 The main window of the Slope Stability Module 97 The main features of the Slope Stability module include e Presence of water modeled by pore pressure imported from HYDRUS results e Arbitrary number of surcharges strip trapezoidal concentrated loading e Arbitrary number of anchors e Simple mo
187. erature Parameters for constructed wetlands are entered in the Constructed Wetland Model Parameters I and II dialog windows for the CW2D Fig 38 and 40 respectively and CWM1 Fig 39 and 41 respectively modules Table 11 Comparison of CW2D and CWM1 components CW2D CWM1 Langergraber and Simunek 2005 Langergraber et al 2009 Components Soluble components S 1 SO Dissolved oxygen O2 1 SO Dissolved oxygen O2 2 CR Readily biodegradable soluble 2 SF Fermentable readily biodegradable soluble COD COD 3 CS Slowly biodegradable soluble 3 SA Fermentation products as acetate COD 4 SI Inert soluble COD 4 Ch Inert soluble COD 5 SNH Ammonium and ammonia nitrogen 5 XH Heterotrophic bacteria 6 SNO Nitrate and nitrite nitrogen 6 XANs Autotrophic ammonia oxidizing 7 SSO4 Sulphate sulphur bacteria Nitrosomonas spp 8 SH2S Dihydrogensulphide sulphur 7 XANb Autotrophic nitrite oxidizing Particulate components X bacteria Nitrobacter spp 9 XS Slowly biodegradable particulate COD 8 NHA4N Ammonium and ammonia 10 XI Inert particulate COD nitrogen 11 XH Heterotrophic bacteria 9 NO2N Nitrite nitrogen 12 XA Autotrophic nitrifying bacteria 10 NO3N Nitrate nitrogen 13 XFB Fermenting bacteria 11 N2 Elemental nitrogen 14 XAMB Acetotrophic methanogenic bacteria 12 PO4P Phosphate phosphorus 15 XASRB Acetotrophic sulphate reducing bacteria Organic nitrogen and org
188. ers for each particular material can be selected from the catalog using the Select from Catalogue button or can be defined individually Also a Safety Factor for which slope stability is considered satisfactory is given here The value of the Safety Factor must be in the interval of 1 5 The global parameters for the Slope Stability module are set in the Default Parameters for Slope Stability Module dialog window Fig 44 These parameters are not specific for one particular project but are the default parameters that are used in new projects dealing with slope 98 stability In addition to the default values for the Safety Factor and the Influence of Water it is also possible to edit here the Catalog of Soil Characteristics The initial soil catalog is based on the Hydrus soil catalog using the classification based on the USDA textural triangle Users can change the names of materials and their parameters and can also extend or reduce this catalog using New or Delete commands They can also reorganize soil textures in the catalog using the commands Up and Down Soil Characteristics as defined in this catalog can then be automatically assigned in new projects to materials taken from HYDRUS on the basis of matching their material names see the check box Assign soil characteristics gE Default Parameters for Slope Stability Module es Default type of water influence Analysis Water influence Pore Pressure X Default
189. es 143 ATi Dimensions oheari lo Ea EEE OE R A A dales delaee 145 AT D5 SG DELS sat cds ohek cate odad sia sb eden atid sade oeck eked odnds bs Sadanowet ats sbheaeae tends PEA 146 AT Os Bitmaps Textures seinrotenheorctsandeseried usin a ona sinnd unset a a a ides 147 ATA CFOS SECU ONS ie Pee CS BES el aN Ot I i les ea 148 ATT ACS NT ANOS 2a ie 8 ae i de hati ue i dR i satiate E A asa een dae 148 A IOs Backer und Layers irinenn eei Deca aa E i aaa 150 AS Other Notes on Objects sicnnipinrere inian ari sda EE TE EA E a EA 153 4 8 1 APOC Number misii tiiit a i a a Ma edilint 153 4 8 2 Relations among Objects o eoeessooesssssessssseeessseseesseseesssserssssereessereesssseessssreses 153 4 8 3 References among Objects and Convention for Writing a List of Indices 153 4 9 Import Geometry from a Text File icisiciGi ch cat tras Sethe ta wsaas het ged bet beasts telas iaascatale eases 153 4 10 Import Geometry from a DXF File sss si costoadcrtededs asadaniteaiidesionis ae Geena 156 4 11 Import Geometry from a TIN File onooeoneneennnneennsseseessssesssssssssssereesseseesssseesssseee 156 Finite Element Mesh ceisissnuctyssstrcsaconeacsesovbouastenwteonuaieaubouneauddesa ina o E siaSi i Sa 157 5 1 Finite Element Mesh Generator ccvi kind aie and han Galea 157 5 2 Structured Finite Element Mesh Generator scccscciccegsshecvented test passeesiaseteieisadieada eats 157 5 3 Unstructured Finite Element Mesh Parameters oscense 160
190. es with calculated negative pressure heads are not associated with a Dirichlet boundary condition but rather with a zero flux A fluctuating water level in a stream or furrow is an example of this type of boundary condition While positive pressure head values are below the water table negative values occur above the water table d This is similar to c except that an atmospheric boundary condition is assigned to nodes with negative calculated pressure heads 185 e This is similar to c except that a seepage face boundary condition is assigned to nodes with negative calculated pressure heads Note that a Seepage Face boundary condition needs to be assigned to all boundary nodes for which this option is to be used f When this type of system dependent boundary condition is selected then HYDRUS treats the time variable flux boundary conditions similarly as atmospheric fluxes This means that pressure heads have two limiting values with the maximum pressure head equal to hCritS and the minimum pressure head equal to hCritA g While in version 2 x of the code the flux across the nonactive part of the seepage face was always equal to zero the new version can apply atmospheric boundary conditions on a nonactive seepage face h When heat transport is simulated simultaneously with water flow and atmospheric boundary conditions then snow accumulation on top of the soil surface can be simulated The code then assumes that when the air temper
191. es x fiean Soil Hydraulic Properties ey aona ons Advanced FE Mesh Generation gt Run Time Information Cross Sections i Meh line p F4 Calculate Current Project anday bais p F3 Calculate All Open Projects Select Projects to Calculate Mass Balance Information Chemical Mass Balance Information Convert Output to ASCI Inverse Solution Results Fluxes across mesh lines Time Layer gt Charts gt Flowing Particles GR Delete Results Figure 159 The HYDRUS Menus II Insert Calculations and Results Tools Options Window Hel Show Grid Snap to Grid Window Sas Developers Windo 1 New Window E Arrange Symbols Rendering Mode r Graph Type gt Display Options gt E Main and Secondary Define Work Plane Im o Sa f5 Coordinate System rogram Options E Tile Horizontally E Tile vertically Color Scale gt T Cascade y Iranslate T3 Rotate At Mirror R Context Sensitive Help Shift F1 operties Material Distribution 40 Stretch B Help Contents and Index Fl a Skew Hydrus User Manual W Intersect Lines amp Hydrus Technical Manual Split Lines Hydrus Online Insert Points on Line gt A Troubleshooting ke Check Geometry Hydrus License and Activation E Repair Geometry w About Hydrus il Generate Domain Surfaces h Create Video File Figure 160 The HYD
192. esh the FE Mesh refinement dialog window Fig 106 1 A global Targeted FE Size Fig 98 is the main variable of the FE Mesh process Although a default Targeted FE Size is specified by the program this value should be adjusted by users in most applications The default value is used to generate at least a reasonable initial mesh even for inexperienced users 2 The finite element mesh can be adjusted locally in the domain by using FE Mesh Stretching Fig 99 and 112 or FE Mesh Refinement Figs 48 35 and 106 FE Mesh Refinement can be implemented for various geometric objects including Points Lines or Surfaces Fig 106 When several FE Mesh Refinements overlap in one location such as when the FE Mesh Refinement is defined for both a point and a line then the FE Mesh Refinement specified for the lower level objects 1 e a point rather than a line is used The boundary nodal distribution determines in a very substantial manner the ultimate quality and size of the unstructured finite element mesh Optimally distributing nodes along the boundaries of relatively complicated domains e g a very irregular anisotropic domain can be a very difficult problem and may require some experience Table 18 Definition of terms related to the boundary discretization Boundary Nodes Boundary nodes are points marked by green squares which discretize boundary curves These nodes are generated along every boundary curve and are ordered in a co
193. ext files with values defined at specified locations 6 6 1 Import Initial Condition from HYDRUS Projects The initial condition can be imported from the results of previous calculations from an existing HYDRUS project using the Import command Edit gt Initial Condition gt Import or Insert gt Initial Condition gt Import After clicking on any of these two commands an Open dialog window appears with Files of type preselected for HYDRUS applications i e h3d2 One then needs to browse for the HYDRUS project from which the initial condition is to be imported After selecting a particular project the Import Initial Conditions dialog window appears Fig 132 This window provides information from which project the initial conditions will be imported Import data from Hydrus project and offers quantities that can be imported as initial conditions Select quantities to import Users must then also decide in the Select Time Layer part of the dialog if values for The Last Final Time Layer or for any intermediate time layer using Time Layer No from the lower list box are to be imported Time Layers correspond with Print Times Fig 16 for which the output in the existing project was calculated Import data from Hydrus 3D project C ussl HYDRUS3D 2 0 Examples 2D_Tests Unsatchem h3d2 Select quantities to import C Pressure Head O Solution Composition C Exchanged Species O Solid Species C CO2 Concentration Sel
194. factor of safety 1 5 Catalogue of Soil Characteristics Name Sand Loamy Sand Sandy Loam Unit weight 19 kN m 3 Loam Silt Angle of internal friction 35 9 Silty Loam Sandy Clay Loam Cohesion of soil 0 kPa Clay Loam Silty Clay Loam Saturated unit weight 18 kn m 3 Sandy Clay Silty Clay Clay Options 7 Assign soil characteristics to HYDRUS materials automatically according to names in the catalogue Gea Figure 44 The Default Parameters for Slope Stability Module dialog window The command Printout Report and Results Fig 45 produces a standard Report that summarizes results obtained by the Slope Stability module Users can then edit and modify this report 99 Document Edit View Page Be OB steer bi eo so OQQn OR Water E Document matches its settings ians i AM 2104297 cm Figure 45 An example of the Print and Export document generated by the Slope Stability module 100 4 Geometry of the Transport Domain The transport domain may be defined using relatively simple two dimensional rectangular Fig 10 or three dimensional hexahedral Fig 11 objects In that case the dimensions and other parameters of the transport domain are specified numerically using either the Rectangular Fig 10 or Hexahedral Domain Definition Fig 11 dialog windows In both of these cases the transport domain is discretized into a structured finite eleme
195. fault All Default Figure 103 The FE Mesh Parameters dialog window Tab MG Options 164 The following parameters are specified in the FE Mesh Quality group Maximum Number of Overall Remeshing Iterations This number defines the maximum number of iterations during finite element mesh remeshing In most cases the resulting mesh is obtained within fewer iterations than the default value of 10 In some cases the repeated adding and removing of nodes can cause an infinite loop In that case or when the mesh generation process converges very slowly the code terminates after reaching the maximum number of iterations as defined by this value Number of Intensive Smoothing Steps Intensive smoothing repeats the operations of Delaunay remeshing and smoothing until there are no more changes during the Delaunay remeshing step This parameter specifies the number of intensive smoothing cycles in the beginning of the mesh generation process which can significantly influence the mesh smoothness However too many smoothing cycles can significantly slow down the mesh generation process The recommended value is between 1 less smoothing and 3 more smoothing Number of Internal Iterations for Intensive Smoothing This number defines the maximum number of iterations during one intensive smoothing step This number guaranties that intensive smoothing will stop after a specified number of iterations even when the prescribed criterio
196. finite element mesh with three FE Mesh Stretchings assigned to areas below the domain surface These Stretchings were defined either using the Menu Command Insert gt FE Mesh gt Mesh Stretching Dialog or the Edit Bar Command Insert Mesh Stretching All Local FE Mesh Stretchings can be deleted using the Edit Bar Command Delete All Stretching r z HYDRUS 2 04 MestStretching o B amp File Edit View Insert Calculation Results Tools Options Modules Window Help Deaae amp el 2 2 BOR le e ELp Project Navigator Data AX r Edit Bar FE Mesh ajx _ E MestStretching FE Mesh BCE i Project Data Edit FE Mesh ka MestStretching FE Mesh Parameters El Insert Mesh Refinement Delete All Refinements 5 Project Information 6 0 Flow and Transport Parameters B FE Mesh g FE Mesh Parameters il FE Mesh Statistics 6 FE Mesh Refinements Hi Insert Mesh Stretching Delete All Stretchings Delete FE Mesh fill Fe Mesh Statistics E Remove Selected Elements FE Mesh Advanced Options FE Mesh Sections hd 4 Generate Sections 0 Initial Conditions 9 Boundary Conditions 5 Auxiliary Objects Mesh Stretching 5 2 Results Graphical Display T Results Other Information 6 Add on Modules No Z Geometry i FE Mesh F Domain Properties QJ Initial Conditions A 1 W MestStretching FE Mesh Stretc
197. g objects graphically they can also be selected using their Indices or by means of Sections Double clicking on selected objects or simultaneous holding the Alt Enter buttons recalls dialogs for editing properties of particular objects Most dialogs support multiple editing i e if edit boxes with different values remain empty the original values will not change This feature allows for example Z coordinates of multiple selected points to be changed while leaving the X and Y coordinates unchanged When different objects are selected simultaneously e g points and curves double clicking causes a dialog window to appear from which objects can be selected for editing 8 1 6 Pop up Menus Context sensitive menus with useful commands for a particular object can be called from the View window when clicking the right mouse button While the commands are accessible also from the main menu right clicking the mouse is much faster Menus for multiple selections that may contain different types of objects operate in the same way When the right mouse button is clicked a default menu will appear when no object is close to the cursor When one clicks with the right mouse button on the view window the pop up menu of Figure 150 will appear This menu will allow users to a select different views View i e Isometric in X direction in Y direction in Z direction Reverse X direction Reverse Y direction Reverse Z direction or a perspective view
198. gas phases are to be multiplied by a tortuosity factor according to the formulation of either Millington and Quirk 1961 or Moldrup et al 1997 2000 Check this box if the solute transport and reaction parameters are assumed to be temperature dependent Water Content Dependence Check this box if the solute reaction parameters are assumed to be Attachment Detachment Filtration Theory Fumigant Module d Iteration Criteria water content dependent Walker 1974 Check this box if the solute is assumed to be subject to attachment detachment to from the solid phase This process is often used in simulations of the transport of viruses colloids or bacteria Check this box if the attachment coefficient is to be calculated from filtration theory Additional options related to fumigant transport e g tarp removal temperature dependent tarp properties additional injection of fumigants can be used with this module The advection dispersion solute transport equation becomes nonlinear when nonlinear adsorption is considered Similarly as for the Richards equation an iterative process must then be used to obtain 63 solutions of the global matrix equation at each new time step During each iteration a system of linearized algebraic equations is derived and solved using either Gaussian elimination or the conjugate gradient method After inversion the coefficients are re evaluated using the initial solution and the new equatio
199. gs into the USB HASP also called a dongle is a software copy protection device that port of the computer Upon startup the application looks for the key and will run only if the key contains the appropriate code Hardware keys are very effective copy protection devices because they cannot be duplicated by the user 1 The HASP for HYDRUS is sent by PC Progress by mail and its use is very simple You just connect it to the computer via the USB port and HYDRUS is then immediately authorized The HYDRUS software then does not require any further activation 2 Although the drivers for the HASP should normally be installed automatically when it is connected to the USB Windows operating system and Plug and play should take care of that we still recommend to install the drivers at the same time when the Hydrus software is installed during the HYDRUS installation In one of the dialog windows that appears during installation there is a special check box Install the hardware key driver Fig 182 which needs to be checked see the picture below v HYDRUS 2 xx Setup aos Choose Destination Location Select folders where setup will install files Setup will install HYDRUS 2 xx in the following folders To install to these folders click Next To install to different folders click Browse and select other folders Destination Folder for HYDRUS Program Files C Program Files x86 PC Progress HYDRUS
200. h Refinement at a given point can be defined in the FE Mesh Tab 105 Edit Point General FE Mesh Point No Edit Point General FE Mesh Point Type Point No El Coordinates Coordinate system No Coordinate X Coordinate Z Reference Point 5 Cartesian v gt E 40 00 cm 100 00 cm Comment 9 FE mesh Refinement FE Mesh Refinement oS at Point S 2 cm P X Y Z Global FE Size cm Figure 48 The Edit Point dialog window Although Cartesian Coordinates are usually used it is possible to use also other coordinate systems Coordinate Systems in 3D Projects Coordinate Systems in 2D Projects Cartesian X cylindrical Y cylindrical Z cylindrical Spherical e Cartesian e Polar Reference Point Point coordinates are usually related to the defined origin of the coordinate system They can nevertheless be also related to another existing point whose index is specified in the box Reference Point No Locations of all related points are automatically adjusted when the location of the reference point is changed The dependence of points on the Reference Point is however canceled during more complex operations such as Copy Rotate or Drag and Drop The coordinates of such points are then recalculated using absolute Cartesian coordinate system Point Type Current version of HYDRUS recognizes two types of points e Standa
201. h displays boundary codes for all boundary nodes in the View window the command Codes by Pointer which displays boundary codes only for the node closest to the cursor Numbering Options which changes the Navigator Bar to the View Tab and Numbering option Boundary Conditions Options which allows additional system dependent boundary conditions for water flow see the Technical manual and Fig 118 and Help which is similar as discussed above The Edit Bar for Initial Conditions and Pressure Head h displays a color spectrum that is used to draw the initial conditions and lists the minimum and maximum values that are used in the entire domain This Edit Bar also includes a Edit Commands Set Values and Values by Pointer When nodes for which the initial conditions are to be specified are already selected then the Set Values command calls the Water Flow Initial Condition dialog window Fig 116 When no nodes are selected then clicking on the Set Values command causes a square cursor to appear which may be used to select particular nodes after which the Water Flow Initial Condition dialog window appears The command Values by Pointer again displays the initial pressure head of the node closest to the cursor b Two Chart Tools commands The Cross Section Chart and the Boundary Line Chart The Cross Section Chart command allows users to display a particular variable between any two points of the transport domain The Boundary Line Chart co
202. has two tabs one related to Graphics Fig 161 and one to Program itself Fig 162 Contains basic input parameters of the Slope Stability module Opens the add on Slope Stability module which carries out required slope stability calculations Produces a standard Report that summarizes results obtained by the Slope Stability module Sets the global parameters for the Slope Stability module Open a new View window 267 Arrange Symbols Main and Secondary Tile Horizontally Tile Vertically Cascade Close All Help Context Sensitive Help Help Contents and Index Hydrus User Manual Hydrus Technical Manual Hydrus Online Troubleshooting Hydrus License and Activation About Hydrus Arranges minimized windows as icons at the bottom of the View window Displays open View windows as main and secondary windows Tiles open View windows horizontally Tiles open View windows vertically Cascades open View windows Closes all open View windows Help for various objects of GUI Displays help information Displays a PDF version of the HYDRUS User Manual Displays a PDF version of the HYDRUS Technical Manual Launches Internet Explorer Browser and opens the HYDRUS web page Launches Internet Explorer Browser and opens the Troubleshooting page of the HYDRUS web page Displays the Hydrus license and activation information the HYDRUS License and Activation dialog window Fig 165 Displays the version and authors of the H
203. have to ask for Number of remaining attempts 3 4 Authorization process succeded Activation complete IMPORTANT NOTICE Before any hardware changes or reinstallation of Windows or if you want to move your license to another computer you should deactivate HYDRUS on this computer See Help how to deactivate HYDRUS properly Figure 176 Window confirming successful HYDRUS authorization 285 Note that the Request Code and a Computer ID are displayed in the upper part of the Step 3 Tab Remember that your Request Code and Computer ID are hardware dependent After upgrading your hardware e g BIOS hard drives you will very likely have to request new Activation Code You are eligible to obtain those codes for free although subject to some limitations ask for details When the activation fails three times likely due to incorrectly entered information the request keys will change and windows shown in Figure 177 will be displayed providing instructions on how to proceed further User will be requested to send a report to the HYDRUS support so that the cause of the problem can be analyzed HYDRUS 2 xx xi The activation Failed request codes have been changed and H YDRUS has created an error report IF you are sure that you entered the correct activation code please save the error report and send the file to the HYDRUS customer support support pc progress cz for analysis IMPORTANT NOTICE You MUST send us the err
204. he Edit Bar during the process of graphically defining a Comment Selection of the Comment Position Comment Text Font and Color left and Offset right Bitmap No Bitmap Preview 1 D C Position F Visible C Pick D Pick Properties Size 430300 pixels Size 1292 kB Comment Sl tinct Gi Figure 89 The Edit Bitmap dialog window 147 4 7 4 Cross Sections In the HYDRUS 2D software package one could click at any two points of the transport domain to display results of selected variables between those two points i e along a specified cross section The exact location of these cross sections was not saved and they had to be redefined whenever a new graph was required In HYDRUS one can define the cross sections and save their locations so that graphs along the cross sections can be recalled at any time by simply clicking at them Graphs along pre defined cross sections can be display for both the initial conditions and the output results For example if a plot of the pressure head along a predefined cross section at a particular time is needed one needs to display the pressure head outputs find a particular time and then click on the predefined cross section The graph is displayed instantaneously Specifying the cross section within a two dimensional domain is straightforward For three dimensional domains one can use the Cross Section dialog wind
205. he standard module is simulated Concentration of kinetically sorbed solute s MM T displayed when solute transport in the standard module is simulated and when the two site sorption model is considered Concentration in the immobile water Cim MeLw 1 displayed when solute transport in the standard module is simulated and mobile immobile water or dual porosity models are considered Temperature T C displayed when heat transport is simulated Major ions Ca Mg Na K HCO3 SO4 Cl tracer sorbed Ca sorbed Mg sorbed Na sorbed K calcite gypsum dolomite nesquohonite hydromagnesite sepiolite displayed when the Unsatchem module is used Various variables used in the two constructed wetlands modules CW2D and CWM1 see the Wetlands module manual for details Subscripts c s and w refer to contaminant soil and water 210 Table 22 Alternative variables that can be displayed in the View Window of the Results tab Pressure Head Total Pressure Head Water Content Mobile Water Content Immobile Water Content Total Water Content Velocity Total Value x component y component z component Concentration Options Liquid Equil Phase Conc Sorbed Equilibrium Conc Sorbed Total Concentration Gas Phase Concentration Total Concentration Standard display Total Pressure Head H h z L alternative display Standard display Water content in the mobile phase or default display Water content in the
206. heir data Displays recently opened projects Closes open projects and leaves the program This command informs users before exiting the application whether or not the input data of open projects were changed during the application run If changes did occur users are given an option to save data before exiting the application Reverses the last edit action Repeats the last edit action Copies a selected object Pastes a selected object Selects objects by means of a rhomboid Selects objects by means of a circle Selects objects by means of a polygon Add new object to existing selection Remove objects from existing selection Selects objects by means of a quadrilateral Displays properties of a selected object Finds an object Deletes a selected object Deletes all objects Specifies whether the flow and transport problem occurs in a two or three dimensional transport domain and whether the domain is simple or complex using the Domain Type and Units dialog window Fig 6 Specifies parameters dimensions and slopes for simple rectangular or hexahedral transport domains using the Rectangular Fig 10 or Hexahedral Domain Definition Fig 11 dialog windows Calls Edit 3D Layered Domain dialog window for editing the object Deletes 3D Layered Domain Edits selected points Edits selected lines using the Edit Curve dialog window Fig 50 Edits selected surfaces Edits selected openings Edits selected thickness ve
207. heir integration 7 Surfaces cannot partially cover each other see also 6 8 Points located outside of Surfaces are ignored when generating FE Mesh 4 2 4 Internal Objects Internal Objects are objects of the type Point Curve or Opening integrated in the Surface object Objects are by default integrated into the Surface automatically see Option Autodetect in Figure 1 It is possible to edit objects manually when the Autodetect option is turned off bmct Internal_Object_Dlg bmp Edit Surface General Integrated FE Mesh Surface No Objects Integrated in Surface Openings Lines Points Figure 68 The Integrated Tab of the Edit Surface dialog window 125 Main reasons for integrating objects into a Surface e Objects integrated in a Surface are respected when the FE Mesh is generated On the other hand objects that lie in a Surface but are not integrated in it are ignored during the FE Mesh generation e Internal Points allow users to precisely define location of Observation Points and other objects e Internal Curves allow users to precisely define geometric boundaries inside of the transport domain They can be used for many different purposes e g Mesh Lines Material Boundaries etc e Curves integrated in a Surface that is used as a Base Surface for the 3D Layered Solid are projected also at the Upper Surface and enable thus more precise modeli
208. hing Factor i Mesh stretched in __SetNo Stretching x direction with factor Stretching Direction Fs 3 0 X direction Y direction Pick i surfaces erly projects graphically V Parallel Le V Perpendicular 3 5 3 5 ZA Geometi FE Mesh Domain Properties Initial Conditions 0 Comment Data View amp Sections A y g esh J l J A ee For Help press F1 Figure 102 An example of the FE Mesh with three FE Mesh Stretchings assigned to areas below the domain surface 163 The MG Options Tab Parameters for the unstructured triangular finite element generator are given in the MG Options Meshgen Tab of the FE Mesh Parameters dialog window Fig 103 The parameters are divided into FE Mesh Limits which limits the number of elements and FE Mesh Quality which affects the smoothness of the FE mesh groups The following parameters are specified in the FE Mesh Limits group Maximum Number of Nodes on Boundary Curves This is the maximum total number of nodes on all boundary curves for two dimensional applications or on all boundary curves defining the bottom plane base surface for three dimensional applications Maximum Number of FE Mesh Nodes 2D Mesh This is the maximum total number of finite element nodes in two dimensional domains or on the bottom plane base surface of three dimensional domains Both parameters are mainly informative and may lead to a
209. hten Mualem model van Genuchten 1980 b the van Genuchten Mualem model with an air entry value of 2 cm c the modified van Genuchten type equations Vogel and Cislerova 1988 d the equations of Brooks and Corey 1964 e the lognormal distribution model of Kosugi 1996 and f a dual porosity model Durner 1994 Additionally user can select two dual porosity nonequilibrium flow models with mass transfer between the mobile and immobile zones assumed to be proportional to either g the water content or h the pressure head im nek et al 2003 For a detailed description of these models see the technical manual of HYDRUS Two other approaches a dual permeability model and look up tables are not available in the current version of HYDRUS 53 Hysteresis When the van Genuchten model is used either a a non hysteretic description No Hysteresis b a hysteretic description only in the retention curve Hysteresis in Retention Curve or c hysteretic descriptions in both the retention curve and the hydraulic conductivity curve Hysteresis in Retention Curve and Conductivity can be used When hysteresis in the soil hydraulic properties is assumed users must specify whether the initial condition is associated with the main wetting Initially Wetting Curve or main drying Initially Drying Curve retention curve The HYDRUS code incorporates hysteresis by using the empirical model introduced by Scott et al 1983 This model was also emp
210. icence No Time4imited License Yes Expiry Date 2011 07 01 Request Code 1 311157192 1 Send the authorization request all information above by e mail to your HYDRUS reseller or to support pc progress cz 2 You can close this dialog and HYDRUS After receiving the activation code run HYDRUS and insert the code on the next page of this dialog Step3 Figure 172 The Activation by E mail dialog window Tab Step 2 Information entered during Step 1 on Tab Step 1 is summarized in the Authorization Request Codes section of the Step 2 Tab This information can be copied to the clipboard using the Copy to Clipboard button and then sent by email to the HYDRUS support or other HYDRUS distributors The command Send Request Codes by E mail will attempt to start emailing program e g Microsoft Outlook directly and copy there automatically an email address of the HYDRUS support support pc progress cz and all required information see an example of such email displayed in Outlook in Fig 173 282 On the basis of this information the HYDRUS support or other resellers will promptly email HYDRUS Activation Requeste Mes i l o Is uea gee o zm Format Text Adobe PDF e f aia 6 hle 43 Send Paste Basic Names Mei PE Spellin X Text X 7 Send Clipbo Proofin Subject HYDRUS Activation Request HYDRUS version 2 01
211. ick on the Edit Bar on the particular boundary condition e g constant head They subsequently need to move the mouse to the selected position and click the left mouse button Implementation of the boundary condition terminates with a repeated click of the left mouse button 184 The boundary nodes will acquire the same color as the corresponding type of the boundary condition See the rules for specifying boundary conditions as described in Chapter 8 of the Technical Manual im nek et al 2010 Alternatively users can first select boundary nodes and then assign desired boundary conditions by clicking at a particular boundary condition at the Edit Bar Note that the Free Drainage and Deep Drainage boundary conditions cannot be specified simultaneously in one project Similarly when the Gradient Boundary Conditions is specified see description below the Time Variable Flux 4 Boundary Condition is disabled In addition to system dependent boundary conditions available in version 2 x of HYDRUS 2D several new options are available in HYDRUS These new options are specified in the Boundary Condition Options dialog window Fig 118 that is called using the menu command Edit gt Boundary Conditions gt Boundary Conditions Options or from the Edit Bar for Water Flow Boundary Conditions version using the BDRC Options command This dialog window has three tabs a Time Variable Head Flux 1 BCs b Special Boundary Conditions and c Triggered Irriga
212. icular video format OpenGL acceleration should be disabled when problems occur when creating Video File Create Video File Video File C FlowAnimation avi Video Codec Type Microsoft MPEG 4 Video Codec 2 v About Qual 1005 4 Recording Frequency Real Time Changed Frames Only Figure 186 The Create Video File dialog window Animation files avi created by the HYDRUS command Create Video File can be displayed using a standard video software such as the Windows Media Player Animation files can also be inserted directly into PowerPoint presentations using the menu command Insert gt Movie gt Movie from File and selecting whether animation starts Automatically or When Clicked Animation can then be stopped and restarted using additional mouse clicks Notes on Video Editing 1 Video records only changes in View Thus if nothing changes in the View window only the first picture is recorded When one records animation of flow or transport then while the View window is redrawn each change is recorded Similarly one could record video 298 for any other manipulation of the View which requires its redrawing e g rotation of the model If the option Real Time is on each recorded View has an assigned time which elapsed between redrawing of the View window This means that the video is then played at approximately the same rate as redrawing of the View windo
213. ifies a constant pressure head boundary condition along a selected part of the boundary Specifies a constant flux boundary condition along a selected part of the boundary Flux is positive for inflow Specifies a seepage face boundary condition along a selected part of the boundary Specifies a variable pressure head boundary condition along a selected part of the boundary Specifies a variable flux boundary condition along a selected part of the boundary Flux values are negative for inflow Specifies a free drainage boundary condition along a selected part of the boundary Specifies a deep drainage boundary condition along a selected part of the boundary Specifies an atmospheric boundary condition along a selected part of the boundary Specifies a first type boundary condition for solute transport along a selected part of the boundary Specifies a third type boundary condition for solute transport along a selected part of the boundary Specifies a volatile type boundary condition for solute transport along a selected part of the boundary Specifies a first type boundary condition for heat transport along a selected part of the boundary Specifies a third type boundary condition for heat transport along a selected part of the boundary Inserts a cross section graphically Inserts a cross section using the dialog window Inserts a mesh line graphically Inserts a mesh line using the dialog window 264 Dimension Comment
214. ig 50 Inserts a surface either graphically or numerically Inserts a planar surface either graphically or numerically Inserts a Quadrangle surface either graphically or numerically Inserts a Rotary surface either graphically or numerically Inserts a Pipe surface either graphically or numerically Inserts a B Spline surface either graphically or numerically Inserts an opening either graphically or numerically Inserts thicknesses either graphically or numerically Inserts solids either graphically or numerically Inserts Layered solids either graphically or numerically Inserts General solids either graphically or numerically Inserts new FE mesh refinement graphically the FE Mesh refinement dialog window Fig 106 Defines new FE mesh refinement graphically the FE Mesh refinement dialog window Fig 106 Specifies the spatial distribution of soil materials Specifies the spatial distribution of root water uptake Specifies the spatial distribution of nodal recharge Specifies the spatial distribution of the hydraulic conductivity scaling factors Specifies the spatial distribution of the pressure head scaling factors Specifies the spatial distribution of the water content scaling factors Specifies the spatial distribution of the angle of local anisotropy for two dimensional applications Specifies the spatial distribution of the first component of local anisotropy for two dimensional applications Specifies the spati
215. igation starts Irrigation can start in the left node of the boundary and then the wetting zone will be spreading to the right From left to right it can also starts in the right node of the boundary and then the wetting zone will be spreading to the left From right to left or it can start in the arbitrary middle node of the boundary Center Node and spread in both direction From the center Seepage Face with a Specified Pressure Head This type of boundary condition is often applied to laboratory soil columns when the bottom of the soil column is exposed to the atmosphere gravity drainage of a finite soil column The condition assumes that the boundary flux will remain zero as long as the pressure head is negative However when the lower end of the soil profile becomes saturated a zero pressure head is imposed at the lower boundary and the outflow calculated accordingly This type of boundary condition is often used for lysimeters User can specify a pressure head value other than zero Pressure Head for triggering flux across the seepage face in several experimental settings a negative pressure can be applied at the bottom of laboratory columns or lysimeters 188 Boundary Conditions Options Time Variable Head Flux 1 BCs Special Boundary Conditions Triggered Irrigation Gradient Boundary Conditions instead of Free Drainage BC Gradient in the x direction positive against the x axis Gradient 1 he y direct
216. imensions Deletes all dimensions Edits a comment Deletes selected comments Deletes all comments Geometric objects that are imported to HYDRUS and are used as templates for defining HYDRUS geometries Edits a selected Background Layer Moves a selected Background Layer Rotates a selected Background Layer 261 Mirror Stretch Skew Delete All View Geometry FE Mesh Domain Properties Initial Conditions Boundary Conditions Results Navigator Edit Bar Tabs in View Status Bar Toolbars Arrange Toolbars Customize Toolbars Standard View Zoom by Rectangle View All Previous View Dynamic View Scroll Zoom Rotate View Stretching Perspective Auto Rotate Display Whole Domain View in Direction Isometric In X direction In Y direction In Z direction Reverse X direction Reverse Y direction Reverse Z direction Mirrors a selected Background Layer Stretches a selected Background Layer Skews a selected Background Layer Deletes all Background Layers Sets the View window to View Edit Domain Geometry mode Sets the View window to View Edit FE Mesh mode Sets the View window to View Edit Domain Properties mode to edit materials Sets the View window to View Edit Initial Conditions mode to edit pressure head initial conditions Sets the View window to View Edit Boundary Conditions mode to edit water flow boundary conditions Sets the View window to View Results mode to view pressure head distrib
217. immobile phase q im displayed when dual porosity model is used Total water content O 6m displayed when dual porosity model is used Standard display Darcy s flux LT default display x component of the Darcy s flux q LT y component of the Darcy s flux q LT z component of the Darcy s flux q LT Liquid phase concentration c M Ly default display Concentration of instantaneously sorbed solute sf M M Sorbed concentration s s s M M Gas phase concentration g Kyc M La Total concentration mass S M L gt Sorbed Concentration Options Sorption Sites 1 Sorption Sites 2 Total Sorbed Conc Sorbed concentration on first kinetic sorption sites se M M Sorbed concentration on second kinetic sorption sites sof M M Total sorbed concentration s s y s M M Subscripts c s a and w refer to contaminant soil air and water 211 Table 23 Definition of various concentration modes for linear sorption model Equilibrium Mobile immobile Two site Two kinetic model model sorption model sites model Sorbed Equilibrium Kc K fc f K pc Kpc Concentration M M Sorbed Nonequil K U f cin sk st sk Concentration M M Sorbed Total Kpc Kp fen a f cm f Kpe s K ct si s Concentration M M Gas phase K c Kpc Kpc Kpc concentration M L Solute mass in the c C 9 Cin in c0 c0 liquid phase S M
218. implest menu command is the New Section from the View command alternatively one can use the Create New Section from Current View command from the Edit Menu of the Sections Tab of the Navigator Bar which creates a newly named section from currently displayed objects in the View window The New Section from Selection menu command alternatively one can use the Create New 232 Section from Selected Objects command from the Edit Menu of the Sections Tab of the Navigator Bar creates a newly named section from currently selected objects or the FE Mesh The Display Whole Domain View All and Display Whole FE mesh commands causes the entire computational domain or FE Mesh to be displayed Geometric Sections can be created manually as described above or automatically The automatically generated Geo Sections are generated as follows An object above each part of the Base Surface in the 3D Layered Domain forms a Column which is divided into Layers depending on how many vertical layers the domain is divided into Each such Layer of each such Column then forms one Object a Domain Section When we have N Columns that is N parts in the Base Surface and the domain is divided into M horizontal Layers then the number of generated objects is N M At the same time Surfaces belonging to each of these objects are also generated Some of these Surfaces are Horizontal and some are Vertical although these terms are only approximate Surfaces can then be u
219. in the given direction which can be desirable for problems that for example require different spatial steps mesh sizes in the X and Y directions FE Mesh Parameters Main Stretching Options 1 Options 2 Mesh Sections Stretching Factor Fs 1 Mesh stretched in Ese NoSbetchi x direction with factor o Stretching Es 3 0 Stretching Direction Or z O General Vector Y Previous Apply All Default Figure 99 The FE Mesh Parameters dialog window Tab Stretching The Stretching Direction is defined either by the direction of main X Y and Z coordinates in both 2D and 3D projects or by a general vector V with two coordinates Vx and Vz for vertical 161 two dimensional domains and Vx and Vy for horizontal two dimensional domains An example of a mesh stretched using a Stretching Factor of 3 in the x direction is shown in Figure 112 One can define a Global FE Mesh Stretching using the Stretching Tab Fig 99 of the FE Mesh Parameters window or a Local FE Mesh Stretching using the Insert gt FE Mesh gt Mesh Stretching command While a Global FE Mesh Stretching is applied to the entire transport domain a Local FE Mesh Stretching can be assigned to individual Surfaces On Surface No A local FE Mesh Stretching can be defined in the direction of main coordinates or parallel V Parallel or perpendicular V Perpendicular to a general vector V which is defined by two or three coordinates Vx an
220. inclined Z coordinate m of the lower point of the first layer of the Thickness Vector a point denoted N1 in Figure 79 of the User Manual When P N1 this coordinates is the same as the 3 coordinate Z coordinate m of the upper point of the first layer of the Thickness Vector Z coordinate m of the upper point of the second layer of the Thickness Vector Z coordinate m of the upper point of the last layer of the Thickness Vector i e the coordinate of the surface of the solid Here is an example of the file for the import of a Solid divided into three Geo Layers OBJECT THICKNESS_ARR3Z_NLAYERS 4 500000e 000 4 000000e 000 0 000000e 000 0 000000e 000 1 300000e 000 2 100000e 000 3 300000e 000 5 500000e 000 2 500000e 000 0 000000e 000 0 000000e 000 1 300000e 000 2 200000e 000 3 400000e 000 7 000000e 000 4 500000e 000 0 000000e 000 0 000000e 000 1 400000e 000 2 300000e 000 3 000000e 000 7 000000e 000 2 500000e 000 0 000000e 000 0 000000e 000 1 200000e 000 2 600000e 000 3 500000e 000 6 500000e 000 9 999999e 001 0 000000e 000 0 000000e 000 1 600000e 000 2 400000e 000 3 600000e 000 5 000000e 000 2 000000e 000 0 000000e 000 0 000000e 000 1 200000e 000 2 500000e 000 3 700000e 000 4 500000e 000 2 000000e 000 0 000000e 000 0 000000e 000 1 400000e 000 2 400000e 000 3 400000e 000 5 000000e 000 9 999999e 001 0 000000e 000 0 000000e 000 1 500000e 000 2 500000e 000 3 300000e 000 5 500000e 000 9 999999e 001 0 000000e 000 0 000000e 000 1 100000e
221. indow c ccesseceeeseeeeeteeees 216 The use of intermediate isolines 4 23 oi ne ene au Ee cee 217 The Colot dialo WIN Wy dire ane ds ed each Roe sae aT Does edema 218 Adjusting scale in the Edit Isoband Value and Color Spectra dialog window 219 The use of the Custom Scalesiac cciwiniei ion ares lil a eel 220 The COLOR SIT OLIN asin E a ac A aoa age teen aca van Sew 221 An example of the Project_Property_Isolines txt text file eg Furrow_Pressure_Head_Isolines txt an excerpt for the Furrow project displayed in the top OF the fig re isissscassusvassaedserenctaanscceds Deedavsavaradeesnds ewearvcnsaeesguranceammesterevens 222 x y graph dialog window displaying pressure heads in observation nodes 223 The Convert to ASCII dialog window cccccssececseececsseceeseeceesneceeseeeeeseeeeeaeeees 226 The Grid and Work Plane dialog window c ceessceceseeceeeeececeneeeeneeeeseeeenaeeees 228 The View Stretching Factors dialog WindOW cesccecsseceeeeeceeseeeeesteeeenteeeenaeeees 229 The Rendering part of the View Tab of the Navigator Bar 0 0 0 eee eeeeeeeeeeeeees 230 The Pop up Menu from the View window esecesscsseecsseeeseeeeseeceaeceseessneeeaeees 232 Options for Generation of Geo Sections and FE Mesh Sections dialog window 233 Selected Navigator Bars Data Tabs on the left and in the middle the View Tab onthe Ti IN e cen a e e E a mane 236 Selected Edit Bars f
222. ine additional matrix of N N internal nodes which allows one to curve the inside of a Surface One needs to define a number of internal nodes N and an order of the Surface Spline Internal nodes are created automatically when a B Spline Surface is defined Their coordinates can be subsequently edited An order of the Surface Spline is an order of the polynomial which is used for modeling the surface either quadratic or cubic A Rotary Surface is defined by an Axis of Rotation defined using two nodes a Rotated Curve of arbitrary type as long as the created surface make sense and an Angle of Rotation from 0 to 360 degrees A Pipe Surface is defined by an Axis Curve a smooth curve of an arbitrary type only a polyline does not have to be smooth and a radius Rotary Curved Surface Quadrangles Figure 67 Examples of Curved Surfaces Rotary Pipe B Spline and Quadrangle Surfaces 122 4 2 1 3 Partial Surfaces A Partial or Component Surface Fig 85 is created by an Intersection of Surfaces or Solids see Section 4 6 which divides an original Surface into smaller Sub Surfaces or the so called Component Surfaces Although this Surface has its own number and can be used to define for example a Solid its shape and boundaries are defined generated by the shape of its original Surface and a given Intersection A list of Components resulting from division of the original Surface by an Intersection can be found on
223. ines which other optional modules are necessary for a particular application The module contains a project manager and both the pre processing and post processing units The pre processing unit includes specification of all necessary parameters to successfully run the HYDRUS FORTRAN codes grid generators for relatively simple rectangular and hexahedral transport domains a grid generator for unstructured finite element meshes for complex two dimensional domains a small catalog of soil hydraulic properties and a Rosetta Lite program for generating soil hydraulic properties from soil textural data The post processing unit consists of simple x y graphics for graphical presentation of soil hydraulic properties as well as such output as distributions versus 19 time of a particular variable at selected observation points and actual or cumulative water and solute fluxes across boundaries of a particular type The post processing unit also includes options to present results of a particular simulation by means of contour maps isolines spectral maps and velocity vectors and or by animation using both contour and spectral maps Version 2 0 which includes the 3D Professional Level of HYDRUS includes many new features as compared to version 1 0 New features and changes in the HYDRUS GUI 1 2 3 4 5 6 7 8 9 Supports for complex general three dimensional geometries Professional Level Domain Properties Initial Conditions
224. ion 28000 54400 47800 75800 160000 KFE Growth XFB Lysis XAMB xASRB SOB Fraction of S generated Lysis Yield Coefficient for S4MB Yield Coefficient for XASRB Yield Coefficient for SOB N Content of xl N Content of Biomass Previous Figure 41 The Constructed Wetland Model CWM1 Parameter II dialog window 95 Table 16 Temperature dependences stoichiometric parameters composition parameters and parameters describing oxygen transfer in the CWM1 biokinetic model Langergraber et al 2009 Parameter Description unit Value Temperature dependences activation energy J mol for Arrhenius equation Tdep_HyKh activation energy Hydrolyses J mol 28000 Tdep_HyKX activation energy factor KX for hydrolyses J mol 54400 Tdep_H activation energy for processes caused by XH J mol 47800 Tdep_A activation energy for processes caused by XA J mol 75800 Tdep_KNHA activation energy for factor KNHA for nitrification J mol 160000 Tdep_mueFB activation energy for XFB growth J mol 47800 Tdep_bFB activation energy for XFB lysis J mol 0 Tdep_AMB activation energy for processes caused by XAMB J mol 0 Tdep_ASRB activation energy for processes caused by XASRB J mol 0 Tdep_SOB activation energy for processes caused by XSOB J mol 0 Stoichiometric parameters Say
225. ion posit 1g Subsurface Drip Characteristic Function for Time Variable Flux 1 BC V Dripper Characteristic Function Opt Flux o _ Exponent 05 Surface Drip Boundary Condition for Time Variable Flux 1 BC urai Drip Seepage Face with Specified Pressure Head Pressure Head em 100 Figure 119 The Special Boundary Conditions tab of the Boundary Condition Options dialog window 6 3 3 Triggered Irrigation Triggered Irrigation can be specified on the third tab of the Boundary Condition Options dialog window Fig 120 Irrigation can be triggered by a user specified Pressure Head Triggering Irrigation input reached in the selected Observation Node Triggering Irrigation The irrigation starts after a user specified Lag Time input at a user specified Irrigation Rate or Pressure Head input The Duration of Irrigation has to be also specified This option is currently available only for two dimensional and axisymmetrical geometries 189 Boundary Conditions Options Time Variable Head Flux 1 BCs Special Boundary Conditions Triggered Irrigation Triggered Irrigation by Specified Pressure Head in a Observation Node Triggered Irrigation Observation Node Triggering Irrigation 1 Pressure Head Triggering Irrigation cm 1000 Boundary where irrigation will be applied Irrigation Rate em day Variable Head Boundary Irrigation Duration days Atmospheric Boundary L
226. ion energy factor KX for hydrolyses J mol 53000 Tdep_KNHA activation energy for factor KNHA for nitrification J mol 160000 Stoichiometric parameters Saya production of CI in hydrolysis 0 0 JBm cr fraction of CR generated in biomass lysis 0 1 fema fraction of CI generated in biomass lysis 0 02 Yuet yield coefficient for XH 0 63 Yans yield coefficient for XANs 0 24 Yanp yield coefficient for XANb 0 24 Composition parameters incr N content of CR g N g CODcr 0 03 incs N content of CS g N g CODcs 0 04 incl N content of CI g N g CODc1 0 01 N BM N content of biomass g N g CODgm 0 07 P CR P content of CR g P g CODer 0 01 ip cs P content of CS g P g COD s 0 01 p cI P content of CI g P g CODc 0 01 p BM P content of biomass g P g CODpm 0 02 Oxygen cO2_sat_20 saturation concentration of oxygen g m3 9 18 Tdep_cO2_sat activation energy for saturation concentration of oxygen J mol 15000 rate_O2 re aeration rate 1 d 240 94 Solute Transport Constructed Wetland Model No1 CWM1 Parameters II Temperature Dependence Hydrolysis KX Hydrolysis xH xA KNHA nitrification Stoichiometric Parameterss Production of SI Hydrolysis Fraction of SF Generated Lysis Yield Coefficients Yield Coefficient for XH Yield Coefficient for 4 Yield Coefficient for FB Composition Parameters N Content of SF N Content of SI N Content of XS 02 Saturation Temp Dep 02 Saturat
227. ional domain include various Labels or define permanent Cross Sections or Mesh Lines 4 7 1 Dimensions Dimensions can be added to describe spatial properties of the computational domain in the View window using the IJnsert gt Auxiliary Objects gt Dimensions command or the Dimensions command from the Insert Object part of the Domain Geometry version of the Edit Bar Then one needs to click on two points defining the computational domain and drag Dimensions to the required position Figure 107 shows an example of how Dimensions can be used After a command for defining a Dimension is selected a user needs to first select by a cursor two existing points the distance of which is to be labeled The Edit Bar lists during this operation the two definition points and the Dimension number Fig 86 left After the second point is selected a cursor in the View window and the Edit Bar Fig 86 right change and allow a user to define where a Dimension is to be displayed In which plane a Dimension is to be displayed can be done on the Edit Bar Fig 86 right xi zix Domain Geometry M Domain Geometry rH 2 umber for new Set new Dimension a g 5 Number for new BSE Dimension il Dimension Type Definition Points ne Paint 1 1 Point 2 0 Odz Apply Apply see Help Help PN Ke Step 2 of 3 Ke Step 3 of 3 Set second point of the new Set position of the new Dimension Dimension K Press Esc
228. ions Display Show All Hide All Previous demonstrates the use of FE Mesh Sections OBJECT INDEXES_AT_POINTS 200000e 000 000000e 000 500000e 001 500000e 001 700000e 001 000000e 001 200000e 000 7 200000e 000 7 200000e 000 7 200000e 000 7 200000e 000 7 200000e 000 7 450580e 009 450580e 009 450580e 009 450580e 009 450580e 009 450580e 009 WWWW WY 180 6 Domain Properties Initial and Boundary Conditions Initial and boundary conditions for both water flow and solute heat transport and the spatial distribution of other parameters characterizing the flow domain e g the spatial distribution of soil materials hydraulic scaling factors root water uptake parameters and possible hydraulic anisotropy and or observation nodes are specified in a graphical environment with the help of a mouse The program automatically controls the logical correspondence between the water flow and solute transport boundary conditions Various spatially variable properties e g material distribution initial and boundary conditions can be specified in Version 2 0 of HYDRUS Standard and Professional not Lite either a directly on the finite element mesh as done in Version 1 0 or b on geometric objects e g boundary curves rectangles circles surfaces volumes The main advantage of the latter approach is that when the FEM is changed these properties a
229. ions Sets the View window to View Edit Boundary Conditions Execute Calculation View Results e Time Layer Toolbar mode to edit water flow boundary conditions Executes a HYDRUS version 3 0 FORTRAN application Sets the View window to View Results mode to view the pressure head distribution Time 1 0 20 days vin o gt mW em List box of Time Layers First Time Layer Previous Time Layer Next Time Layer Last Time Layer Flow Animation Displays a list box with Time Layers with available results Displays the first time layer Displays the previous time layer Displays the next time layer Displays the last time layer Displays time layers of a particular variable consecutively and continuously 245 8 5 HYDRUS Menus The main window of HYDRUS contains a menu that has ten submenus 1 e File Edit View Fig 158 Insert Calculations Results Fig 159 Tools Options Windows and Help Fig 160 Table 25 lists the main groups the main menu items as well as the main submenu and sub submenu commands Table 26 then provides brief descriptions of all menu commands Edit View Insert Calculation Re Edit iO New Open Close Save Save As Save All Save Special Import and Export Print Print Preview Print to the Clipboard Print Options Printer Setup Project Information Project Manager 1 C USSL 3D_Tests Test2 H3D 2 C USSL Furrow H3D 3 C USSL
230. iption serves for the future identification of a particular computer in the electronic licensing system and is usually characterized by a user or its location e g John Laptop Harry Lab 001 7 Online Activation Information about you and your license License Number 1001 Activation Key Specify the required authorization level Select HYDRUS Level to activate 3D Professional Z Time limited Authorization Network Installation Expiry Date 77 122011 v Computer Description to identify this computer in the future Computer Description Home PC Activate Now Figure 169 The Online Activation dialog window After clicking on the Activate Now button you will be asked to confirm all specified parameters Fig 170 note that you may be prompted by your firewall to allow communication between your computer and the license server of PC Progress At this point all specified information will be verified against the data of our electronic licensing system and if confirmed the actual activation of HYDRUS will occur This communication applies only to data entered in the Online Activation window and no other information stored on your PC is transferred In case of unsuccessful activation an error message is displayed explaining the problem After correcting the problem you can use again the Activate Now command 279 p HYDRUS 2 xx i Please review the parameters for the
231. is higher than cRoot the excess solute stays behind Set equal to zero if no fifth time independent boundary condition and no solute uptake by roots is considered cWell Value of the concentration for the sixth time independent boundary condition ML 3 If internal sources are specified then cWell is automatically used for the concentration of water injected into the flow region through internal sources Set equal to zero if no sixth time independent boundary condition and no internal sources are specified cBnd7 Concentration of the incoming fluid for a volatile type boundary condition at the soil surface ML Set equal to zero if no volatile boundary condition is specified cAtm Concentration above the stagnant boundary layer gam ML for a volatile type boundary condition Set equal to zero if no volatile boundary condition is being specified d Thickness of the stagnant boundary layer d L for a volatile type boundary condition Set equal to zero if no volatile boundary condition is being specified When the parameter estimation option is selected then users have to provide initial estimates of the optimized solute transport parameters specify which parameters are to be optimized select appropriate checkboxes and provide parameter constraints for the optimization Zero values for minimum and maximum values signify that the parameters are unconstrained The Solute Transport and Reaction Parameters dialog window for the inverse
232. isplays options k How to set Initial Con gt Next Boundary Condi Back Domain Propert F 3 Tools xixi 000 Results Water Content th 0 429 0 412 0 394 0 376 0 359 0 341 0 323 0 305 0 288 0 270 0 252 0 234 0 429 0 234 af Time Layer Time 0 0 00 days lt j i C Flow Animation Chart Tools a Cross Section Chart E Boundary Line Chart e Display Values at Nod Help x Ke Right click on the Color Scale displays options Back Boundary Cond Figure 153 Selected Edit Bars from left to right for Material Distribution in Domain Properties Water Flow Boundary Conditions Pressure Head Initial Conditions and Water Content Results 237 As an example the Edit Bar for Domain Properties and Material Distribution displays materials that can be assigned to selected nodes in this case Materials 1 2 and 3 the Command Edit Materials which calls the Water Flow Parameters dialog window Fig 19 the command Values by Pointer which displays the material number for a node closest to the cursor and Help The Help part of the Edit Bar usually contains help on a particular process How to and the direction of the data inputting process next or backwards The Edit Bar for Boundary Conditions and Water Flow displays the various boundary conditions that can be specified along boundaries of the transport domain as well the command Display Codes whic
233. ite Element Size S 2 60 4 om Current Global Targeted Size of Finite Elements 7 90 cm Comment FE mesh Refinement on Surface No 2 g FE Size S 2 cm gt jj Surface No t lt Global FE Size 5 cm Figure 106 The FE Mesh Refinement dialog window for the MeshGen2D module with four different types of refinements applied to a Point a Line with a given FE size or the number of Points and to a Surface As an example Figure 107 shows the transport domain 700 650 cm and the finite element mesh of a problem with a furrow and a drain The mesh was generated with a Targeted FE Size 169 of 50 cm and three FE Mesh Refinements Fig 107 top Refinement with a finite element size of 10 cm was assigned to nodes 1 2 4 and 5 refinement 2 5 cm to node 3 and refinement 3 15 cm to nodes 8 and 9 There were 15 nodes on the drain boundary due to the command Minimum Number of Points on Each Closed Boundary Curve The resulting finite element mesh is shown in Figure 107 bottom Figure 107 Example of FE Mesh Refinements top and FE Mesh bottom 170 5 4 2 Finite Element Mesh Refinement for Genex T3D While the MeshGen2D module discretizes the computational domain into unstructured FE mesh using triangles in 2D and tetrahedrals in 3D the Genex T3D module uses primarily quadrilateral in 2D and hexahedral in 3D finite elements Genex T3D uses triangles only in parts of
234. l 0 0 16 15 0 07 0 18 15 0 02 0 13 15 0 0 2 15 0 0 28 15 0 18 15 0 08 15 0 14 15 0 11 15 0 11 15 0 11 15 0 11 15 Linear interpolation of time between the initial and final time J Surface area associated with transpiration Help Add Line Delete Line 1 2 3 4 5 6 8 ow ai ooo ol ol o o o o o oa oa oro oi oa ol ol ol ol o o a a e M lt W olololololojlololojololo Figure 37 The Time Variable Boundary Conditions dialog window The following variables are specified in the Time Variable Boundary Conditions dialog window Time Time for which a data record is provided T Boundary condition values are specified for the time interval preceding time given at the same line Thus the BC values specified on the first row are for the time interval between the initial time and time specified on the same line Precip Precipitation rate LTH in absolute value applied to the atmospheric boundary Evap Potential evaporation rate LT in absolute value applied to the atmospheric boundary Trans Potential transpiration rate LT in absolute value hCritA Absolute value of the minimum allowed pressure head at the soil surface L applied to the atmospheric boundary Var Fl1 Drainage flux LT across the bottom boundary or another time dependent prescribed flux boundary condition positive when water leaves the flow region set to zero when no time dependent f
235. l boundary one or more Internal Curves which entirely lies inside of a Surface An Opening can be formed by clicking with the right mouse button in the View Window on the closed internal boundary and selecting from the popup menu the Create Opening command Additional information can be found at Openings 5 Geometry Check The consistency of the geometry can be verified at any time using the command Check Data Consistency Tools Menu 6 Remarks e Any change in geometry can be undone using the undo command or redone using the redo command A number of undo or redo step is limited by the buffer memory which can be set in the Program Options dialog window Tab Options and Directories e When the Computation Domain is formed by several subdomains with different properties e g different materials and so on one can form this domain from multiple Surfaces corresponding to these subdomain An advantage is that after the FE Mesh is generated it is possible to automatically form Mesh Sections for particular Surfaces and use them to easily define materials and other properties or initial and boundary conditions Additional information can be found at FE Mesh Sections Section 5 7 4 2 3 Several Notes on Rules for Correct Definition of Surfaces 1 Contrary to the old HYDRUS 2D program internal curves can touch or cross other internal curves and can touch boundary curves A point where two curves intersect or touch must be a definition p
236. lbars Users can use various toolbars that allow an easy access to the most frequently used commands These commands are grouped into five toolbars that can be displayed using the command View gt Toolbars Fig 156 Users can also create their own toolbars and customize them in various ways using the Customize dialog window Fig 157 Toolbars KIKIKI Ihar me ooibar name Standard Show Tooltips C Large Buttons Customize Toolbars Commands Categories Buttons File YUROU De Edit Seep ee en ks View ms a a a a a i E 5 _ A BEARERS Window Calculation Select a category then click a button to see its description Drag the button to any toolbar Description Figure 157 The Customize Toolbars dialog window 242 The default toolbars i e Standard Toolbar Tools Toolbar View Toolbar GUI Toolbar and Time Layer Toolbar are briefly summarized below definitions in each case are from left to right a Standard Toolbar eee New Project Creates a new project Open a Project Opens an existing project represented by the project_name h3d2 file Save Project Saves the input data of the current project specified in the main program module if the data were either newly created or changed during an application run Project Data Manager Calls the project manager to manage data of existing projects helps to locate open copy delete or rename the desired projects a
237. le 5 0 ikl Number of Copies 0 parce Definition of the Axis of Rotation Help Definition of the Mirroring Plane Point and Parallel Axis O 2Points Pick Point and Parallel Plane YZ Cancel O 3Points Pick Coordinates x Y Z is r 1 Point 0 00 0 00 0 00 fem 1 Point 24 31 00 em 2 Point 200 0 00 0 00 em Pick cm Pick 3 Paint 0 00 0 00 0 00 cm Numbering Copy ann Numbering hat wl Be Br Na Coos te epee Point Automatic Automatic Lines Automatic Automatic Surface Automatic Automatic Solids Automatic Automatic Slope Definition Variable coordinate X coordinate Stretching Factors OK Y coordinate In Direction Cancel e Slope Angles tangents In Direction dz dx In Z Direction Origin Origin Center of the Bounding Box Center of the Bounding Box D User Defined Point Pick User Defined Point Pick 0 00 x 0 00 em 0 00 Yy 0 00 cm Apply 0 00 0 00 cm Options Figure 58 The Stretch left and Skew right dialog windows 115 Lines between Points 7 Create new lines between the selected nodes and their copies Lines between Points Surfaces between Lines Create new surfaces between the selected lines and their copies Solids betw
238. length it is recommended to set the radius not too small in order to avoid acute angled triangular finite elements in the refinement area For a Rectangular Refinement a rectangular refinement area is defined around a node in all directions Users need to specify the Side Length of the refinement area and the Inner Targeted FE Size i e a FE size immediately around a point Fig 111 Figure 108 Circular left and rectangular right refinements around a node FE Mesh Refinements assigned to a Line are handled in Genex T3D similarly as in MeshGen2D One can again define either the size spacing Line through FE Length or the number a specific number of equidistant sub divisions Line through Division of finite 171 elements along a line In the former case one needs to define the Target FE Length in the latter case the Number of Division FE Nodes However while in MeshGen2D there was a gradual increase in sizes of finite elements away from the Line in Genex T3D the refinement affects only one row of finite elements Figure 109 ea eee AMAAAAAN VVVVVV VI ia Sh ENE Figure 109 Refinement on a line by defining either the size or the number of finite elements along a line It is also possible to define Fe Mesh Refinements for Surfaces or Solids Figure 110 In both cases users need to s
239. lerance usually 0 1 mm 4 2 5 Check and Repair Geometry 127 The Check Data Consistency command performs a consistency test of the domain boundaries It checks especially whether each domain component is bounded by an outer boundary curve and whether or not the curves are intersecting each other When the geometry is not correct the code sends a warning and select those curves which do not fulfill the rules for a correct definition of boundaries The command Repair Geometry may then be used to fix existing problems The Repair Geometry command attempts to fix errors in the ill defined Geometry that were found using the command Check Data Consistency This command calls the Repair Domain Definition dialog window Fig 71 The List of Corrections section of this dialog lists various operations that can be used automatically by the program when attempting to correct the ill defined Geometry Some of these corrections depend on the model precisions which are defined in the Model Precision and Precision of Corrections section Users can define these precision criteria or use those suggested by HYDRUS pair Domain Definitio Model Precision and Precision of Corrections Model precision Eps 0 0041 em F Automatic Corections precision Eps2 0 4100 em V Automatic List of Corrections Replace arcs with length L lt Eps2 and incorrectly defined arcs by abscissas Remove overlapping points i e points with dist
240. lications respectively Since this variable is usually specified in individual nodes it is uncommon to specify it here Mater Material number Roots Root distribution AXZ Scaling factor for the pressure head Bxz Scaling factor for the hydraulic conductivity Dxz Scaling factor for the water content Temp Initial temperature K Conc Initial concentration of the equilibrium phase ML Sorb Initial concentration of the nonequilibrium phase kinetically sorbed MM or of the immobile region ML 181 Values from each line are assigned to the entire layer within the FE Mesh with the exception of Code the boundary condition code which is assigned only to boundary nodes When multiple values are encountered within the single layer when initiating the table the cell is left empty instead of displaying any particular value Unless changed this variable will not be assigned in a particular layer after closing the dialog with OK and original values will remain unchanged The three commands Copy Sel Copy All and Paste MS Excel Import Export facilitate the transfer of data from this HYDRUS dialog window to the Excel or other spreadsheet The command Set Boundary Conditions for Solute Transport and Heat Transport for changed Codes leads to assigning Cauchy boundary conditions for solute and heat transport to nodes where the Code was changed Default Domain Properties Properties of Horizontal Layers Layer 2 cm
241. lied globally to all selected surfaces e g a single point with the lowest z coordinate is found for all selected surfaces Nodes that are at the boundary line shared by two surfaces or at the surface shared by two volumes are assigned the property value with a higher number The sequence in the list of properties can be adjusted using the command Sort Property where Property is either Material Scaling Factor etc at the Edit Bar Fig 127 The option to assign Properties at Geometric Objects is not available for simple parametric i e Rectangular or Hexahedral Geometries available in the Lite Version of HYDRUS Name One can provide a Name for each newly defined Property Object When user does not define a Name for a Property Object the GUI will automatically generate a generic name that is then used throughout the project e g on the Navigator and Edit Bars When different values are specified on Geometric Objects and FE mesh a warning Different Values on FE Mesh is displayed in the Help section of the Edit Bar A similar warning is also issued in such case before calculations are started All properties can be transferred from Geometric Objects to FE Mesh using the menu command Edit gt Transfer all Properties to FE Mesh 201 6 6 Import of Domain Properties and or Initial and Boundary Conditions Various domain properties and initial and boundary conditions can be imported either from existing HYDRUS projects and from data t
242. lines arcs circles splines surfaces openings thickness vectors solids Points A point is a basic geometric object which is used to define Curves and other objects A point location is defined using two or three coordinates depending on dimensions of a particular problem Curves A curve is a set consisting of a finite number of objects connected by boundary nodes Except at point nodes objects cannot intersect each other or themselves A curve can be open or closed Outer Boundary Curves An outer boundary curve is a boundary curve with the following properties the curve is closed positively oriented i e in a counter clockwise direction does not intersect any other curve or itself and has the computational domain surface located on its left side in the sense of positive orientation while the right side is not part of a computational domain Internal Curves An internal curve must be located entirely within the computational domain It can touch but not intersect the outside boundary of the computational domain at its definition points An internal 102 curve can be open or closed and can intersect itself provided the intersect occurs at a definition point of the internal curve Openings An opening is defined by one or more boundary curves that form a closed boundary Lines Lines and polylines are the most commonly used objects for describing boundaries of a domain or internal curves Lines are defined by
243. lly deactivated on this computer Please keep the deactivation code safe without it you may not be able to reactivate HYDRUS again Warning After deactivation HYDRUS will run as a demo version Do you want to continue i Hydrus has been deactivated on this computer You will be presented with a code which serves as a proof that you have deactivated HYDRUS on this computer Warning If you fail to present the code you will not be able to activate HYDRUS on an another computer Figure 181 Window confirming successful deactivation of HYDRUS by email 9 2 4 Extending Activation Prior to the expiration Expiry Day of the Time Limited Authorization user will be alerted about it and the license can be easily repeatedly extended using the Extend Activation On Line button This button will appear instead of the Activate on line button on the Status Tab of the HYDRUS Authorization Status window Fig 165 To extend the activation you will need again the Activation Key either for the entire license or for a particular Workspace 289 9 2 5 Hardware Key Starting with version 2 02 the network authorization of the HYDRUS program can be done either as in previous versions using the software key activation or newly using a Hardware Key HASP The software key can be used to authorize only separate computers while a Hardware Key is required for the network or server installations designated for remote access A Hardware Key plu
244. lly have to lie in the same plane However if a spline is used to define a boundary of a surface then all its definition points need to lie in this surface A spline can be defined either 111 graphically using a command on the Edit Bar or in the dialog where we select a particular type of spline HYDRUS allows three types of splines cubic spline i e a curve defined by multiple polynomials of the third order It passes smoothly through all points Bezier s curve a smooth curve that passes through boundary points but does not have to pass through internal points B spline a general Bezier s curve More information can be found at http mathworld wolfram com BezierCurve html http mathworld wolfram com B Spline html Once a command for defining a new spline graphically is selected a cursor in the View window will become a cross with a small empty circle in the middle The coordinates of the location of the cursor will be displayed next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 54 The Edit Bar will also show which point and curve their numbers are being defined and what reference coordinate system the current coordinate system the grid origin or the last inserted point is used One node is specified after the other A user can also select on the Edit Bar the type of the spline standard spline B spline or Bezier curve The process of defining a new s
245. log Window Figs 6 and 7 appears this window can be also selected from the Pre processing Menu From this point on the program will navigate users through the entire process of entering input files Users may either select particular commands from a menu or allow the interface to lead them through the process of entering input data by selecting the Next button Alternatively clicking the Previous button will return users to the previous window Pre and post processing commands and processes 24 are also sequentially listed on the Data Tab of the Navigator Bar Green arrows on the Edit Bar always direct users to subsequent or previous input processes for a particular command Many commands and processes can be alternatively accessed using either the Toolbars and Menus or the Navigator and Edit Bars 25 26 1 Project Manager and Data Management A Project Manager called by the command File gt Project Manager Figs 2 and 3 is used to manage the data of existing projects and helps to locate open copy delete and or rename desired projects or their input or output data A Project represents any particular problem to be solved by HYDRUS The project name as well as a brief description of the project Fig 4 helps to locate a particular problem Projects are represented by a file project_name h3d2 the final 2 refers to version 2 of HYDRUS extension h3d was used with version 1 0 that contains all input and output data when the Tempor
246. lor spectrum Displays a selected variable using isosurfaces Displays a selected variable using color points Displays a selected variable using color edges Displays velocities using velocity vectors Figure 155 shows two more Edit Bars i e those for Domain Geometry and FE Mesh The Insert Object of the Domain Geometry Edit Bar allows users to Insert Objects with which a 239 transport domain is defined i e points lines arcs circles splines surfaces as well as auxiliary objects such as dimensions and comments The Edit Objects part allows objects to be edited using various actions such as Move Copy Rotate and Mirror This Edit Bar also provides Help on how to Edit Domain Geometry and to Check Domain Definition The FE Mesh Edit Bar allows quick access to various commands needed for editing and generating the finite element mesh Edit FE Mesh such as the FE Mesh Generator Fig Error Bookmark not defined FE Mesh Parameters Figs 98 through 104 Insert Mesh Refinement Fig 106 Delete All Refinements Generate FE Mesh Delete FE Mesh and FE Mesh Information Fig 113 The FE Mesh Edit Bar also allows users to generate the finite element mesh step by step FE Mesh Advanced i e using individual steps such as Fundamental Triangulation Mesh Refinement Delaunay Retriangulation Convex Retriangulation and Mesh Smoothing This Edit Bar additionally provides tools to work with FE Mesh Sections allows users to selec
247. loyed by Kool and Parker 1987 who modified the formulation to account for air entrapment While relatively simple to implement the above model has been found to suffer sometimes from a so called pumping effect in which the hysteresis loops can move to physically unrealistic parts of the retention function As an alternative we also incorporated in HYDRUS the hysteresis model of Lenhard et al 1991 and Lenhard and Parker 1992 that eliminates pumping by keeping track of historical reversal points Hysteresis in Retention Curve no pumping Bob Lenhard 54 3 7 Water Flow Parameters Parameters for the soil hydraulic models are specified in the Water Flow Parameters dialog window Fig 19 In all models i e Brooks and Corey 1964 van Genuchten 1980 Vogel and Cislerova 1988 Kosugi 1996 and Durner 1994 6 Qr and 8 Qs denote the residual and saturated water contents respectively K Ks LT is the saturated hydraulic conductivity and is a pore connectivity parameter The parameters Alpha Ly and n are empirical coefficients affecting the shape of the hydraulic functions The modified van Genuchten model has four additional parameters 6 Qa a water content smaller or equal to 6 8 Qm a water content larger or equal to 0 K Kk LTH the unsaturated hydraulic conductivity at water content amp and amp Qk the water content associated with Kz r
248. lt Profile which corresponds to the table described in 4 4 2 above One can create new profiles change their thicknesses or delete them One can simultaneously also see a list of Thickness Vectors where the selected Profile is used 135 A desired Profile can be associated with a particular Thickness Vector after opening a dialog with its properties e g by double clicking on a vector and selecting a Profile from a Combo Box Thickness Profile No see Fig 79 This operation can even be carried out globally by first selecting desired Thickness Vectors then opening a dialog with their properties Alt Enter and finally repeating the above described process Note that one Profile can be associated with many Thickness Vectors which enables one to change easily Thicknesses of Layers on all Thickness Vectors by changing a single Profile 4 4 2 4 Steps to Define a 3D Layered Domain 1 Definition of the Base Surface The Base Surface is a 2D domain of an arbitrary shape How to specify the Base Surface is described in Building a Two Dimensional Domain 2 Definition of Thickness Vectors One inserts one or more Thickness Vectors in points that lie in the Base Surface so that the shape of a Solid is defined as needed 3 Definition of a Solid On the Edit Bar or the Menu command Insert gt Domain Geometry one clicks on the Solid gt Extruded command and selects clicks on one of the Surfaces defining the Base Surface This o
249. lues for the minimum and maximum values signify that parameters are unconstrained The Heat Transport Parameters dialog window for the inverse problem is not further shown here Notice that thermal conductivity and volumetric heat capacity parameters have units of Wm K 4 and Jm3K respectively These units when converted to basic SI units are ML T K and MLT K respectively and thus contain time to the negative second or third power which needs to be taken into account during any time conversion 76 3 18 Root Water Uptake Model Users may select a particular Water Uptake Reduction Model and a Solute Stress Model in the Root Water Uptake Model dialog window Fig 33 Root Water and Solute Uptake Model Water Uptake Reduction Model Feddes S Shaped Critical Stress Index Solute Stress Model O No Solute Stress Additive Model Multiplicative Model Active Solute Uptake Model Active Solute Uptake 01 Michaelis Menten Constant Minimum Concentration for Uptake Critical Stress Index for Active Solute Uptake Reduced Potential Solute Uptake due to Reduced Water Uptake Help Previous Figure 33 The Root Water Uptake Model dialog window a Water Uptake Reduction Model Either a water stress response function suggested by Feddes et al 1978 or an S shaped function suggested by van Genuchten 1985 can be used to reduce the potential root water uptake to th
250. lux Cumulative Variable Boundary 3 Solute Flux Cumulative Variable Boundary 4 Solute Flux Constant Boundary Flux Seepage Face Flux Variable Boundary Flux 1 Actual Atmospheric Flux Drain Boundary Flux Free and Deep Drainage Boundary Flux Variable Boundary Flux 2 Variable Boundary Flux 3 Variable Boundary Flux 4 All Solute Cumulative Fluxes All Solute Fluxes Soil Hydraulic Properties Pressure Head Water Content Log Pressure Head Soil Water Capacity Water Content Hydraulic Conductivity Log Hydraulic Conductivity Effective Water Content Pressure Head Log Pressure Head Run Time Information Time Level Time Step Time Number of Iterations Cumulative Number of Iterations Peclet Number Courant Number Number of Solute Iterations This graph is given for each solute The x y graphs have only a limited capacity and can display at most 6 000 data points and 20 lines If a dataset to be displayed has more data points then allowed then automatic selection is made by the program only each n data point is displayed and a warning File is too big to be displayed entirely Automatic selection has been made is issued If the number of observation nodes is larger than 20 only the first 20 observation nodes are displayed Additional text output is provided under the command Mass Balance Information on the Data Tab of the Navigator Bar also at the Results Menu This output gives the total amount of water heat and solute inside each specified
251. lux boundary condition is specified Same for 84 Var Fl2 Var Fl3 or Var Fl4 The Var Fl4 value is used for internal time variable nodal flux sinks or sources if they exist Var H 1 Groundwater level L usually negative or other time dependent prescribed head boundary condition set equal to zero when no time dependent head boundary condition is specified Same for Var H 2 Var H 3 or Var H 4 The Var H 4 value is used for internal time variable nodal pressure head sinks or sources if they exist TVall1 The first time dependent temperature K that can be used for nodes with time variable boundary conditions atmospheric BC variable head flux BC is not specified when heat transport or time variable boundary conditions are not considered TVal2 The second time dependent temperature K that can be used for nodes with time variable boundary conditions is not specified when heat transport or time variable boundary conditions are not considered CVal1 The first time dependent solute concentration ML3 that can be used for nodes with prescribed time variable boundary conditions atmospheric BC variable head flux BC not specified when solute transport is not considered This column should be used preferably only for the atmospheric boundary because the concentration value is adjusted based on values of precipitation and evaporation as follows cVall Precip Precip Evap cVall The cVall is adjusted to be zero when Evap gt Pr
252. lux from a simulated transport domain is equal to the potential transpiration T L T multiplied by the Surface boundary Area length in 2D Associated with Transpiration see Figure 2 2 of the Technical Manual It is usually the entire soil surface usually the boundary area length with an 85 atmospheric boundary condition By dissociating this value 1 e the surface area associated with transpiration from the surface boundary area length of the transport domain we provide HYDRUS users with more flexibility how to specify transpiration e g for sparsely vegetated soil surface or for row crops or trees In any case the definition of the Surface Area Associated with Transpiration depends on how the potential transpiration T is calculated which is usually done for the entire soil surface 86 3 22 Constructed Wetlands Two biokinetic model formulations can be chosen 1 the biokinetic model as described in CW2D Langergraber and im nek 2005 2006 and 2 the CWM1 Constructed Wetland Model 1 biokinetic model Langergraber et al 2009 In CW2D aerobic and anoxic transformation and degradation processes for organic matter nitrogen and phosphorus are described whereas in CWMI aerobic anoxic and anaerobic processes for organic matter nitrogen and sulphur Comparisons between CW2D and CWM1 components and processes is given in Tables 11 and 12 respectively Details about both modules can be found in the above referenced lit
253. m 180 00 Figure 52 The New Line Arc dialog window An object circle is always defined internally using three definition points However to simplify its specification it is possible to define a circle also using a center and a radius Three definition points are then created automatically Again circles can be entered either graphically using the cursor most common or using the New Line dialog window Fig 52 A new circle can be entered graphically by selecting the command Jnsert gt Domain Geometry gt Arc Circle gt Graphically from the menu or by using one of the following commands a Circle by 3 Points or b Circle by Center and Radius from the Insert Object part of the Domain Geometry version of the Tool Bar at the right side of the View Window and then entering lines using the cursor The list of points defining the circle must be entered in the General Tab Fig 53 left while coordinates of points defining the circle its center and radius are entered in the Circle Tab Fig 53 right When a Circle is defined by Center and Radius graphically then the first definition point is created at the mouse click while the other two are at the circle circumference at 90 and 180 degrees Adjustable Point When a radius or the center of an arc is modified it is usually also necessary to modify the location of one of the arc definition points An adjustable point enables one to choose a point whose co
254. m HYDRUS 2 03 File Version 1 Isoline 1 Value 60 000 Segment 1 Description C1 x coordinate m C2 z coordinate m 2 761816e 000 8 381839e 001 2 670929e 000 8 391035e 001 2 577883e 000 8 403773e 001 2 559808e 000 8 406094e 001 2 542170e 000 8 409753e 001 Hj 537666e 000 477832e 000 Koj 790872e 001 000000e 000 ji men Figure 144 An example of the Project_Property_Isolines txt text file e g Furrow_Pressure Head_Isolines txt an excerpt for the Furrow project displayed in the top of the figure 222 7 2 Results Other Information Additional information such as boundary fluxes and or soil hydraulic properties can be displayed using x y graphs Results Other Information on the Data Tab of the Navigator Bar or Results Menu Fig 145 Figure 145 shows the x y graph dialog window that displays pressure heads in observation nodes Table 24 gives an overview of the different graph options that are possible Two list boxes at the top of the x y graph dialog window provide various combinations of graphs that are possible to display Table 24 Browsing through various graphs is additionally also enabled using the Previous and Next command Double clicking at various objects of the x y graph e g axis title captions legend will allow users to redefine them i e to change their text colors or fonts When the right mouse button is clicked above the graph a pop up menu will appear tha
255. mber four digits and the Activation Key hexadecimal 32 characters You should receive both numbers from the HYDRUS distributor from whom you purchased the license for HYDRUS or from HYDRUS customer support support pc progress cz Enter both numbers into the Online Activation dialogue window Fig 169 After clicking the Activate Now command HYDRUS establishes a connection over the Internet with the license server and performs its activation B Activation by E Mail when encountering problems with on line activation The activation process by email consists of generating two request codes that need to be sent to the HYDRUS distributor together with information about the license customer and workplace Based on this information the HYDRUS distributor will generate a corresponding activation code and send it back to the HYDRUS user Different HYDRUS functions will be activated after inserting the activation code depending upon the type of purchased license In the dialog window Activation by E mail Fig 184 generate Request Codes Send the Request Codes by email to support pc progress cz or to the HYDRUS distributor from whom you purchased the license for HYDRUS After that you will receive by email the Activation Code which you enter into the dialog window Activation by E mail the Step 3 Tab Fig 175 and activate HYDRUS 9 2 2 Detailed Description of HYDRUS Activation Using a Software Lock The HYDRUS Authorization Sta
256. mmand allows users to display a particular variable between any two points on the boundary of the transport domain or along any line that is drawn along edges of finite elements within the transport domain This line hence does not have to be straight but can turn in any direction along finite element edges c The Help commands as before The Edit Bar for Results and Water Content displays similarly as for the initial conditions a spectrum that is used to draw results and the minimum and maximum values for the entire domain This bar further includes a A Time Layer command to specify which time layers corresponding to print times specified in the Output Information dialog window Fig 16 are to be displayed Time layers can be chosen either from the list box or from a scroll bar It is also possible to perform animation of results by clicking on the Flow Animation check box b Two Chart Tools commands Cross Section Chart and Boundary Line Chart which have the same purpose as above for the initial condition The last command i e Display Values at Nodes again causes the value of a particular variable e g water content of the node closest to the cursor do be displayed 238 c The Help command One useful feature of the Help command here is the Right click on the Color Scale displays options a right click displays the Edit Isoband Value and Color Spectra dialog window Fig 138 Right clicking results in the display of the pop
257. modified using the RS1 relative size at the top and RS2 relative size at the bottom factors below General Vertical Coordinates The element sizes are then proportionally distributed Smaller RS factor leads to smaller elements The upper boundary is by default parallel with the bottom boundary Any possible vertical deviations from this parallel line can be defined using dz values in the Horizontal Discretization in X Direction part of the window Relatively general domains can still be defined by properly adjusting the dz values see Fig 8 157 Rectangular Domain Discretization Horizontal Discretization in X Direction OK Count 11 1 2 3 4 5 GANA x em 0 00 100 00 20000 300 00 400 00 dz em 0 00 000 000 OOO OOF OO Help Vertical Discretization in Z Direction Generate Vertical Coordinates Count 1 1 A Set relative size of finite elements 1 2 3 4 5 6 7 8 3 Previous a o Figure 96 The Rectangular Domain Discretization dialog window A similar approach can be used to discretize simple hexahedral domains in three dimensions Hexahedral domains must have similar properties as rectangular domains in that they are defined by vertical planes at the sides a horizontal plane possibly with a certain slope at the bottom boundary and with only the upper boundary not having to be a plane The discretization of the hexahedral domain is then defined in the Hexahedral Domain Discretizati
258. multiplied by a constant lt 1 usually between 0 3 and 0 9 d If during a particular time step the number of iterations at any time level becomes greater than a prescribed maximum usually between 10 and 50 the iterative process for that time level is terminated The time step is subsequently reset to Ar 3 and the iterative process restarted 51 We note that the selection of optimal time steps Af during execution is also influenced by the adopted solution scheme for solute transport Table 6 Time Step Control variables Lower Optimal Iteration When the number of iterations necessary to reach convergence Range for water flow is less than this number the time step is multiplied by the lower time step multiplication factor the time step is increased Recommended and default value is 3 Upper Optimal Iteration When the number of iterations necessary to reach convergence Range for water flow is higher than this number the time step is multiplied by the upper time step multiplication factor the time step is decreased Recommended and default value is 7 Lower Time Step If the number of iterations necessary to reach convergence for Multiplication Factor water flow is less than the lower optimal iteration range the time step is multiplied by this number time step is increased Recommended and default value is 1 3 Upper Time Step If the number of iterations necessary to reach convergence for Multiplication Factor water flo
259. n be achieved by pressing various buttons on the keyboard Rotating is achieved by holding simultaneously the Ctrl button on the keyboard and the left mouse button Scrolling occurs by holding simultaneously the Shift button on the keyboard and the left mouse button And finally zooming is achieved by holding simultaneously the Alt button on the keyboard and the left mouse button Zoom by Rectangle View All Previous view In Reverse Z direction View Commands Isometric View Perspective View View Stretching Factors Rendering Commands Full Model Transparent Model Wire Model Sections Commands Cut with Rectangle Cut with Indexes Zooms in on a certain part of the View window using a rectangle Shows the default view of the View window Shows the previous view of a certain part of the View window Sets the view of the transport domain in the reverse Z direction Shows a pop up menu with the following commands Isometric In X direction In Y direction In Z direction In Reverse X direction In Reverse Y direction In Reverse Z direction Perspective Default View Specifies the isometric view Specifies the perspective view Calls the View Stretching Factors dialog window Fig 148 Displays a menu with three commands on how to display the transport domain see 8 1 4 Displays the transport domain as a full object Displays the transport domain as a transparent object Displays the transport domain as a wired object Display
260. n be used for soil with less nonlinear soil hydraulic properties e g loam Minimum Time Step Minimum permitted value of the time increment Atmin T The minimum time step must be smaller than a the initial time step b interval between print times and c interval between time variable boundary condition records Always specify a small minimum allowed time step on the order of 1 s This value may never be used but it provides the code with flexibility when it may be needed e g when there is a sudden change in boundary fluxes and HYDRUS may not converge with larger time steps Maximum Time Maximum permitted value of the time increment Atmax T This is Step relatively unimportant parameter and a large value may be specified Since HYDRUS automatically selects its optimal time step there is usually no need to constraint that The only time when there is a need to constrain the time step is likely for cases when HYDRUS is asked to generate internally intra daily variations in temperature or in evaporation and transpiration fluxes Then there is a need to have time step smaller e g 1 h so that these daily variations can be properly modeled 47 3 4 Output Information The Output Information dialog window Fig 16 contains information governing output from the computational module of HYDRUS Output Information Print Options Print Times K Cl T Level Information Count 24 t days S Cancel C Interval Out
261. n interruption of the FE mesh generation process The mesh generation is interrupted by the message Achieved the maximum number of nodes This means that the maximum allowed number of nodes either on the boundary curves or in the two dimensional domain was reached during the mesh generation process This is usually a consequence of having too many nodes along the boundaries the number of mesh nodes inside a domain increases approximately with the square of the number of boundary nodes It is then necessary to decide whether or not so many nodes are needed for the envisioned triangular mesh If the answer is yes then the maximum number of nodes must be increased in this dialog window If the answer is no then it is necessary to decrease the Targeted FE Size Figs 98 or to increase the Smoothing Factor in the FE Mesh Quality group discussed below Main Stretching MG Options Options Sections Expott FE mesh limits Max number of nodes on boundary curves 5000 Max number of FE mesh nodes 2D mesh 200000 FE mesh quality Max number of overall remeshing iterations Number of intensive smoothing steps Number of internal iterations for intensive smoothing Number of internal iterations for standard smoothing Smoothing factor gt 1 Previous 7 Check distances between neighboring FE mesh ET points on domain boundaries and refine the mesh BPPN automatically if the ratio is greater than F De
262. n is not reached i e some changes would still occur during Delaunay remeshing Number of Internal Iterations for Standard Smoothing This number defines the maximum number of iterations while solving the elliptic equations a process needed during mesh smoothing it significantly influences the final smoothness of the mesh A higher number of iterations improves the mesh smoothness It serves little purpose to increase the number above 20 since the mesh is then virtually constant anyway while the whole process of mesh generation would be slowed down significantly Smoothing Factor The smoothing factor is the ratio of the maximum and minimum height of a finite element triangle For a triangle with equal sizes this factor is equal to 1 which is theoretically not achievable for finite element meshes The smoothing factor can be decreased to a value of about 1 1 when a highly smooth finite element mesh is required and vice versa can be increased when a course mesh can be tolerated The smoothing factor significantly affects the final number of elements In general the default values in the FE Mesh Parameters dialog window should be preserved only experienced users should modify the various parameters needed for the mesh generation process When the option at the bottom of Figure 103 is checked HYDRUS compares distances between the neighboring nodes on the domain boundaries When the ratio of distances between two neighboring nodes is l
263. n menu or in the popup menu in Navigator Data Tree V Move Background Layer so that its bottom left corner is positioned at the Origin 0 0 0 v Update Grid and Workspace according to the Background Layer template dimensions You can Move Rotate or Stretch the Background Layer later by commands available in the OK Cancel Figure 94 The New Background Layer dialog window 151 STL is a file format native to the stereolithography CAD software created by 3D Systems This file format is supported by many other software packages it is widely used for rapid prototyping and computer aided manufacturing STL files describe only the surface geometry of a three dimensional object without any representation of color texture or other common CAD model attributes The STL format specifies both ASCII and binary representations Binary files are more common since they are more compact An STL file describes a raw unstructured triangulated surface by the unit normal and vertices of the triangles using a three dimensional Cartesian coordinate system The STL file specifications are at http en wikipedia org wiki STL _ file_format TIN files are used for storing triangulated irregular networks using a simple set of xyz coordinates The TIN file specifications are at http www ems i com wmshelp Files File_Formats TIN_Files htm The project may have at the same time multiple Background Layers virtually any number
264. n multiple ways using a three points on its circumference b a center a radius two angles starting and final angle and its orientation or c by two points a center and a radius Again arcs can be entered either graphically using a cursor most common or using the New Line dialog window Fig 52 When entering a new arc or circle graphically a user must select the command Insert gt Domain Geometry gt Arc gt Graphically from the menu or one of the following commands a Are by 3 Points b Arc by 2 Points and R or c Arc by Center R and Angle from the Insert Object 108 part of the Domain Geometry version of the Tool Bar at the right side of the View Window and then enters arc using a cursor Graphical definition of Arcs and Circles is rather similar to the definition of Points and Lines Differences occur when Radii or Angles are used to define these objects For example when user defines Arc by 2 Points and Radius he she first needs to define the two points after which both the cursor and the Edit Bar change Fig 51 left for the definition of the third type of information defining the arc This can be a radius an internal angle or a height The selection can be made on the Edit Bar that also displays the magnitude of this variable R A and a step dR dA in which it can be increased xi a Domain Geometry Set new Arc a Numbers for new Curve E xl Point 14 Domain Geometry Set new
265. n the View Orde via 3 Points HER Auxiliary Objects EZ Update Grid and Workspace according to the template dimensidnis Grete via Center and Radius i Dimensions X Sine Comments REMARK A Planar Sut Rect Bitmaps Yau can Move Rotate or Stretch the Background Layer later by commands available in the il Plorar Suface via Rectangle A Cross Sections main menu or in the popup menu in Navigator Data Tree Solid Brick Mesh Lines ED Solid Boundary Surfaces Be Backgr yna yA E 1 WP New Background Layer Cancel zea Conert P TE Transform Object a fr od FEC Intersect Lines esults Ot Project Information 2 Insert Points on Line T 2S Spit Line Help a Ka How to Edit Domain 1a Check Domain Definition gt Next FE Mesh Ee Data 6x View amp Sections Geometry FEMesh FA Domain Properties Ga Initial Conditions Boundary Conditions M Resuts R Tools Inserts a Background Layer a DXF drawing or other formats that can be used as a template for graphical input Figure 93 An example of the Background Layer E New Background No Name 1 Source File File Type HYDAUS project h3d h3d2 DXF points and lines dxf STL Unstructured triangulated surface ASCII stl TIN Triangulated irregular network tin BMP Bitmap bmp File Path m Target Position and Transformations Make visible in View REMARK mai
266. n the tab Integrated Objects and in the edit box Points insert a list of integrated points it is possible to do a graphical selection Generated 3D FE Mesh will then have some of its nodes located exactly in points with imported values thereby achieving a higher accuracy when interpolating values to the rest of the FE Mesh nodes 2D General domain The procedure is the same as in item 2 above except instead of 3D points we have 2D points which will be integrated into Surfaces 2D Simple a 3D Simple Here the situation is quite difficult because the locations of FE Mesh nodes can be defined only using coordinates in the tables for generating structured FE Mesh 207 208 7 Graphical Output Graphical output is divided into two main parts In the first part variables which change spatially throughout the transport domain are displayed by means of contour maps isolines isosurfaces or isobands Results Graphical Display on the Data Tab of the Navigator Bar or Options gt Graph Type Additional information such as boundary fluxes and or soil hydraulic properties are displayed using x y graphs Results Other Information on the Data Tab of the Navigator Bar or using the Results Menu 7 1 Results Graphical Display Results of a simulation can be displayed by means of contour maps isolines isobands isosurfaces color points color edges spectral maps and or velocity vectors Graph Type at the View Tab of the
267. n yariables sre eena sata a ha teionsaam dan et erie otis 47 Time Step Control variables 20 ie Be A BES ee eS 52 Soil hydraulic parameters for the analytical functions of van Genuchten 1980 for twelve textural classes of the USDA soil textural triangle according to Carsel and Parrish 1988 ie a A N BEE OE AAO 57 Soil hydraulic parameters for the analytical functions of van Genuchten 1980 for twelve textural classes of the USDA textural triangle as obtained with the Rosetta Lite program Schaap et al 2001 ooeeseeeeeeeeesseesseesseseesesseserssressessresressersreseesseesese 57 Soil hydraulic parameters for the analytical functions of Brooks and Corey 1964 for twelve textural classes of the USDA soil textural triangle according to Carsel and PGPFFISH TOSS sete hd Scots eh See E EAE E AEE A E EEE EE O cod oleh 58 Soil hydraulic parameters for the analytical functions of Kosugi 1996 for twelve textural classes of the USDA soil textural triangle eee eeeceeeeeceeeteceeeteeeenteeeenaeeees 58 Comparison of CW2D and CWM1 components 0 eeecceeeeeeeceseeeeeeeeeeeeeeenaeeeenaeeees 87 Comparison of CW2D and CWM1 processes ceeeesseeeseceseeeseeesneecaeceaeenseeeeneees 88 Kinetic parameters in the CW2D biokinetic model Langergraber and Simunek DENY ots srs caatenus a oe sae Ea rill is ta meets haa hagas dead A ducal eel clade d yaa 90 Kinetic parameters in the CWM1 biokinetic model Langergraber et al 2009
268. nal computational domain that is formed either by the base surface and thickness vectors 3D Layered Solids or boundary surfaces 3D General Solids which can be either planar or curved e g Quadrangle Rotary Pipe or B Spline Computational Domain A Computational Domain is a continuous part of a two or three dimensional space for which water flow or solute transport is simulated The Domain Geometry term relates to the shape of this space The Domain Geometry can be defined for simple cases using parameters using a Generalized Rectangle in 2D projects or a Generalized Hexahedral in 3D projects and for general cases using boundaries boundary curves for two dimensional domains and boundary surfaces for three dimensional domains 103 In the 3D Standard version the Geometry is defined using the Base Surface which is a 2D domain of an arbitrary shape and a set of Thickness Vectors that define the variable thickness of the 3D domain or thicknesses of an arbitrary number of Geo Layers the term Sublayers was used in version 1 and is used alternatively in the text below Such domain is then called the 3D Layered domain Although such domains cannot be fully general they allow definition of a majority of realistic 3D problems In the 3D Professional version the Geometry is defined using three dimensional objects Solids bodies of general shapes which are formed by boundary surfaces which can be either planar or curved A Comput
269. napping to already existing objects points 2 Numerically Objects can be entered numerically by defining their X Y and Z coordinates and indexes in a dialog window The dialog is obtained by using the Menu command Insert gt Domain Geometry or the Navigator Bar command Data Tab gt Domain Geometry and selecting the desired object type with a click of the right mouse button and the New command 3 Import from a File Particular objects with a large number of nodes spline polyline or the entire Geometry can be read from the text file using several formats More detailed information is at Read points from a text file and Import Geometry from a Text File The order of inputting particular objects is arbitrary 2 Definition a Surfaces 123 Boundary Curves do not yet form the Computational Domain The Computational Domain is formed using one or more Surfaces that need to be defined A Surface is defined using a list of Curves that form a closed external boundary A Surface can be defined Graphically by sequentially clicking on particular Boundary Curves or Numerically in a dialog where one can define a list of indexes of Boundary Curves 3 Internal Objects Any surface can have an arbitrary number of Openings Holes Internal Curves or Internal Points Additional information can be found at Internal Objects 4 Openings Each surface can have an arbitrary number of Openings Holes An Opening is defined by an closed interna
270. nd degradation processes in subsurface flow constructed wetlands In the wetland module two biokinetic model formulations can be chosen 1 the biokinetic model as described in CW2D Langergraber and Simunek 2005 2006 2011 and 2 the CWMI1 Constructed Wetland Model 1 biokinetic model Langergraber et al 2009 In CW2D aerobic and anoxic transformation and degradation processes for organic matter nitrogen and phosphorus are described whereas in CWM1 aerobic anoxic and anaerobic processes for organic matter nitrogen and sulphur The Major Ion Chemistry Module UNSATCHEM im nek and Suarez 1994 can be used instead of the standard solute transport module Detailed description of the UNSATCHEM Module is given in the UNSATCHEM user manual im nek et al 2012c More detailed description of concepts used in the UNSATCHEM module is provided in the HYDRUS 1D manual im nek et al 2008 which provides all relevant information about the one dimensional version of this module The C Ride module simulates two dimensional variably saturated water flow colloid transport and colloid facilitated solute transport in porous media The module accounts for transient variably saturated water flow and for both colloid and solute movement due to advection diffusion and dispersion as well as for solute movement facilitated by colloid transport Detailed description of the C Ride Module is given in the C Ride user manual im nek et al 20
271. nd their data Figs 2 and 3 Print Ctrl P Prints the content of the View window Navigator Window Displays or hides the Navigator Window Edit Bar Displays or hides the Edit Bar b Tools Toolbar 2 a ae a A Undo Reverses the last edit actions Redo Repeats the last edit actions Tools for Selection Select by Rhomboid Selects objects using rhomboid Select by Circle Selects objects using circle Select by Polygon Selects objects using polygon Add to Selection Add additional objects to existing selection Remove from Selection Remove objects from existing selection Standard Selection Mode Grid and Work Plane Settings Calls the Grid and Work Plane dialog window Fig 147 Show Grid Shows a Work Plane axis and origin of the grid in the View window Set Grid Origin Redefines the origin of the grid Snap to Grid Mouse moves in steps given by the grid Set XY Work Plane Sets Work Plane to the XY plane Set YZ Work Plane Sets Work Plane to the YZ plane Set XZ Work Plane Sets Work Plane to the XZ plane c View Toolbar CARa EE are g E 243 Rotate View Scroll View Zoom View Allows objects in the View windows to be rotated using the mouse while holding the left mouse button Allows moving scrolling of objects in the View window using the mouse while holding the left mouse button Allows zooming of objects in the View window using the mouse while holding the left mouse button Similar functions ca
272. nd then solved using either Gaussian elimination or the conjugate gradient method After solving the matrix equation the coefficients are re evaluated using this solution and the new equations are again solved The iterative process continues until a satisfactory degree of convergence is obtained i e until for all nodes in the saturated unsaturated region the absolute change in pressure head water content between two successive iterations becomes less than some small value determined by the imposed absolute Pressure Head or Water Content Tolerance The first estimate at zero iteration of the unknown pressure heads at each time step is obtained by extrapolation from the pressure head values at the previous two time levels Iteration Criteria Iteration Criteria Maximum Number of Iterations Water Content Tolerance Pressure Head Tolerance cm Time Step Control Lower Optimal Iteration Range Upper Optimal Iteration Range Lower Time Step Multiplication Factor Upper Time Step Multiplication Factor Internal Interpolation T ables Lower Limit of the Tension Interval crm Upper Limit of the Tension Interval crm Initial Condition In Pressure Heads In Water Contents Figure 17 The Iteration Criteria dialog window In the Iteration Criteria part of the dialog window one specifies the maximum number of iterations during one time step and the water content and pressure
273. nded to create FE nodes exactly in the points with measured values This task depends on the type of the domain 1 3D Layered Domain Here we recommend that you first import the projection of the points locations to the Base Surface Points obtained in this way will then become Internal Points of the Base Surface and FE nodes generated in other layers above these base points will then be very close to locations with imported values thereby increasing the accuracy of interpolated values In practice this can be done as follows assuming that the Base Surface lies in the x y plane and its z 0 A Make a copy of the file with coordinates of points with imported values and values themselves prepared for the import of values and delete the last column values B In HYDRUS use the command File gt Import gt Import Points from Text File and read points coordinates from this file C You will need to move imported points to the Base Surface Select all imported points press Alt Enter and in the dialog for editing points set z 0 3D General Domain Here it is possible to make the points with imported values to be directly part of the FE mesh as follows A Import the 3D points as described in item 1 above but omit the projection to the Base Surface item 1C above B Include the imported points into the Solids that form the Computational Domain as Integrated Points Click on the Solid either in View or Navigator ope
274. nent O Two Surfaces Intersection Curve Two Solids 8 A Intersecting Objects Intersecting Objects Pe i Surface A No il a Solid A No 4 Pi SufaceB No 2 gt Solid B No 5 Pic Lines generated by the intersection J Lines generated by the intersection A Surface2 Pipe Surfaces generated by the intersection Surfaces generated by the intersection Solid A Comment Surface Planar Comment Figure 84 The Edit Intersection dialog window for two Surfaces left and two Solids right 143 A Partial or Component Surface Fig 85 is created by an Intersection of Surfaces or Solids which divides an original Surface into smaller Sub Surfaces or the so called Component Surfaces Although this Surface has its own number and can be used to define for example a Solid its shape and boundaries are defined generated by the shape of its original Surface and a given Intersection A list of Components resulting from division of the original Surface by an Intersection can be found on the Tab Components Inte cre ctim af SURFACES Figure 85 An example of an Intersection of two Surfaces and a resulting Partial Surface and Intersection Curve 144 4 7 Auxiliary Objects In addition to objects that define the computational domain the HYDRUS GUI allows users to employ several Auxiliary Objects that can be used to for example add Dimensions to the computat
275. next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 47 left The Edit Bar will also show which point its number is being defined and what reference coordinate system the current coordinate system or the grid origin is used The process of defining new points is ended by pressing the Esc keyboard button the right mouse button see the Help part of the Edit Bar or clicking the Stop button on the Edit Bar x a Domain Geometry Set new Line a xl Numbers for new a Domain Geometry DESE E Set new Point a Point 5 Number for new Point Coordinates x 319 40 cm Coordinates zZ 520 15 cm x 568 66 cm Z 335 08 cm Ref Coord System Current CS Ref Coord System Grid Origin Current CS O Last Point Grid Origin Apply Stop Help a Help a Ke Step 1 of 2 ire Sann Pork pone point of the new K Press Esc or right mouse i F baomer EA Ke Press Esc or right mouse button to end the tool Figure 47 The Edit Bar during the process of defining graphically a new point left and a new line right Double clicking on an existing point will recall the Edit Point dialog window Fig 48 In addition to the General Tab Fig 48 left in the New Point dialog window the Edit Point dialog window has also the FE Mesh Tab Fig 48 right Coordinates of a point and its number are entered in the General Tab while the FE Mes
276. ng of its shape see Figs 69 and 70 bA HYDRUS Test Domain Geometry C Eile Edit wiew Insert Calculation Results Tools Options Window Help Lees 228 aleli alae See Az Geometry aA FE Mesh Domain Pro g Initial Condit A Boundary C o Results For Help press F1 System Default Figure 69 An example of internal objects 126 bA HYDRUS Test Domain Geometry C Eile Edit wiew Insert Calculation Results Tools Options Window Help X Denas HS sea amn eles F A Geometry aA FE Mesh Domain Pro Initial Condit A Boundary C 000 Results For Help press F1 System Default Ph Figure 70 An example of an Upper Surface definition using Internal Curves and Thickness Vectors There are several rules that must be followed when defining Internal Objects e An Internal Curve must be entirely within a Computational Domain e An Internal Curve can touch but can not intersect the outside boundary of a parent Surface at its definition points definition points of its boundary curves e An Internal Curve can be open or closed and can intersect itself provided that the intersect occurs at a definition point of an Internal Curve An Internal Curve or an Opening must lie entirely inside of the parent Surface Common reasons why a Curve or an Opening are not automatically integrated into a Surface is that there exist small deviations between them and a Surface that are not visible but are larger than allowed to
277. ng to Delaunay criterion Corrects possible errors which may appear during smoothing and retriangulating Smoothes the mesh by solving a set of coupled elliptic equations using a recursive algorithm Carries out calculations for the currently active project Carries out calculations for all currently open projects Opens the Project Manager to select projects to be calculated Displays results in terms of pressure heads Displays results in terms of water contents Displays results in terms of velocities Displays results in terms of concentrations Displays results in terms of nonequilibrium concentrations kinetically sorbed or in the immobile water Displays results in terms of temperatures Graphical presentation of pressure heads at different boundaries and in the root zone Graphical presentation of potential and actual boundary water fluxes at different boundaries Graphical presentation of potential and actual cumulative boundary water fluxes Graphical presentation of actual and cumulative boundary solute fluxes Graphical presentation of changes in water content pressure head temperature and or solute and sorbed concentration at specified observation nodes Graphical presentation of the soil hydraulic properties 265 Run Time Information Mass Balance Information Chemical Mass Balance Information Convert Output to ASCII Inverse Solution Results Fluxes across Mesh Lines HP2 Text Output Time Layer Firs
278. nimum and maximum values of a particular variable and then leaves the scale invariant in time between these two values The scale however can also be automatically adjusted for each time level by specifying the minimum and maximum values for a particular variable and a particular print time when the option Min Max glob in time from the Color Scale View Options of the View Tab of the Navigator Bar is deselected Similarly the scale can be automatically adjusted for a particular layer of the FE mesh a section the minimum and maximum values for a particular variable and a particular section when the option Min Max glob in space from the Color Scale View Options of the View Tab of the Navigator Bar is unselected 217 After clicking on the color panel with the left mouse button the Color dialog window Fig 140 appears in which one can redefine colors to be used in displays By default a Standard Palette is used If a Custom Scale exists for a displayed variable colors for this scale will be displayed even when Standard Scale was currently used since the Standard Scale can not be edited Palettes with newly defined colors can be saved Save Palette under a new name and used for different purposes The new palette can be saved locally and used with the given application or globally and used for all HYDRUS applications Users hence can in this way define different palettes for displaying water contents pressure heads concentrations or temper
279. ns are again solved This iterative process continues until a satisfactory degree of convergence is obtained i e until at all nodes the absolute change in concentration between two successive iterations becomes less than some concentration tolerance defined in HYDRUS as the sum of an Absolute Concentration Tolerance and the product of the concentration and a Relative Concentration Tolerance the recommended and default value is 0 001 The Maximum Number of Iterations allowed during a certain time step needs to be specified recommended value is 10 When the Maximum Number of Iterations is reached then the numerical solution is either a terminated for problems involving transient water flow or b restarted with a reduced time step for steady state flow problems e Initial Conditions Initial Conditions can be specified either using liquid phase concentrations in units of mass of solute M per volume of water M Lv or using total concentrations in units of mass of solute per volume of soil M L In the latter case the liquid phase concentration is calculated from the total concentration depending on the distribution coefficients e g Ka or Henry s constant between different phases Rather then specifying directly the initial values of the nonequilibrium phase concentrations e g concentrations in the immobile water for the dual porosity models or concentrations kinetically sorbed to the solid phase for the two site sorption model
280. nsor K and Ky together with the angle w between the principal direction of K and the x axis of the global coordinate system for each element Fig 21 Edit Local Anisotrophy Local Anisotrophy Angle and Components Number of Selected Elements 1 Angle 0 Specify All Components Simultaneously Component 1 1 Component 2 1 Figure 21 The Edit Local Anisotropy dialog window for two dimensional applications This has been simplified for three dimensional problems where user can specify one or more Tensors of Anisotropy Fig 22 which may be assigned to different parts of the transport domain The anisotropy tensor is defined by three principal components K ConAX Ky ConAY and K ConAZ and six coefficients aij that represent the cosine of angles between the ith principal direction of the tensor K and the j axis of the global coordinate system 1 e Cos X x Cos Y y Cos Z y Cos X y Cos X z Cos Y z Tensors of Anisotropy Tensors of Anisotropy for Hydraulic Conductivity Number of Tensors of Anisotropy 1 niz CondX Con Y Con Z Cosf lt x CosfY y Cos Z z Cos lt y Cos lt z 1 1 1 1 1 1 1 D Previous Figure 22 The Tensors of the Anisotropy dialog window 60 3 10 Solute Transport Basic information needed for defining solute transport problem are entered in the Solute Transport dialog window Fig 23 In this window users specify the Sp
281. nt mesh Alternatively a more general two dimensional geometry can be defined from basic boundary objects such as points lines splines polylines arcs and or circles Boundary curves can consist of any combination of polylines arcs circles or cubical splines The program permits one to specify internal boundaries e g drains wells impermeable objects as well as internal curves A user can define from these boundary objects either a two dimensional transport domain the base plane base surface of the three dimensional layered domain or multiple surfaces that can then define the three dimensional general domain In the former two cases the two dimensional transport domain or the base plane of the three dimensional domain is discretized into an unstructured finite element mesh 4 1 Boundary Objects The computational domain the two dimensional transport domain or the base surface of the three dimensional domain is formed by an arbitrary number of mutually nonintersecting curves Each curve can be formed by connecting an arbitrary number of objects Objects are defined by nodes the positions of which can be specified either graphically with the mouse with possibilities to use grid alignment Fig 147 or by numerically defining their coordinates X Y and Z It is also possible to read in the objects with a large number of nodes spline polyline from a file containing the x y and z coordinates for each node using the command Inser
282. nt view or in a different open project The operation terminates by holding the Esc button or by clicking the right mouse button Drag and Drop can be used for most geometric objects but also for auxiliary objects such as comments labels and bitmaps Holding the Shift button during the Drag and Drop operation leads to movement of selected objects in a direction perpendicular to the current Working Plane available only for three dimensional objects 8 1 8 Sections Sections serve do divide complex objects models into simpler parts Only the simpler parts are then displayed in the View window while the remaining parts are hidden Two types of sections exists those for geometric objects Geo Sections and those for the FE Mesh FE Mesh Sections see also Section 5 7 and Table 19 New sections for both types can be created and named a list of which is displayed on the Section Tab of the Navigator Bar Clicking on the Section of the Navigator Bar causes the Section to be displayed in the View window Multiple Sections can be displayed simultaneously by holding the Shift button during the selection Undesired to be displayed parts can be cut off and hidden from the View window using the Cut with Rectangle command This leads to a temporary section that is remembered by the program and renewed after the project is closed and reopened New sections can be named and listed in the Navigator Bar by using commands to create new sections The s
283. ntains three tabs Fig 183 In the General Tab a user selects whether the content of the View window Picture is to be printed with or without a Legend Page Orientation Portrait or Landscape and Page Margins In the Picture Tab users further select Print Quality the Standard print quality which can be changed by users is 5 000 5 000 pixels whether the Frame is to be printed in black or color Colors and Frame and Text Size Finally in the Legend Tab users select what texts Legend Rows are to be printed with what Font and how far from the picture Users can use a predefined text or can write their own Print Options Print Options a General Picture Legend General Picture Legend Print Page Orientation Print Quality Colors and Frame Portrait Landscape Page Margins i Draw Frame f DERE Lines and Text Black Max 5000 x 5000 pixels O User Defined All Colored ao Text Size Symbol Size and Line Width Top Proportional to Picture Size Proportional to Picture Size Right I Constant O Constant Facto 100 Factor Default Print Options General Picture Legend Legend Rows Row Text Content i M Project 000 Project Info he FE Mesh Picture Desc o o Text Size Height 4002 mm 0 00 mm Font Default OK Cancel Help Figure 183 The G
284. nts applied to a Circular or a Rectangular Point a Line with a given FE size or a number of points to a Surface and to a Solid 174 5 5 Unstructured Finite Element Mesh Generator MeshGen2D The MeshGen2D module may be used to discretize a two dimensional flow region or a base plane of the three dimensional domain into an unstructured triangular mesh The algorithm used for this purpose is general and can be applied to virtually any two dimensional computational domain The first step of the mesh generation process discretizes the boundary curves while the second step generates the unstructured triangular mesh Generation of Boundary Points The first step of the mesh generation process involves discretization of the boundary curves During this step boundary nodes are generated on all boundaries and internal curves by dividing them in abscissas i e short boundary edges If no previous boundary nodes existed the program automatically generates a default equidistant point distribution Boundary nodes can be edited by users to optimize the lengths of the boundary edges using the FE Mesh Parameters dialog window Figs 98 through 104 The local density of the mesh can thereby be determined in any part of the domain also taking into account the use of internal curves There are two ways to obtain appropriate distributions of the boundary nodes i e by 1 specifying the Targeted FE size Figs 98 the Main Tab and 2 refining the FE M
285. o M Sakai and M Th van Genuchten The HYDRUS 1D Software Package for Simulating the Movement of Water Heat and Multiple Solutes in Variably Saturated Porous Media Version 4 0 HYDRUS Software Series 3 Department of Environmental Sciences University of California Riverside Riverside California USA pp 315 2008 303 im nek J M Th van Genuchten and M ejna Development and applications of the HYDRUS and STANMOD software packages and related codes Vadose Zone Journal doi 10 2136 VZJ2007 0077 Special Issue Vadose Zone Modeling 7 2 587 600 2008 im nek J and J W Hopmans Modeling compensated root water and nutrient uptake Ecological Modeling doi 10 1016 j ecolmodel 2008 11 004 220 4 505 521 2009 im nek J D Jacques M ejna and M Th van Genuchten The HP2 Program for HYDRUS 2D 3D A Coupled Code for Simulating Two Dimensional Variably Saturated Water Flow Heat Transport and Biogeochemistry in Porous Media Version 1 0 PC Progress Prague Czech Republic 71 pp 2012a im nek J M ejna S A Bradford and M Th van Genuchten The C Ride Module for HYDRUS 2D 3D Simulating Two Dimensional Colloid Facilitated Solute Transport in Variably Saturated Media Version 1 0 PC Progress Prague Czech Republic 43 pp 2012b im nek J M ejna and M Th van Genuchten The UNSATCHEM Module for HYDRUS 2D 3D Simulating Two Dimensional Movement of and Reactions Between Major
286. of 2 Set thickness of the new Select a Surface to extrude Solid Ke Press Esc or right mouse gt Press Esc or right mouse button to end the tool button to end the tool Figure 74 The Edit Bar during the process of graphically defining a Solid by extruding a Base Surface Selection of a Surface left and definition of a Thickness Vector right A Solid can be created graphically nsert gt Domain Geometry gt Solid gt Graphically from the menu or alternatively the command Solid Extruded on the Insert Object part of the Domain Geometry version of the Tool Bar by clicking on one point defining the Base Surface and extruding the base to form a three dimensional solid During the first part of the operation the Edit bar Fig 74 left displays numbers for a Solid a Thickness Vector a Point and a Surface while during the second part it Fig 74 right displays the Thickness Vector length and increment and in which direction it is created a Perpendicular to the Base Surface b in X direction c in Y direction or d in Z direction A user should during the first step select click 131 on the Base Surface that is to be used to define the Solid It is also possible to click on any Point that defines the Base Surface The second step depends on whether Thickness Vectors are already defined in Points of the Base Surface If they are they are used to define the Solid and the second step is not done If they are not the thicknes
287. oint of both curves must be a part of the Geometry This point can be found automatically using commands Intersect Lines Tools gt Intersect Lines or Intersect Lines from the Edit Bar or Repair Geometry Tools gt Repair Geometry 2 Curves cannot lie upon each other 3 Multiple points can not be defined at the same location A frequent error is when initial and final points of a curve are defined at the same location The curve is then not closed and a surface can not be defined using this curve Initial and final points of a closed curve must be defined using the same point 124 4 A point cannot lie on a curve without being its definition point All above mentioned errors in definition of the Geometry can be automatically solved using the command Repair Geometry Tools gt Repair Geometry 6 Contrary to the old HYDRUS 2D program the number of Surfaces is virtually unlimited up to 30 000 Surfaces can touch each other in a point or on a boundary line or one Surface can lie inside of the other Surface In this case one needs to first create an internal Hole in the first Surface and then insert the second Surface into this hole This process can be recursive i e it is possible to crease a Hole in the internal Surface and insert an additional Surface there When defining a new Surface graphically e g using a rectangle HYDRUS recognizes when the new Surface is located inside of the existing Surface and automatically offers t
288. omewhat different format HYDRUS will automatically detects that and loads the correct values from the block TABLE_01 NODAL INFORMATION Data in columns can be entered in free format a column width is not fixed spaces tabs and semicolons can be used as column separators Points in which values are defined should not overlap nor should be very close to each other The best way is to use points in a regular grid 2D or 3D covering the entire computational domain The minimum number of points is 3 for 2D domains and 4 for 3D domains The points must be linearly independent i e they cannot lie in a straight line 2D or in a plane 3D The maximum number of points is not limited but an excessive number of points gt 10 000 may lead to extremely long calculation linear interpolation of values for generally located nodes requires relatively complex geometric calculations or to other problems Once the text file is read by the GUI a dialog window Import of Values from Scattered Points shows up a This window first summarizes imported information in the top section Imported Values i e the number of imported points minimum and maximum values and minimum and maximum x y and z coordinates for points with given values Users can then select whether or not a Linear interpolation of values or a Linear interpolation extrapolation of values should be done when transferring values from Scattered Points to the FE
289. on dialog window Again one needs to specify the number of nodes Count on the horizontal Horizontal Discretization in X Horizontal Discretization in Y and vertical Vertical Discretization in Z Direction sides of the hexahedral region and their nodal coordinates Fig 97 The relative size of finite elements on the vertical side can again be modified using RS1 relative size at the top and RS2 relative size at the bottom factors General Vertical Coordinates The vertical final element sizes are then proportionally distributed Any possible vertical deviations from the plane parallel with the bottom of the domain can be defined using the dz values in the Horizontal Discretization in X and Horizontal Discretization in Y parts of the window This feature still allows relatively general domains too be created see Fig 9 158 Hexahedral Domain Space Discretization Horizontal Discretization in x 0 00 250 00 500 00 750 00 0 00 0 00 0 00 0 00 0 00 100 00 20000 30000 40000 500 00 0 00 0 00 0 00 0 00 0 00 0 00 gt Generate Vertical Coordinates Set relative size of finite elements RS1 Generate RS2 Figure 97 The Hexahedral Domain Discretization dialog window 159 5 3 Unstructured Finite Element Mesh Parameters Parameters for generating the Unstructured Finite Element Mesh are specified in the FE Mesh Parameters dialog window Figs 98 through
290. only for a single solute not for multiple solutes Details about the root water and solute uptake can be found in the Technical Manual or Simiinek and Hopmans 2009 78 3 19 Root Water Uptake Parameters Parameters for the water and salinity stress response functions are specified in the Root Water Uptake Parameters dialog window Fig 34 and Fig 35 respectively Root Water Uptake Parameters Feddes Parameters PO Pot 2 P2H Pa 800 K P3 20 800 Cancel r2L Database Previous Previous Figure 34 The Root Water Uptake Parameters dialog window for the water stress response function of Feddes et al 1978 left and van Genuchten 1985 right The Root Water Uptake Parameters for the water stress response function suggested by Feddes et al 1978 Fig 34 left are described in detail in the HYDRUS technical manual Water uptake in this model is assumed to be zero close to saturation i e wetter than some arbitrary anaerobiosis point P0 Root water uptake is also zero for pressure heads less more negative than the wilting point P3 Water uptake is considered optimal between pressure heads Popt and P2 whereas for pressure heads between P2 and P3 or PO and Popt water uptake decreases or increases linearly with pressure head PO Value of the pressure head L below which roots start to extract water from the soil POpt Value of the pressure head
291. onse function associated with salinity stress L Root water uptake at this osmotic head is reduced by 50 Both salinity stress response functions require a coefficient Osmotic Coefficient that transforms concentrations into equivalent osmotic pressure heads Fig 35 The osmotic coefficients should be negative for the additive model to be added to negative pressure heads and positive for the multiplicative model Note that this conversion needs to be made mainly when one uses the Additive Model That is because then one needs to add pressure heads i e units of m or cm and osmotic heads calculated from concentrations which likely have units of dS m If one uses the Multiplicative Model then one does not need to use this conversion and can keep Osm Coeff equal to one since a both water stress and salinity stress response functions can have their own units and b both the Threshold Model parameters specified above and selected concentrations units are likely already the same e g units of EC dS m A database of suggested values for different plants for the threshold slope salinity stress model is provided based on the work by Maas 1990 The database for the threshold model provides suggested values based on the electric conductivity of the saturation extract EC in dS m These values are converted internally in the GUI into the electric conductivity of soil water at the field capacity as follows EC ke EC where ke is appr
292. op and general bottom two dimensional geometries 35 Figure 9 Example of a hexahedral three dimensional geometry 2D Domain Options Two dimensional flow and transport can occur in a horizontal or vertical plane or in an axisymmetrical quasi three dimensional transport domain When a three dimensional axisymmetrical system is selected the z coordinate must coincide with the vertical axis of symmetry A typical example of the selected 2D or 3D geometry is shown in the preview part of the dialog window The simple geometries are defined in the Rectangular Fig 10 or Hexahedral Domain Definition Fig 11 dialog windows for two dimensional and three dimensional problems respectively In each of these windows users need to specify the vertical and horizontal dimensions of the transport domain as well as a possible slope of the base of the domain in different directions if applicable a is in the x direction and is in the y direction The preview in the middle of the dialog window of a simple example showing all geometry parameters should help users in specifying their desired transport domain Dimensions and Slope Rectangular Domain Definition Dimensions Lx 1000 00 Lz 200 00 Slope o Previous Figure 10 The Rectangular Domain Definition dialog window 36 Hexahedral Domain Definition Dimensions Lx 1000 00 1000 00 200 00 Figu
293. or Estimating the Hydraulic Properties of Unsaturated Soils University of California Riverside CA pp 233 248 1992 Maas E V Crop salt tolerance In K K Tanji ed Agricultural Salinity Assessment and Management ASCE Manuals and Reports on Engineering practice No 71 NY 1990 McNeal B L Prediction of the effect of mixed salt solutions on soil hydraulic conductivity Soil Sci Soc Amer Proc 32 190 193 1968 Millington R J and J M Quirk Permeability of porous solids Trans Faraday Soc 57 1200 1207 1961 Moldrup P T Olesen D E Rolston and T Yamaguchi Modeling diffusion and reaction in soils VII Predicting gas and ion diffusivity in undisturbed and sieved soils Soil Sci 162 9 632 640 1997 302 Moldrup P T Olesen J Gamst P Schjgnning T Yamaguchi and D E Rolston Predicting the gas diffusion coefficient in repacked soil water induced linear reduction model Soil Sci Soc Am J 64 1588 1594 2000 Parkhurst D L and C A J Appelo User s guide to PHREEQC Version 2 A computer program for speciation batch reaction one dimensional transport and inverse geochemical calculations Water Resources Investigations Report 99 4259 Denver Co USA 1999 Perrochet P and D Berod Stability of the standard Crank Nicolson Galerkin scheme applied to the diffusion convection equation some new insights Water Resour Res 29 9 3291 3297 1993 Rawls W J D L
294. or report before applying for a new activation code Do you want to save the error report Press Yes to save the error report Press No to cancel the activation if you know that you used an incorrect activation code HYDRUS 2 x a xi i Would you like to send the report by e mail or to save it to a file Press Yes to e mail the report as an attachment to your HYDRUS reseller and or to support pc progress cz Press No to save the report Figure 177 Window reporting a failure of HYDRUS authorization 9 2 3 Reinstallation Moving to another Computer With a single user license you are eligible to install and use HYDRUS on two computers for example a computer in your office and your notebook If you reinstall HYDRUS on an activated computer or if you install a newer HYDRUS version then your previous authorization will remain active 286 Deactivation of HYDRUS and or Reinstallation to another computer Users should deactivate HYDRUS before a any hardware change motherboard hard drives graphic card BIOS etc b reinstallation of the Windows OS c reformatting the hard drive with HYDRUS d changing the network path to HYDRUS applies to the network installation and e moving HYDRUS license to another computer The HYDRUS software package is deactivated using the HYDRUS Authorization Status dialog window Fig 165 that is called using the command Help gt Hydrus License and Activation Similarly as for HYDRUS a
295. ordinates are to be changed 110 New line General Circle General Circle Curve No Circle No 5 z Curve Type Definition Points List of Points 1 3 Comment Circle Center Circle Parameters x 50 00 em r 50 25 em Y 500 em z 000 em Figure 53 The New Line Circle dialog window 4 1 4 Curves and Splines The term Curve is used in the program and its documentation in two ways while the meaning depends on where it is used 1 The term Curve is a general term for objects Line Polyline Arc Circle Spline 2 The term Curve can also refer to multiple objects ad 1 connected in their boundary points This meaning of the term Curve is mainly used in connection with Boundary Curve Internal Curve and so on There are several rules that need to be followed during the definition of a Curve e Curves cannot intersect each other or themselves except at their definition nodes e No point that is not either its definition or Parametric Point can lie on a Curve Curves are always defined using their definition points their indexes The list of indexes can be checked or changed using the Edit Curve dialog the first Tab General A Spline is a set of more than 2 points connected smoothly by cubic arcs Splines are general smoothed curves defined using points in the 2D or 3D space Three dimensional splines do not genera
296. ork Plane Origin Point No __ 0 00 em 0 00 em 0 00 em Grid Options Grid Type Number of Grid Points Snap Cartesian Show O Polar Direction 1 30 30 Direction 2 30 30 C Dynamic update Grid Point Spacing Distance b 50 00 em Distance h 50 00 cm Rotation oog l Figure 147 The Grid and Work Plane dialog window 228 8 1 3 Stretching Factors In many applications one direction of the transport domain dominates the other direction or the other two directions To facilitate work in the graphical environment HYDRUS allows stretching of the domain in one or two direction s using Stretching Factors This is done using the View Stretching Factors dialog window Fig 148 that is called with the command View gt View Stretching View Stretching Factors Stretching Factors InX direction 1 In Y direction a Factors InZ direction 0 0217391 2 A No Method for Calculation of Stretching Factors Strict All non uniform dimensions will be stretched Fx Dmin Dx Mild Only extremal dimensions will be stretched if Dx lt Dmin N Fx 1 else Fx Dmin N Dx or if Dx gt Dmax N Fx 1 else Fx Drmax N Dx where N 5 Figure 148 The View Stretching Factors dialog window Two options of View Stretching are available a Strict Stretching when all transport domain dimensions will be
297. ossible to adjust the Display of the Scene using the mouse scroll wheel as follows e Simultaneously holding the mouse scroll wheel and moving the mouse will move the Scene in the same direction as the mouse i e to the left right up or down e Simultaneously holding the Ctrl keyboard button and the mouse scroll wheel while moving the mouse rotates the Scene around the center of the displayed object available only for three dimensional objects e Simultaneously holding the Shift keyboard button and the mouse scroll wheel while moving the mouse leads to zooming in or out of the Scene from the center of the View window e Rotating the scroll wheel up or down while pointing the mouse to a particular point in the View window results in zooming in or out the Scene from this point e Simultaneously holding the right mouse button and the mouse scroll wheel while moving the mouse rotates the Scene around the center of the displayed object available only for three dimensional projects The above described operations are available not only during selection on existing transport domain but also when defining basic geometric objects This allows users to adjust the View window as needed without interrupting the process of graphically defining objects of the transport domain b Commands to define the Content of the Scene In every view one can independently specify what is to be displayed e g a variable the type of graph or
298. ound Layer dialog window Figure 94 one selects a the format of the imported file i e either HYDRUS formats h3d and h3d2 or DXF STL TIN or BMT formats b units of the imported file c whether or not to place the Background Layer so that its bottom left corner is located in the origin of the coordinate system d whether or not to make the Background Layer visible in the View window and e whether or not the Grid and Workspace settings should be adjusted according to the Background Layer dimensions 150 HYDRUS 2 xx DXF_Test Domain Geometry E File Edit View Inset Calculation Results Tools Option a x SHES e A ees No Name aaanw xl 2 My Background layer zixl Project Dat 4 gt W Project Data DXF Source File drawing to be used as a Template Domenie iwi DXF_Test Insert Object a Bly Project Information G Tmp_Data DXF_Okna 2_1 A2000 CW50 SC 6 15 6 def Browse K Point Domain Geomet n A olenemata Units of Length used in the DXF fie m X lt 7 Une Abaceas Flow and Transport Parameters _ _ XI Line Polyine fll FE Mesh Template Position and Transformations Arc via 3 Points Domain Properties N XU Arc via 2 Points and R i I Initial Conditions Z Move Background Layer so that its bottom left comer is positiobed at the Origin 0 0 0 3S Avia Center Rand Ande eel Boundary Conditions T Make visible i
299. oundary Conditions The following Special Boundary Conditions Fig 119 can be selected from the second tab of the Boundary Condition Options dialog window 1 Gradient Boundary Conditions 2 Subsurface Drip Characteristic Function 3 Surface Drip Irrigation with a Dynamic Evaluation of the Wetted Area 4 Seepage Face with a Specified Pressure Head Gradient Type Boundary Condition Version 1 of HYDRUS implements the Gradient Type Boundary Condition only as the Free Drainage boundary condition or the unit gradient boundary condition However in many situations one needs a non unit gradient BC For example it is difficult to select appropriate boundary conditions for vertical boundaries for flow in a hill slope where the side gradient is more or less parallel with the direction of the slope In version 2 of HYDRUS users can specify a gradient other than one unit gradient This option i e non unit gradient boundary condition needs to be selected from the Special Boundary Conditions tab of the Boundary Conditions Options dialog window Gradients are positive for flow against a particular axis i e from right to left in the x direction and from back to front in the y direction and should be used only or mainly on sides of the transport domain In 3D the gradient BC can be specified only in one direction i e either in x or y direction Subsurface Drip Characteristic Function Infiltration rate of water from a subsurface cavit
300. ow 58 3 8 Neural Network Predictions The HYDRUS code was coupled with the Rosetta Lite DLL Dynamically Linked Library Fig 20 which was independently developed by Marcel Schaap at the U S Salinity Laboratory Schaap et al 2001 Rosetta implements pedotransfer functions PTFs which predict van Genuchten s 1980 water retention parameters and the saturated hydraulic conductivity Ks in a hierarchical manner from soil textural class the soil textural distribution bulk density and one or two water retention points as input Rosetta has its own help features containing all relevant information and references Rosetta provides soil hydraulic parameters for the analytical functions of van Genuchten 1980 for twelve textural classes of the USDA textural triangle Table 8 ee Rosetta Lite v 1 1 June 2003 Select Model Textural classes SSCBD water content at 33 kPa TH33 O Sand Silt and Clay SSC Same water content at 1500 kPa TH1500 Sand Silt Clay and Bulk Density BD Input Output Textural Class Theta r cm3 cm3 0 0737 Sand Theta s em3 cm3 0 4291 Silt Alpha 1 cm 0 0078 Clay nH 1 5577 BD gr cm3 Ks om day 1423 TH33 em3 cem3 Figure 20 The Rosetta Lite Neural Network Predictions dialog window 59 3 9 Anisotropy in the Hydraulic Conductivity For two dimensional problems users may need to specify the principal components of the anisotropy te
301. ow Fig 90 for this purpose Cross Section Description a Son Cross Section P Cross Section Definition Points definition ine A Help x1 0 00 cm 0 00 cm yi 0 00 em 0 00 em ale 0 00 crn 0 00 crn Direction ae lt We gt Cross Section Y Cross Section f Inx Vector 0 00 cm direction Y curve vector intersection Ony 0 00 cm Olnz 0 00 cm Figure 90 The Cross Section dialog window 4 7 5 Mesh Lines Mesh Lines are very similar to Cross Sections except that Mesh Lines follow edges of the finite elements and do not have to be straight They are used similarly to Cross Sections to display selected variables along defined Mesh Lines Similarly to Cross Sections the locations of Mesh Lines are saved and can be recalled at any time 148 Mesh Line Description 1 Meshline to calculate flux Cancel Mesh Nodes for example 1 2 3 4 Help 573 423 302 204 139 248 427 389 311 588 377 102 386 239 172 _ Alow arbitrary indexes not only adjacent nodes Fluxes V Calculate Fluxes across this Mesh Line Figure 91 The Mesh Line dialog window A description of the Mesh Line is given in the Mesh Line dialog window Fig 91 which contains the Mesh Line number its description a list of nodes defining the Mesh Line and whether or not the computational module shoul
302. ox if the hydraulic properties are considered to be temperature dependent Using capillary theory the influence of temperature on the soil water pressure head is then quantitatively predicted from the influence of temperature on surface tension while the influence of temperature on the hydraulic conductivity is predicted from the influence of temperature on viscosity and the density of water Soil Catalog The hydraulic parameters of selected soils were included into a catalog from which users can make selections The van Genuchten parameters were taken from Carsel and Parrish 1988 Table 7 the Brooks and Corey parameters are from Rawls et al 1982 Rawls et al 1982 used multiple linear regression to estimate the Brooks and Corey parameters from a large database of some 2540 soil horizons Their regression equations were subsequently used also by Carsel and Parrish 1988 but the results were further manipulated statistically to get van Genuchten parameters probability density functions superficially the van Genuchten parameters are the same or closely related to the BC parameters such as n lambda 1 Hence the Carsel and Parrish 1988 parameters were statistically derived from the Rawls et al 1982 estimates they were not fitted independently to the Rawls database Some caution is needed when using these parameter values since they only represent very approximate averages for different textural classes The soil hydraulic parameters in th
303. oximately 2 Skaggs et al 2006 Consequently the threshold value of Maas 1990 is multiplied by 2 ke and the slope is divided by 2 A user is responsible for converting these values in the regular HYDRUS further to the osmotic pressure in the head units L or concentration units used in your project For guidance see Eqs 13 3 and 13 4 in Maas 1990 The threshold slope salinity stress model is implemented in the standard HYDRUS solute transport model as R 1 0 01 c c s while in the UNSATCHEM module as R 1 h hyp Ss where cr is the concentration threshold gr is the osmotic head threshold s is the slope in HYDRUS and s is the slope in UNSATCHEM 81 3 20 Root Distribution Parameters The spatial distribution of the roots can be specified using the Root Distribution Parameters dialog window Fig 36 The following two and three dimensional root distribution functions are implemented in HYDRUS Vrugt et al 2001 2002 x Aea b x z N gt ous X y Z gt k k e b x y z 1 X 1 Y 1 Z e d i m where Xm Ym and Zm are the maximum rooting lengths in the x y and z directions L respectively x y and z are distances from the origin of the plant tree in the x y and z directions L respectively px py pz x L y L and z L are empirical parameters x y and z are in Fig 36 indicated as Depth of Naum Intensity or Radius of Maximum Intensity parameters px py and p are assumed to be
304. pecify the Targeted FE Size which will be set as target size of the finite elements for the entire surface or solid EH ecetcs ceecaceunaas g 4 aa HEHEH Figure 110 Refinements on a surface left or solid right 172 New FE Mesh Refinement New FE Mesh Refinement Apply FE Mesh Refinement to Point Rectangular O Line through FE Length O Line through Division O Surface O Solid Parameters Radius 1 900 m Targeted FE Size Innes 0 210 m Outer 0 630 m Current Global Targeted Size of Finite Elements 0 630 m FE mesh Refinement at Point S 20cm R 200cm Apply FE Mesh Refinement to Point Circular Rectangular Line through FE Lenath O Line through Division O Surface O Solid Parameters Side _ Lenath 1 900 Targeted FE Size Global FE Size 50 cm Inner 0 210 m Current Global Targeted Size of Finite Elements 0 630 m FE mesh Refinement at Point S 20cm L 100cm Global FE Size 100 cm Comment Apply FE Mesh Refinement to Point Circular Point Rectangular Line through Division O Surface O Solid Parameters Target FE Length 0 210 m Current Global Targeted Size of Finite Elements 0 630 m ee Ne
305. peration creates the 3D Layered Solid One can do this even when no Thickness Vectors are defined In such case after clicking on the Base Surface a graphical tool is started using which one can extrude the Solid into the space A Thickness Vector is simultaneously created in the Point on the Base Surface that is closest to the location of the click 4 Formation of a Solid A Solid can be further formed using additional Thickness Vectors and Internal Lines 5 Definition of Geo Layers A Solid can be vertically divided into Layers 4 4 3 3D General Solids Solids in the 3D Professional version are defined using boundary Surfaces either Planar see Section 4 2 1 1 or Curved see Section 4 2 1 2 and identified as 3D General Solids In one project one cannot use at the same time 3D General Solids and 3D Layered Solids created in the 3D Standard Version or the parametric blocks created in the 3D Lite Version It is 136 however possible to convert 3D Layered Solids into 3D General Solids by changing the project type from 3D Layered to 3D General Boundary Surfaces of a Solid must enclose a closed space and cannot intersect each other Interior of a Solid must form a three dimensional simply continuous space i e it must be possible to connect any two internal points using a polyline that is entirely located inside of a Solid Boundaries of a Solid thus can be formed by any number of either Planar or Curved Surfaces Figure 77
306. perties and a Rosetta Lite program for generating soil hydraulic properties from textural information The post processing unit consists of simple x y graphs for graphical presentation of the soil hydraulic properties distributions versus time of a particular variable at selected observation points as well as actual or cumulative water and 23 solute fluxes across boundaries of a particular type The post processing unit also includes options to present results of a simulation by means of contour maps isolines isosurfaces spectral maps and velocity vectors and or by animation using both contour and spectral maps E Hydrus 3D FURROW File Edit View Insert Calculation Results Tools Options Window Help Dehee amp a pla PRAAR T m Dike Ren n3 Concentration A Project Data W FURROW P Project Information Pressure Head h cm Gl Domain Geometry 72 851 Flow and Transport Paramete rs se li FE Mesh 2 a Gj Domain Properties 18 775 Material Distribution 5 255 GE Nodal Recharge 8 264 i Scaling Factors 21 783 Gi SF Pressure Head 35 302 Gil SF Hydraulic Condu 48 821 Gl SF Water Content a pa QM Anisotropy troy to ne A Anisotropy Ist Com A Anisotropy 2nd Con Time Layer Subregions k _______________H_H __ Observation Nodes A Geomety GBFE Mesh Domain Proper gad Initial Conditions g Boundary Condi Time 19 65 00 days v 4 Flowing Particles i Initial Conditions EE FURRO
307. ple of the Path file c program files uss hydrus3d mydirect run1 Example of the Path2 file c program files uss hydrus3d mydirect run2 296 9 8 The HyPar Module a parallelized version HyPar is aparallelized version of the standard two dimensional and three dimensional HYDRUS computational modules h2d_calc exe and h3d_calc exe HyPar uses parallel programming tools and techniques to take advantage of multiple cores and to accelerate calculations on multi core processor computers HyPar currently supports only calculations in the direct mode does not support the inverse mode and it does not support any add on modules e g HP2 UnsatChem Wetland and or C Ride The HyPar module is initialized on the Program Tab of the Program Options dialog window Fig 162 The name HYPAR HyPar is an acronym for Hydrus Parallelized The term which has been suggested by Rien is also intended to indicate a Hyper action when a multiple cores of a PC processor work in unison like a bunch of bees The results of the speedup of the HyPar module compared to the standard modules are presented in Table 27 Table 27 A comparison of the HyPar module to standard computational modules System Info Computer HP Elite 7300 Series MT Operating System W7 64 Processor Intel R Core TM i7 2600 CPU 3 40 GHz Number of cores 8 2D Tests Project Name Processes Number of Elements Standard Module HyPar Module Ratio 2DWater1 2D WF 20 k
308. pline is ended by pressing the Esc keyboard button the right mouse button see the Help part of the Edit Bar or clicking the Stop button on the Edit Bar x a Domain Geometry Set new Spline a Numbers for new ma Curve Point 24 Coordinates X 525 37 cm Z 42 54 om Ref Coord System Current CS Grid Origin O Last Point Spline Type Spline OB Spline O Bezier Curve Apply Help Ke Step 4 of N Set next point of the new Spline Ke Press Esc or right mouse button to end the tool Figure 54 The Edit Bar during the process of defining graphically a spline 112 4 1 5 Common Information for a Graphical Input of Objects A A Numerical Input of Values Edit controls displayed on the Edit Bar can be used to enter some values that are difficult to enter graphically as follows Using a mouse one defines an approximate shape of an object Then using a keyboard one enters selected values numerically While entering values using a keyboard one can not move a mouse or entered values will be lost One needs to use the Tab key or Shift Tab keys at the keyboard to move forward of backward from one edit controls to another one respectively A control of Combo Boxes and Radio buttons is done using a standard way as in dialog windows i e using keys Arrow Up or Arrow Down etc After all values are entered one pushes the Enter key to finish the actual s
309. problem is not further shown here 69 Reaction Parameters for Solute 1 Boundary Conditions Reaction Parameters Mat 1 bulk d Disper L Disper T 1 3 1 5 0 Previous Figure 27 The Solute Reaction Parameters dialog window for the UNSATCHEM module The UNSATCHEM Module When the UNSATCHEM module is used the Solute Reaction and transport Parameters are specified in the Solute Reaction Parameters dialog window displayed in Figure 27 instead of Figure 26 which is used for the standard solute transport module The following Soil Specific Parameters are specified for each soil material Bulk d Dw Disper L Disper T CEC Calc SA Dol SA DOC K Ca Mg K Ca Na K Ca K Bulk density p ML Molecular diffusion coefficient in free water D LTH Longitudinal dispersivity Dz L Transverse dispersivity Dr L Cation exchange capacity CEC meq kg Calcite surface area m dm Dolomite surface area m dm Dissolved organic carbon mmol dm Gapon constant for exchange of calcium and magnesium Gapon constant for exchange of calcium and sodium Gapon constant for exchange of calcium and potassium 70 3 13 Temperature Dependence of Solute Reaction Parameters Several of the diffusion D Dg zero order production Ye first order degradation 44 Lis Hg Hw Hs and Lg and adsorption ks kg P 7 coefficients may be strongly dependent upon tempera
310. project in the bottom left corner of the Project Manager Show Old Projects Shows projects created using earlier HYDRUS versions i e either HYDRUS 2D or version 1 0 of HYDRUS 2D 3D Start on Project Groups Page Opens the Project Manager at the Project Groups Tab 29 The commands New and Rename from the Project Tab of the Project Manager dialog window Fig 3 call the Project Information dialog window Fig 4 which contains the Name and Description of the project as well as information about the Project Group name description and pathway to which the project belongs It also contains information whether or not the input and output data are kept permanently in an external directory the radio buttons Temporary is deleted after closing the project and Permanent result files are kept in this directory Fig 4 m Project Information Project Name Description Furrow Water flow from furrow to a drain Project Group Description 2D_Tests Two Dimensional Examples Path C usslK HYDRUS3D 2 0 Examples 2D_Tests Working Directory C ussl HYDRUS3D 2 0 T emp Hydrus3D_2xx Furrow Temporary exists only when the project is open O Permanent remains open when the project is closed Project Manager Figure 4 The Project Information dialog window New Project Group Project Group Name 3D_tests Description Examples of three dimensional problems Directory C ussiHydrus3D
311. ptions dialog window the FE Mesh Tab In the Mesh Limits part of the FE Mesh Tab Fig 163 one can a specify the Recommended maximum number of finite elements for 2D projects b specify the Recommended maximum number of finite elements for 3D projects In the Export Options part of the FE Mesh Tab one can select various export options such as a whether to Export intermediate points on boundary curves 273 b whether to Include internal curves in Boundary Information Table and c whether to Write Description Tables Finally in the Preferred Generator for 2D Meshes part of the FE Mesh Tab one can select whether to use the MESHGEN default or Genex program In the Files and Directories Tab Fig 164 Options one can specify locations of various HYDRUS files and the file having information about display options e Directory for HYDRUS Settings and Authorization Files Working Directory for Temporary Files Default Directory for HYDRUS Projects Configuration file for display options Directory for Thermodynamic Databases for the HP2 program Graphics Program FE Mesh Files and Directories Files and Directories Directory for Program Settings and Configuration Files Working directory for Temporary files C ussl HYDRUS3D 2 0 Temp Default directory for Projects C ussl HYDRUS3D 2 0 Projects Directory for Project Templates C ussl HYDRUS3D 2 0 Templates Configuration file for Display Options C u
312. put Update Screen Output C Press Enter at the End Default log Subregions for Mass Balances won nm Ae wn Number of Subregions 1 Previous Figure 16 The Output Information dialog window In the Print Options part of the dialog window one decides whether certain information concerning mean pressure heads and concentrations mean water and solute fluxes cumulative water and solute fluxes and time and iteration information is printed at each time step T Level Information after n time steps Every n time steps at a certain defined time interval Interval Output or if the information is sent to the screen during the calculations Screen Output When the simulation ends users are by default asked to hit the Enter key of the keyboard to return to the GUI from the computational window This action can be disabled by unchecking the Hit Enter at the End check box T Level Information This check box decides whether certain information concerning mean pressure heads and concentrations mean water and solute fluxes cumulative water and solute fluxes and time and iteration information are to be printed at each time step after n time steps or only at preselected times Print Times or Time Intervals Interval Output Users can specify whether or not information concerning mean pressure heads and concentrations mean water and solute fluxes cumulative water and solute fluxes and time and iteration
313. r content dependence of reaction parameters the Water Content Dependent Solute Reaction Parameters dialog window shown in Figure 29 Specifies various chemical parameters and selections for the UNSATCHEM module the Chemical Parameters dialog window Fig 31 Allows additional application of a specified mass of a chemical into the transport domain a specified location at specified time 258 Heat Transport Parameters Root Water Uptake Root Water Uptake Models Pressure Head Reduction Osmotic Head Reduction Variable Boundary Condition Data for Inverse Solution FE Mesh FE Mesh Generator FE Mesh Parameters Generate FE Mesh Delete FE Mesh Remove Selected FE Elements FE Mesh Statistics Select Mesh Nodes Select Mesh Elements Advanced FE Mesh Generation Fundamental Triangulation Mesh Refinement Homogeneous Retriangulation Check of Convexity Mesh Smoothing Domain Properties Material Distribution Root Distribution Nodal Recharge Specifies heat transport parameters the Heat Transport dialog window Fig 32 Selects the root water uptake stress response models for both salinity and water stress the Root Water Uptake Model dialog window Fig 33 Specifies parameters in the root water uptake water stress response model the Root Water Uptake Parameters dialog window Fig 34 Specifies parameters in the root water uptake salinity stress response model the Root Water Uptake Parameters dialog
314. r more boundary objects forming a closed curve The Edit Bar displayed during the operation will list Boundary Curves defining the Opening similar to Fig 62 left Alternatively an opening can be created using the New Opening dialog window Fig 72 by clicking on the command IJnsert gt Domain Geometry gt Opening gt Dialog from the menu An opening can be edited using the Edit Curve dialog window Fig 50 which specifies the number boundary curves defining the opening its number and has a box for possible comments or a description New Opening Opening No in Surface No 1 limit Boundary Curves Comment Opening representing well Figure 72 The New Opening dialog window 129 4 4 Solids Solids are three dimensional objects defined by the base surface and one or more thickness vectors See also Section 2 Projects Geometry Information There are three types of Solids depending upon the selection made in the Domain Type and Units dialog window Figs 6 and 7 e 3D Layered Hexahedral This type of solid has a Hexahedral Shape and is defined by its basic dimensions Figs 6 and 9 The base can have a certain slope in the X and Y dimensions e 3D Layered General This type of solid is defined by the Base Surface and one or more Thickness Vectors e 3D General This type of solid is defined using a set of surfaces either Planar or Curved Surfaces that form its boundaries
315. rc Circle Spline Surfaces Rectangle Graphically 251 FE Mesh Domain Properties Initial Conditions Boundary Conditions Cross Sections Mesh Line Auxiliary Objects Planar Quadrangle Rotary Pipe B Spline Openings Graphically Dialog Thickness Vectors Graphically Dialog Solids 3D Block Graphically 3D Layered Domain General Solid Mesh Refinement Graphically Mesh Refinement Dialog Mesh Stretching Material Distribution Root Distribution Nodal Recharge Scaling Factor Hydraulic Conductivity Pressure Head Water Content Local Anisotropy Angle First Component Second Component Index Subregions Observation Nodes Drains Flowing Particles Pressure Head Water Content Concentration Nonequilibrium Concentration Temperature Import Water Flow No Flux Constant Head Constant Water Content Constant Flux Seepage Face Variable Head 1 4 Variable Flux 1 4 Gradient Boundary Free Drainage Deep Drainage Atmospheric Boundary Solute Transport First Type Third Type Volatile Type Heat Transport First Type Third Type Graphically Dialog Graphically Dialog Dimension Comment 252 E Calculation F Results G Tools FE Mesh Parameters Generate FE Mesh Delete FE Mesh FE Mesh Statistics Advance FE Mesh Generation Calculate Current Project Calculate All Open Projects Select Projects to Calculate Display Quantity Boundary Information Observation Points Soil Hydraulic Properties
316. rd These are regular points defined using two or three coordinates e Parametric These points are located on a curve and their location is calculated using a specified parameter from the interval 0 1 where 0 and 1 represent the beginning and end of the curve respectively For example a point with a parametric coordinate t 0 5 is located exactly in the middle of the curve A parametric point is not a defining point of a curve i e it does not define its shape On the contrary a shape of a curve defines the location of a parametric point A Parametric Point can be redefined as a Standard Point in the Edit Point dialog window Fig 48 106 Parametric Points can be added on a curve using the command Insert Points on Line on the Edit Bar using the menu command Tools gt Insert Points On Line gt Graphically or by clicking on a curve with the right mouse button and selecting the Insert Points On Line gt Graphically from the popup menu Fig 49 Either the parametric coordinate of a point or its distance from boundary points L of a curve is displayed on the Edit Bar when specifying a Parametric Point EJ HYDRUS sssss Domain Geometry T Fie Edit View Insert Calculation Results EASI Options Developers Window Help KARRAR EROF oe D Uag palles LA Project Data W sssss E Project Information a Domain Geometry a Geometry Information Points i Lines Surfaces Openings Thicknesses Solid
317. re not automatically lost but can be recalculated to the new FEM from their definition on Geometric Objects Which option is used depends on the menu command Edit gt Properties and Conditions on FE Mesh A similar button switch is also available at the end of the tool bar z next to the Results button and at the Edit Bar The latter approach i e on Geometric Objects is described in detail below in Section 6 5 6 1 Default Domain Properties For rectangular two dimensional domains and for layered three dimensional domains immediately after the finite element mesh is generated one can specify the initial Default Domain Properties in the dialog window shown in Figure 115 Values listed in this window are initially assigned to each horizontal layer of the transport domain but can later be modified graphically The following variables are involved Code Code of the boundary condition 0 for no flow 1 for constant flux 1 for constant head 2 for unsaturated seepage face 2 for saturated seepage face 3 7 8 9 for variable flux 3 7 8 9 for variable head 4 for atmospheric 5 for tile drain 6 for free drainage h Initial value of the pressure head L The initial pressure head changes linearly between the first and last layer if one clicks on the command at the bottom of the dialog Linear interpolation of the pressure heads between the first and last layer Q Recharge flux L T and L T for 2D and 3D app
318. re 11 The Hexahedral Domain Definition dialog window In the Domain Type and Units dialog Window Figs 6 and 7 users also select the geometry Units to be used throughout the application mm cm m and the size of the Initial Project Group When units are changed during specification or after reading the input data then all input variables are automatically converted into the new units Initial Project Group This part of the dialog allows users to define the initial dimensions of the graphical view window Model Precision and Resolution Epsilon is a minimum resolution recognized when defining geometric objects Epsilon is by default defined as R 100 000 where R is a domain radius i e a radius of a circle sphere circumscribing the domain Epsilon is used for example for evaluation of positions of two points If their distance is less than Epsilon then the two points are replaced by a single point A user defined epsilon may lead to unstable behavior of the program and it is intended only for advanced users who may need it for special purposes A correct functionality of geometrical calculations and generation of FE meshes is not guaranteed for user defined epsilons Edit Properties on Geometric Objects When the check box Edit domain properties initial and boundary conditions on geometric objects is checked users can specify various properties and conditions on the Geometric Objects See Section 6 5 Defining Properties on Geometric O
319. required activation License Number 1001 Level to activate 3D Professional Time limited License Yes Expiry Date 7 1 2011 Computer Description Home PC Press OK if you are satisfied with the displayed parameters and want to generate request codes Press Cancel if you wish to make any changes to the activation parameters Figure 170 Window requesting confirmation of entered parameters Prior to the expiration Expiry Day of the Time Limited Authorization user will be alerted about it and the license can be easily repeatedly extended using the Extend Activation function 9 2 2 2 Activation by E mail For this option the user is guided through a three step form three Tabs of the Activation by E mail dialog window Fig 184 During the first two steps he she prepares information needed to obtain HYDRUS Authorization and emails it to the HYDRUS distributor In the third step user enters the Activation Code that he receives by e mail on the third Tab Step 3 of the Activation by E mail and activates HYDRUS The first step is to fill in information about the license License Number the name of the license owner Customer and description of the Workspace WP Description This last item i e WP Description serves for future identification of a particular computer in the electronic licensing system and is usually characterized by a user or its location e g John Laptop Harry Lab 001 In the section Required
320. resis is to be considered the Soil Hydraulic Model dialog window Fig 18 Specifies parameters in the soil hydraulic model the Water Flow Parameters dialog window Fig 19 Defines anisotropy tensors for three dimensional applications the Tensors of Anisotropy dialog window Fig 22 Selects the time and spatial weighting schemes for numerical solution of the solute transport equation specifies the number of solutes to be considered the Solute Transport dialog window Fig 23 Specifies the path to the thermodynamic database and components to be considered in PHREEQC calculations Text editors for defining input for PHREEQC Specifies solute transport parameters the Solute Transport Parameters dialog window Fig 25 Specifies solution adsorbed and precipitated concentration combinations for the UNSATCHEM module the Solution Compositions dialog window Fig 30 Specifies solute reaction parameters the Solute Reaction Parameters dialog window Fig 26 Specifies parameters for constructed wetlands the Constructed Wetland Model Parameters I dialog windows Fig 38 Specifies parameters for constructed wetlands the Constructed Wetland Model Parameters II dialog windows Fig 40 Specifies parameters defining the temperature dependence of reaction and transport parameters the Temperature Dependent Solute Transport and Reaction Parameters dialog window shown in Figure 28 Specifies parameters defining the wate
321. retization close to the soil surface to get good estimates of evaporation across the entire transport domain solid Layers can have different Thickness Profiles the Thickness Profiles Tab One profile is created by the code automatically Users can then define one or more Thickness Profiles that are associated with different Thickness Vectors These profiles can then be subdivided into multiple layers that can have either constant or variable thickness T across the transport domain Thicknesses and the mode constant or variable of particular layers are specified in a table Thickness Sum TS is then calculated by adding thicknesses of particular layers At least one layer thickness must be variable The finite element discretization then follows these layers Finally the FE Mesh Tab Fig 76 specifies how many horizontal FE Layers are used to discretize the solid When only one layer exists then users can specify relative finite element spacing spacing of vertical discretization layers on the vertical side FE Mesh Layer Spacing using the RS1 relative size at the top and RS2 relative size at the bottom factors below Generate Mesh Layer Spacing The element sizes are then proportionally distributed The preview part of the dialog window shows the main terms used on each Tab When multiple layers exist then users can specify relative sizes of elements for each layer FE Mesh Density in Layers 132 Edit Solid IX Edit Solid General
322. rmat The E format is then used also on the Edit Bar and for printing only for a particular variable Note that switching from a regular format to the E format represents also switching from the Standard Scale to the Custom Scale see below which is then kept for the display of the same variable at other times Returning to the Standard Scale may be required to adjust the scale as needed to display a given variable at the new time Edit Isoband Values and Color Spectra Scales 100 000 n Standard 143 261 po Empty Eill 186 521 229 782 Fill Max Min 273 043 316 304 359 564 402 825 Palettes ETT Defaut 489 347 532 607 1575 868 C E Format Number of Intermediate Isolines nm ka u ie a o When drawing Isolines Double click on the color panel When drawing Color Contours to change colors nm Figure 138 The Edit Isoband Value and Color Spectra dialog window Users can also define the Isoline scales This can be done by simply changing numbers in the edit boxes next to the colors If the numbers are not in an increasing or decreasing order a 216 warning will be issued Newly created Isoline scales can be saved again locally or globally and used later Users need to specify only the maximum and minimum values the top and bottom edit boxes after clicking the Fill command the program will calculate and fill complete the intermediate numbe
323. rming successful online deactivation of HYDRUS uu 287 The HYDRUS Deactivation dialog WiIndOW cescceesseceeeeeceesteeeenteeeeneeeenaeeees 288 Window confirming successful deactivation of HYDRUS by email 0 0 289 The HYDRUS 2 xx Setup window with a choice to install the hardware key driver The General Picture and Legend tabs of the Print Options dialog window 292 The Coordinate Systems dialog WindOWS ssssssessssseessresseesseesseeesseeesseesseesseessees 294 The Create Video File dialog window xsi ts Jene eid ane Ae ntii ala ieee eee 298 Result of commands Print Preview or Copy to the Clipboard ee eeeeeeeeeees 293 The About HYDRUS dialog window the Program tab top and the Authors tab DOCLOMD ss 58 55 ste esses ts TE A E ER E E 300 15 16 Table 1 Table 2 Table 3 Table 4 Table 5 Table 6 Table 7 Table 8 Table 9 Table 10 Table 11 Table 12 Table 13 Table 14 Table 15 Table 16 Table 17 Table 18 Table 19 Table 20 Table 21 Table 22 List of Tables Commands in the Project Manager 3 4 scs 3 cceess as aseltoaseeeasteacaaiee casted Rec 29 Data types for the objective function Inverse Problem cceeseeseeeseceeeeeeeeeeeeees 44 Definition of the column X in Fig 14 based on Data Type Inverse Problem 44 Definition of the column Y in Fig 14 based on Data Type Inverse Problem 45 Hime ntormatio
324. rom left to right for Material Distribution in Domain Properties Water Flow Boundary Conditions Pressure Head Initial Conditions and W ater Content ReStlts niesi Bade snin E E Bate tie EE E i EE 237 The Color Scale Display Options menu essesssesssssssssresseessessseeesseeesseesseesseessees 241 Selected Edit Bars for Domain Geometry and FE Mesh ceescceeeseeeesteeeeeee 241 The Toolbars dialog WOW hse oasis etieh seciee Pe eieaaetsaige ve eae dae sen asians oe neue 242 The Customize Toolbars dialog Window cccssccecssececesececeneeecsneceeseeeeneeeenaeeees 242 The HYDRUS Menus I File Edit and View c cccccccccssssssssecececeeeessssnseceeeeees 246 The HYDRUS Menus II Insert Calculations and Results 0 0 0 0 ccceesesseeeeeees 247 The HYDRUS Menus II Tools Options Windows and Help eeseeeeeeeees 247 The Program Options dialog window the Graphics Tab ceccceeeseeeesseeeeeteeees 271 The Program Options dialog window the Program Tab ceccceceseeeesseeeeeteeees 272 14 Figure 163 Figure 164 Figure 165 Figure 166 Figure 167 Figure 168 Figure 169 Figure 170 Figure 171 Figure 172 Figure 173 Figure 174 Figure 175 Figure 176 Figure 177 Figure 178 Figure 179 Figure 180 Figure 181 Figure 182 Figure 183 Figure 184 Figure 185 Figure 186 Figure 187 The Program Options dialog window the FE Mesh Tab eseese 273 The Program
325. roup has its own name description and pathway Figs 2 and 5 A Project Group can be any existing accessible subdirectory folder HYDRUS is installed together with two default Project Groups 2D_Tests and 3D_Tests which are located in the HYDRUS3D folder The 2D_Tests and 3D_Tests Project Groups contain test examples for two and three dimensional problems respectively We suggest that users create their own Project Groups e g the My_2D_Direct My_2D_Inverse and My_3D_Direct Project Groups and keep the provided examples intact for future reference Projects can be copied with the Project Manager only within a particular Project Group Users can copy projects between Project Groups or share 28 their HYDRUS projects with colleagues and clients using standard file managing software such as Windows Explorer In that case one must copy only the project_name h3d2 file when the radio buttons Temporary is deleted after closing the project is used Fig 4 When temporary data are kept permanently in the working directory 1 e the radio button Permanent results files are kept in this directory is selected Fig 4 the working directory must be copied together with the project_name h3d2 file In addition to a Name and a brief Description of a Project the Project Manager also displays dimensions for a particular problem Type the dimensions are either 2D or 3D and the geometry is either Simple S Layered L or General G see Se
326. rs by interpolation A specified Number of Intermediate Isolines can be drawn between the main isolines using When drawing Isolines or When drawing Color Contours This number is by default equal to zero Five intermediate isolines are used in Figure 139 sms Bia aa E PRAG 2 C pAr 2andarw od View Optra w rrara E O Doman Geometry b dan A O E FE Moth Sectors j Presse Head h fcm s f r e7 251 OE Doman Propane Ao ze OF Vr Contor reem 852 E OG Boundary Condtons Emery 2 M Rests fa ss WD Premue Head OW Water Cortert faMauMn OW Tenperstue OW voc OW Corcertesten 1 OW Corcertaten 2 ow Concerteston 3 OW Flewng Pacie BH FEMeh DG Nose AG Sutace Edger 48 8271 C 8 Voume Edges XT AG Sutace Facets OB Ninbeng 75 860 J E Number of Intermediate lsoines Og Abey Obyrcts Fes og Rerderrg Model JE Format Wien i oe DZ Giph Type wng lioine Lighting Double check on the color When daeng Color Contours Fi Crott Secton Chart OG Coke Scale atk mem ohare E Boundary Line Chat AF Daplap Values at Nodes Help FA Right cick on the Coder Scale dipi opion Back Boundary Conditions FY Sg l i o 4 C Flow Animation Figure 139 The use of intermediate isolines Minimum and maximum numbers of the scale are automatically adjusted to a particular problem and for a particular variable By default HYDRUS searches all output time levels of a particular project for the mi
327. ructed Wetland Model CW2D Parameters II Temperature Dependence Heterotrophic Organisms Autotrophic Organisms Stoichiometric Parameterss Production of Cl in Hydrolysis Fraction of CR in biomass Lysis Yield Coefficients Yield Coeff for Heterotr Yield Coeff for N Somonas Composition Parameters N Content of CR N Content of CS P Content of CR P Content of CS 02 Saturation Temp Dep 02 Saturation Hydrolysis Factor KX for Hydrolysis Factor KNHA for Nitrification Fraction of Cl in biom Lysis Yield Coeff for N Bacter N Content of CI N Content of biomass P Content of Cl P Content of biomass Rate 02 93 28000 53000 160000 Previous Figure 40 The Constructed Wetland Model CW2D Parameter II dialog window Table 15 Temperature dependences stoichiometric parameters composition parameters and parameters describing oxygen transfer in the CW2D biokinetic model Langergraber and Simunek 2005 Parameter Description unit Value Temperature dependences activation energy J mol for Arrhenius equation Tdep_het activation energy for processes caused by XH J mol 47800 Tdep_aut activation energy for processes caused by XA J mol 69000 Tdep_Kh activation energy Hydrolyses J mol 28000 Tdep_KX activat
328. rves that must all lie in the same plane and cannot cross each other In the 3D Professional version also the Curved Surfaces Quadrangle Rotary Pipe or B Spline are available A surface is a closed two dimensional domain that is either the computational domain for two dimensional applications or the base surface that can be extended into a solid for three dimensional applications A surface is defined by the List of Boundary Curves It can be created using either the Insert gt Domain Geometry gt Surfaces gt Graphically or Insert gt Domain Geometry gt Surfaces gt Graphically Rectangle commands Alternative commands on the Insert Object part of the Domain Geometry version of the Tool Bar are Planar Surface via Rectangle and Planar Surface via Boundaries In the first case a cursor appears and users can create a rectangular surface using the mouse The Edit Bar displayed during this operation is similar to the one displayed in Figure 47 right The Edit Bar will also show which point curve and surface their number are being defined In the second case users can create a surface by clicking on a closed curve one or more boundary objects forming a close curve The Edit Bar displayed during the operation will list Boundary Curves defining the Surface Fig 62 left A surface can be edited using the Edit Surface dialog window Fig 62 right which specifies surface type the number of boundary curves defining the surface its number and
329. s Figure 161 The Program Options dialog window the Graphics Tab In the top part of the Graphics Tab Fig 161 OpenGL one can turn on or off the OpenGL Hardware Acceleration OpenGL is a library of functions developed by Silicon Graphics Inc for handling graphical objects and select the speed for OpenGL optimization In the bottom part of the Graphics Tab Options one can select a b c d Simplified display in Move modus whether to Invert direction of mouse scroll wheel when zooming whether or not an object is selected when the cursor hovers above it Pre selection Mark object while hovering above it with cursor whether or not values and properties are displayed numerically when the cursor is close to a selected object Display values properties at pre selected objects 271 e a different background Gradient Background visually more effective background is displayed which may be useful for presentations and f minimum time for one frame during flow animation Simplified Display Mode When the graphics View Window update is too slow this option accelerates it during dynamic rotating moving or zooming When rotating the model only its simplified version is drawn which results into faster display of the model When rotating is finished the full model is displayed again This option is initiated only when the number of refreshments per second falls below the specified number
330. s Flow and Transport Parameters FE Mesh GJ Domain Properties Initial Conditions Boundary Conditions Auxiliary Objects Results Graphical Display Results Other Information Tae Data 60 View amp F Sections Inserts new points on the curve via graphics Show Grid i Snap to Grid Grid and Work Plane Define Work Plane Coordinate System Color Scale g Translate Rotate Mirror WE Intersect Lines Split Lines Insert Points on Line Check Geometry Repair Geometry h Create Video File M Geometry GA FE Mesh n Points Distance Edit Lines Delete Lines Split Lines Graphically Insert Parametric Points Reverse Orientation FE Mesh Refinements main Proper P Initial Conditi System Default n Points Distance a Boundary Con Plane XY X 267 84 cm g Bakta 48 a aa w xl a Domain Geometry Insert Object Point Line Abscissa ED Line Polyline X Arc via 3 Points amp Y Are via 2 Points and A Arc via Center A and Circle via 3 Points Circle via Center and K Spline 1D Surface via Rectangle ig Surface via Boundaries ia Opening via Boundaries EP Solid Brick UP Solid Extruded Mp Thickness Vector re ke Dimension 3A Comment Transform Object Ra Translate TS Rotate Ab Mirror z 3 Tools Y 577 93
331. s for 3D General geometries It is recommended to use Triangular Prisms or Mixed Elements rather than Tetrahedrals since then the number of finite elements is three or more times smaller and thus the calculations are faster r FE Mesh Main Stretching MG Options Options Sections Export OK Main Stretching Options Sections Targeted FE size Cancel Targeted FE size F Automatic Help Automatic Hee TS 10 00 cm 0 630 Number of Mesh Layers Targeted FE Size Type of 3D elements Targeted FE Size NL 21 TS 0 10m Tetrahedral TS 0 10m Dje gt e Mixed Details a Mesh Limits Tope of 3D elements Tetrahedral Max number of nodes 00 m Triangular Prism 4 gt Nmax 200000 Previous OO Previous Appl Appl Lae _ V Detect Collisions ay Default Default _ Al Default All Default Figure 98 The FE Mesh Parameters dialog window the Main Tab for 3D Layered left and 3D General right geometries 160 For 3D General geometries users also need to specify the Maximum Number of Nodes in the FE mesh This is the maximum number of finite element nodes in the entire three dimensional domain Similarly as below for MeshGen when this is specified for a two dimensional domain Fig 103 when this maximum number is reached a warning will appear Achieved the maximum number of nodes This means that the maximum allowe
332. s or for concentrations associated with the solid phase for the attachment detachment models users can specify that the nonequilibrium phase concentrations are initially at equilibrium with the equilibrium phase concentrations Initial conditions need to be then specified only for the liquid phase concentrations and the nonequilibrium phase concentrations are calculated by HYDRUS The UNSATCHEM Module When the UNSATCHEM module is used basic information needed for defining solute transport problem are entered in the Solute Transport dialog window displayed in Figure 24 instead of Figure 23 which is used for the standard solute transport module In this window users specify again the Space and Time Weighting Schemes and additional Solute Information such as mass units Note that all concentrations in the UNSATCHEM module are either in meq L in the liquid phase or meq kg in the solid phase meq mmol The pulse duration is not used in UNSATCHEM and the number of solutes is fixed to 8 i e the number of considered major ions Ca Mg Nat K Alkalinity SO Cl and an independent tracer The number of solution adsorbed and precipitated concentration combinations is specified when simulating the transport of major ions in the UNSATCHEM module This value represents the maximum number of solution adsorbed and precipitated concentration combinations which can be used to specify the initial and boundary conditions 64 Sin
333. s a menu with nine commands for editing sections Create New Section from Selection Create New Section from Current View Display All Display Previous Hide Selection Display only Selection Display Reverse Edit Section Graph Type Commands Displays a menu with five commands 244 Tsolines Colormap Tsosurfaces Color Points Color Edges Velocity Vectors Color Scale Options Color Smoothing Surface Lighting Displays the spatial distribution of a certain variable by means of isolines Displays the spatial distribution of a certain variable by means of color contours Displays the spatial distribution of a certain variable by means of isosurfaces Displays the spatial distribution of a certain variable by means of color points Displays the spatial distribution of a certain variable by means of color edges Displays Darcy velocity vectors Displays menu with seven commands Min Max Values Global in Time Min Max Values Global in Space Standard Scale Custom Scale Edit Scale and Colors d GUI Toolbar View Edit Domain Geometry View Edit FE Mesh View Edit Domain Properties View Edit Initial Conditions Sets the View window to View Edit Domain Geometry mode Sets the View window to View Edit FE Mesh mode Sets the View window to View Edit Domain Properties mode to edit materials Sets the View window to View Edit Initial Conditions mode to edit pressure head initial conditions View Edit Boundary Condit
334. s defining the Geometry of the transport domain from a file in the DXF format AutoCAD DXF Drawing Interchange Format or Drawing Exchange Format is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs Autodesk now publishes the DXF specifications on its website for versions of DXF dating from AutoCAD Release 13 to AutoCAD 2010 The menu command Import Geometry from a DXF File calls the dialog window Fig 95 of the same name that allows users to select or browse for the DXF file with the description of the transport domain and to specify units that are used in this file DF File Large scale domain dxf Units of Length used in the DXF file m Template Position and Transformations V Move Imported Geometry so that its bottom left comer is positioned at the Origin 0 0 0 V Update Grid and Workspace according to the imported Geometry REMARK You can Move Rotate or Stretch imported objects later by commands available in the main menu or in the popup menu in Navigator Data Tree Cancel Figure 95 The Import Geometry from a DXF File dialog window Since local coordinates defining the transport domain in the coordinate system used in the DXF files may include very large numbers users can ask the HYDRUS GUI to convert these coordinates so that the bottom left corner of the transport domain is located in the origin of the computational coordinate sy
335. s described below A thickness of a Layer is calculated as follows e Thicknesses of Layers given in the Table are calculated on the Master Thickness Vector e The sum of Thicknesses of all Layers should be equal to the length of the Master Thickness Vector If it is not so a program will issue a warning and recalculate Thicknesses of Layers automatically A Solid can have more Thickness Vectors of different lengths so that specified Thicknesses of Layers cannot be maintained The program then does the following For Geo Layers with the Constant Thickness Type the specified thickness is maintained at all Thickness Vectors i e over the entire computational domain For Geo Layers with the Variable Thickness Type their thicknesses are linearly increased or decreased so that the sum of Thicknesses of all Layers corresponds with the length of a particular Thickness Vector 4 4 2 3 Individual specification of different Thicknesses of Geo Layers at different Thickness Vectors In the preceding paragraph we have described how to define Thicknesses of Layers on the Master Thickness Vector using a table Fig 75 This table represents the so called Profile i e a particular distribution of thicknesses If one wants to define precisely the division of thicknesses also on other vectors than the Master Thickness Vector then it is necessary to create additional Special Profiles and use then on corresponding Thickness Vectors There is always a Defau
336. s of the solid needs to be defined during the second step The length and direction of the Thickness Vector is defined using a mouse in the Point on the Base Surface closest to the mouse click which selected it How to create a Solid once the Base Surface and multiple Thickness Vectors are defined 1 Graphically Use the Solid Extruded tool and click on the Base Surface A Solid is created using existing Thickness Vectors 2 Numerically By using a command from the Insert menu or by clicking with the right mouse button on Solids in the Data tree of the Navigator Bar From the popup menu select the New Solid command In the New 3D Layered Solid dialog select the Base Surface and Thickness Vectors Since the Autodetect function is automatically on the Base Surface and Thickness Vectors will likely be detected automatically Thickness vectors do not have to be perpendicular to the base surface A Solid i e its base surface and thickness vectors is defined and can be edited in the Edit Solid dialog window Fig 75 that has four tabs General Sub Layers Thickness Profiles and FE Mesh The General Tab provides information on which base surface and which thickness vectors define the solid The Sub Layers Tab informs whether the solid is divided into one or more Layers Layers are other objects that can be used to subdivide a single solid These layers can be used for example to keep constant thicknesses of selected horizons or constant disc
337. second one while the last point of the first line will be the beginning point of the second line Each abscissa is considered to be a single curve When a New Polyline is being created the entire polyline is considered to be a single curve The process of defining new lines is ended by pressing the Esc keyboard button the right mouse button see the Help part of the Edit Bar or clicking the Stop button on the Edit Bar Double clicking on an existing line will recall the Edit Line dialog window Fig 50 Before using the New Line dialog window a user needs to first define points which are then used to define the line In addition to the General Tab Fig 50 left in the New Line dialog window the Edit Curve dialog window has also the FE Mesh Tab Fig 50 right Points defining the line are entered in the General Tab while the FE Mesh Refinement along a given line can be defined in the FE Mesh Tab Edit Curve Edit Curve General FE Mesh General FE Mesh Curve No Are No FE mesh Refinement 1 on Line given by s Curve Type FE Mesh Refinement Polpline L Avallable List of Points 3 4 Comment Global FE Size 5 om Figure 50 The Edit Curve dialog window 4 1 3 Arcs and Circles An arc is part of a circle An object arc is always internally defined using three definition points However to simplify its specification it is possible to define an are graphically i
338. sed to specify Boundary Conditions Mi only if Nsurf lt 50 V only boundary Surfaces 4 Geo Sections for Solids Mesh Sections F Boundary Shell Mesh Layers D Generate i Sections Mesh Sections for generated Geo Sections S a Set Default Mesh Sections for user defined Geo Sections Save as Default Hint You can create custom Mesh Sections or Geo Sections using the Cut with Rectangle tool and other commands available in the Edit Sections Program menu Default Figure 151 Options for Generation of Geo Sections and FE Mesh Sections dialog window Selected Geo Sections and or FE Mesh Sections can be generated using the command Generate Sections in this dialog window Fig 151 obtained using the menu command Edit gt Sections gt Generate Sections Geo Sections can be generated either only for Solids or also for Boundary and or internal Surfaces Since working with Geo Sections can be rather tedious when the number of Surfaces exceeds a certain limit users can select this limit The default setting Program Default is to generate Geo Sections for up to 50 Surfaces Note that the number of Surfaces can be prohibitively large for certain 3D Layered Domains with multiple internal lines and or layers Users can therefore choose to generate FE Mesh Section only for 233 Boundary Surfaces which are useful when specifying the boundary conditions and not for internal
339. seesssse 195 6 5 2 Observation Nodes on Geometric ObjectS esseseessseessseenssereesseseesssserssss 198 6 5 3 Initial Conditions on Geometric Objects ccccccccecsscccceessececesseseeesesseeeensseeess 199 6 5 4 Boundary Conditions on Geometric Objects ccccsscccceessececesssnseceteestecesnsssenees 200 6 5 5 Additional Notes on Properties at Geometric Objects iiccccccccccccceesseceeessteees 201 6 6 Import of Domain Properties and or Initial and Boundary Conditions 01000606 202 6 6 1 Import Initial Condition from HYDRUS Projects 202 6 6 2 Import Data from HYDRUS Project occcccccccccccccessseceeesssececessssceeesssaeeeensseeees 203 6 6 3 Import Data from a Text PU sare 8 caskets tte Ga aip ais Iu Ta les Saale Seana ae 204 5 MGT ICAL OutP t sin senate creates sactasenamesmatun scastaanastaatanctsps a i aS 209 7 A Results Graphical Display ssocccsecswsisiwwredewssaiectisdiendea eataaseeeasaraoesl irate eaters 209 PALS Displayed Variables iiinis niina Crass a i a 210 Wels Dirrplay OH ONS siecle 8 es sens a a a a a a 215 7 1 3 Edit Isoband Value and Color Spectra sci iiccasiacks eiicndiancoteivasusaueons 216 TAA Export TSOURGS pocnngna sioa a ceca eeebeaenetesndouasss 222 Tas Results Other Informauon ccsaivavsdiatspinand sch bended anid aide 223 T2 Convert TO ASCH ce aston tatie cts ta neat aied e id asec ht Cm ama tent tens tates 226 Graphical User Interface Components 0 0 ccccccce
340. serve on the Edit Bar that an index of a preselected point and its coordinates are displayed in edit controls These controls are disabled since displayed values can not be changed Snapping on curves Fig 55 right occurs in addition to Snapping on existing points An automatic calculation of coordinates of a point on a curve and snapping to this point occurs when a center of a cursor comes close to an existing curve A location of this point is marked using a yellow cross which indicates that after this point is entered it becomes a definition point of a curve This is important since entering a point on a curve that is not its definition point leads to the wrongful definition of a domain A Check of a Geometry discovers such errors and the Repair Geometry function will automatically correct it Figure 55 Snap to a point left and snap to a curve right 113 4 1 6 Translate Copy Rotate Mirror Stretch and Skew Operations All boundary objects can be manipulated using the Translate Copy Rotate Mirror Stretch or Skew operations in the Translate Copy Fig 56 Rotate Fig 57 left Mirror Fig 57 right Stretch Fig 58 left and Skew Fig 58 right dialog windows These commands can be access either from the Tools Menu or from the Transform Object part of the Domain Geometry version of the Tool Bar at the right side of the View Window Users first select an object to be manipulated then click on the command and specif
341. shows two examples of 3D General solids While the Solid at the top is formed using 8 Planar Surfaces and 4 Quadrangles the Solid at the bottom is formed by multiple Curved Surfaces Figure 77 Examples of 3D General Solids Top formed by Planar Surfaces bottom formed by Curved Surfaces 137 General Solids can be created in the following ways 1 Using a standard dialog from which Boundary Surfaces can be picked graphically individually or using a Quadrilateral or Rhomboid Selection Tool 2 Creating a Simple Block Brick 3 Extruding a Solid from a Surface one or multiple simultaneously Process of Extruding Approach 1 Start a tool and click on a given Surface which is to be extruded It is important where a click occurs The program finds a closest Node on a Surface Boundary and the extruding distance height is measured in this node The extruding height is measured on a line passing through this node Approach 2 When you want to extrude multiple surfaces at the same time you need to press the Left Shift keyboard button before selecting desired Surfaces you can add or remove Surfaces After a selection is made release the Left Shift button and start extruding selected surfaces Approach 3 First select desired Surfaces and then click the Edit Bar command Solid Extruded This will start the extruding process for all selected surfaces One can extrude Surface in the direction of X Y
342. signs default properties where required e g Materials to the entire transport domain Note that this command does not delete definitions of Properties as done by the Delete All Properties command which thus remain available in the data tree of the Navigator Bar Delete Property Deletes a Property Object selected in the data tree of the Navigator Bar This command is not used for Materials or Subregions the number of which is specified elsewhere Delete All Properties Deletes all Property Objects defined for a particular Property except for a default Property which is defined for those Properties where a default Property is needed Similarly as for the Delete Property commands this command does not exist for Materials and Subregions 194 Sort Properties Calls a dialog window Sort Property Objects which displays all available Property Objects Here the sequence of the Property Objects can be arbitrarily rearranged Transfer to FE Mesh Transfers information about a particular Property defined on Geo Objects to the FE Mesh Note that this command is available only when information about a particular Property on Geo Objects and FE Mesh does not correspond This can occur for example when Property is defined or refined on FE Mesh Edit Property Recalls a dialog window with parameters of a particular Property to edit Note that the word Property is used in place of a particular Property Object such as Domain Property e g
343. simple hexahedral three dimensional geometry i e 3D Simple is given in Figure 9 3D Layered surfaces which can be either Planar surfaces or Curved surfaces Quadrangle Rotary Professional version 3D General Geometries can be formed from three dimensional Pipe or B Spline or more Thickness Vectors see Section 4 5 objects Solids of general shapes Three 3D General Boundary Rep 3D Simple Parametric fully form its SERA Oe PASE augue pees BE ANA AUNA AAT RAA TATT AAAA SAN IRIKA APANIA E I REOR SATAAN FS 4 VAR RETA N KZZ VA APAVATN KERENT TOSE IEAI 2 AZ AE NAS SAADEH PIR aA P KOAK CEK BERK PxISy BOER AEE 3 ONI ae wae iI KIS S lt ey KI gt lt 1 ka D ZI A gt TA AZ WS Di i e Ly i i gt IS Se A oO ne ae Z Z Z B Z A ZA ZA A eA A EZ i TEK N CNN ANY AN KATY oe Z9 gg ER BR RS E T hy BK ATA a K SAI vay T BD as eet SY Vay Vx SEN p DS Nzi eet X SA y va N iW co Z g ar NE i SI S A DY SA KK ANI QANAKS PAVATS AVAVA SERTER Cake AREN DX CERES PR POC KD v RY AVATA A Tari WY TUN Qty Se I Figure 8 Examples of rectangular t
344. sition values Weight is the weight associated with a particular data point The following information can be included into the objective function 43 Table 2 Data Types for the objective function Inverse Problem 0 Cumulative boundary fluxes across a specified boundary K h measurements hydraulic conductivity data point ae Prior knowledge of parameter q 8 Prior knowledge of parametern U U O 9 Prior knowledge of parameter o Depending upon the value of parameter Type the first column X contains the following information Table 3 Definition of the column X in Fig 14 based on Data Type Inverse Problem 0 1 2 3 4 Dummy variable 7 8 9 10 11 Depending upon the value of parameter Type the second Y and fourth Position columns contain the following information 44 Table 4 Definition of the column Y in Fig 14 based on Data Type Inverse Problem Cumulative boundary flux across a specified Code for the specified boundary boundary Pressure head 1 Observation node number _ SC Waterccontent Observation node number __ Averaged water content of the entire flow domain 2 0 Averaged water content of the subregion 2 Negative subregion number _ Concentrations temperatures 4 Observation node number Concentrations for the second solute Negative observation node number a ea es 3 5 Hydraulic conductivity 6 Material number 1 constant pressure head or
345. sscecesececesececseeeeseeeesseeeeseeeesseeees 227 Sls VEC W WIndows iasi aiee a e EE EEEE E EE AEE E i 227 8 1 1 Scene and Viewing Commands bcs cin scirariss iors csbesisrsh nanos sha erin eels 227 8 1 2 Grid and Work Plane vzccsaswedupian nega nunway ei eiin 228 8 1 3 Stretching Factor Socso ninenin a OG ban idak ia Eaa 229 Ou Lil Rendering Model sedesssanicsns nii i T a E 230 8 1 5 Selection and Edit Commands vcincakiu ed Bude 230 8 1 6 Popup Men s crsa s a i a Aa E a E 231 SA7 Drac and DIV OD ccs Susi ds tacos sbaceste a E 232 S 19 DOCH ONS ats oe celle E E abe teak Sie ea dae cs call hedge 232 Sls Navigator BOTS idx crrasraeiatraterinacctua a a E enue a eee wos 235 8 3 Edit BATS cies seaweed aad Gh ee I a aaa phasis 237 SA Toolbars Gis Sok ate tc iat Saath a te es ate alga a Mee das dal etl ah eee 242 Bois HYDRUS Menus Si ie Soe GE Ae ie a A aiaei 246 8 6 Anput Fables in HY DRUS nuserie nde alacant e 269 Miscellaneous Information eee cescesseeneeseeeseceseceaeceeecaeeeeeeseesaeesaecaaecaeesaeeseeeeesaees 271 DV PORTANT OOS ska Sales sae EE la aoa acres Vass aie ds ade E E 271 92 AYDRUS License and ACHVQtHON sist ticcseactieeties a hewn ele hedetad tl deass eevee ceases 275 9 2 1 Brief Description of HYDRUS Activation Using a Software LOCK 0000 275 9 2 2 Detailed Description of HYDRUS Activation Using a Software Lock 275 OO DNs On Line Activa o me e A a EEE R aie 278 9 2 2 2 A
346. ssl HYDRUS3D 2 0 Settings H3DGDI cfg Directory for Thermodynamic Databases C ussl HYDRUS3D 2 0 ThermodynamicDB Figure 164 The Program Options dialog window the Files and Directories Tab 274 9 2 HYDRUS License and Activation HYDRUS is protected either by a Software Lock that is based on information about the hardware on which it is run or starting with version 2 02 using a Hardware Key HASP Starting with version 2 02 the software key can be used to authorize only separate computers while a Hardware Key is required for the network or server installations designated for remote access see Section 9 2 5 Without activation HYDRUS works as a demo version you can run it but you will not be able to run calculations and save your data A customer using a Software Lock can choose to Activate HYDRUS by E mail with the help of the HYDRUS support or directly On line an internet connection is required Using the Online activation system customers can themselves manage their HYDRUS license i e installation de installation and or reinstallation of HYDRUS The HYDRUS software package is activated using the Software Lock using the HYDRUS Authorization Status dialog window Fig 165 that is called using the command Help gt Hydrus License and Activation 9 2 1 Brief Description of HYDRUS Activation Using a Software Lock A On Line Activation recommended To activate online you need to know your License Nu
347. st Code 1 is changed and new activation codes need to be requested 4 We recommend using standard functions Copy amp Paste when inserting activation codes to minimize risk of inserting wrong numbers When starting unauthorized HYDRUS again user is informed that request codes have recently been generated and if he she wants to enter the Activation Code and activate HYDRUS Fig 174 It is important not to regenerate request codes at this time as the Activation Code would then not be active any more since one of the request codes would be changed HYDRUS 2 xx Recently you generated Request Codes for activation of HYDRUS by e mail Would you like to enter the Activation Code now Press OK to enter the Activation Code now Press Cancel to enter the Activation Code later o Figure 174 Window inquiring if the user wants to enter the Activation Code After receiving the Activation Code enter this code on the Step 3 Tab of the Activation by E mail dialog window Fig 175 and click on the Activate Now button You should receive a confirmation that the authorization process was successful Fig 176 284 Enter the activation code exactly as you received it from your HYDRUS distributor For example 269361646 1246593217 1107656901 1001 PC2 627494765 128755978 Caution You have three attempts to enter correct activation code If you enter a wrong activation code three times the request codes will change and you will
348. st copy the input data of the current project to a new project before switching off the solute transport heat transport and or root water uptake options F Dual Permeability Model E Solute Transport 9 Standard Solute Transport Wetland cw2 CWM1 Major Ion Chemistry Unsatchem Colloid Facilitated Solute Transport HP2 Hydrus Phreeqc V Heat Transport F Root Water Uptake E Inverse Solution F Slope Stability Required Add on Modules Figure 12 The Main Processes dialog window 40 For two dimensional problems a user can also select if a Direct or Inverse Problem Inverse Solution is to be solved Inverse problems involve the estimation of selected parameters from available experimental data A new add on module Slope Stability was included in Version 2 04 The Slope Stability module is intended to be used mainly for stability checks of embankments dams earth cuts and anchored sheeting structures see Section 3 23 41 3 2 Inverse Solution HYDRUS implement a Marquardt Levenberg type parameter estimation technique im nek and Hopmans 2002 for inverse estimation of soil hydraulic Hopmans et al 2002 and or solute transport and reaction im nek et al 2002 parameters from measured transient or steady state flow and or transport data The Inverse Solution dialog window Fig 13 appears only when the Inverse Problem in the Main processes dialog window Fig 12 is selecte
349. stem This will likely lead to much smaller values of local coordinates Finally users can ask the HYDRUS GUI to automatically adjust the Grid and Workspace variables to accommodate the imported geometry 4 11 Import Geometry from a TIN File It is possible to also Import the definition of objects defining the Geometry of the transport domain from a file in the TIN format TIN files are used for storing triangulated irregular networks using a simple set of xyz coordinates The TIN file specifications are at http www ems 1 com wmshelp Files File_Formats TIN_Files htm 156 5 Finite Element Mesh 5 1 Finite Element Mesh Generator The Finite Element Mesh Generator dialog window was used in earlier versions to select a structured finite element mesh for relatively simple rectangular or hexahedral domain or a more general unstructured finite element mesh The dialog provided a brief description of each mesh generator and a simple bitmap with an explanation of the main terms involved In later versions after 1 03 a decision which generator to use is made in the Domain Type and Units Window Fig 6 and 7 While the structured finite element generator can be used only for simple rectangular i e the Geometry Type 2D Simple Parametric see the Projects Geometry Information Section 2 or hexahedral domains 3D Simple Parametric the unstructured finite element generator is used for more complicated geometries i e 2D General Boundary
350. subregion and the inflow outflow rates to from that subregion together with the mean pressure head hMean mean temperature TMean and the mean concentration cMean over each subregion see Table 11 6 of the Technical Manual Absolute 225 and relative errors in the water and solute mass balances are also printed to this file Output related to the inverse problem is provided under the command Inverse Solution Results on the Data Tab of the Navigator Bar The Chemical Mass Balance information on the Data Tab of the Navigator Bar or at the Results Menu is provided for the Unsatchem module This file gives mass balances in different phases liquid sorbed solid for all major ions 1 e Ca Mg Na K HCO3 SO4 and Cl The text dialog displaying Mass Balance Information or Inverse Solution Results had only a limited capacity in Version 1 x of HYDRUS If the file to be displayed wass larger than this capacity when there is too many print times or large number of data points in the inverse problem a warning File is too big to be displayed entirely Open it in any text editor was given Users in such case needed to display the Balance out or Fit out files respectively directly using any text editor such as Notepad or WordPad Both files are located in the Temporary Working Directory see Section 1 This capacity problem was overcome in Version 2 and the dialog windows now displays the button Next or Previous which allows browsing
351. t gt Domain Geometry gt Points gt Read from File The order of inputting particular objects is arbitrary the code automatically forms the desired curves In order to have a physically realistic domain only one closed outer curve can exists for multicomponent domains such a curve must exist for each component of the domain The domain can have an arbitrary number of holes or internal curves The consistency of the geometry can be verified at any time using the command Check Data Consistency Tools Menu Any change in geometry can be undone using the undo command up to ten levels backward in time or redone using the redo command again up to 10 levels An object type e g polyline spline arc or circle must be selected first when designing a new object from the Edit Bar on the right side of the view window or from menu e g Insert gt Domain Geometry gt Nodes Then points defining a particular object should be entered The manner in which nodes are entered depends on the selected input style When entering data graphically an appropriate Work Plane x y y z x z and a grid with appropriately set parameters Fig 147 and Section 8 1 2 can be used to facilitate the input while the coordinates X Y and Z of the cursor are continuously displayed in the bottom right corner of the window It is possible to edit existing objects by double clicking on a particular object The current selection displayed in yellow may be modified
352. t Last Previous Next Animation Charts Cross Section Boundary Line Mesh Line Flowing Particles Draw Particles Positions Draw Particles Trajectories Delete Results Tools Show Grid Snap to Grid Grid and Work Plane Define Work Plane Set Origin Define XY Define YZ Define XZ Coordinate System Color Scale Color Smoothing Min Max Values Global in Time Min Max Values Global in Space Standard Scale Custom Scale Edit Scale Translate Rotate Mirror Graphical presentation of information about the number of iterations time step and Peclet and Courant numbers Displays mass balance information and mean profile properties Displays chemical mass balance information Convert binary input and output files into ASCII files Displays information about the inverse solution Displays actual and cumulative water and solute fluxes across selected mesh lines Displays the PHREEQC out text output file Displays a particular variable at the first time layer Displays a particular variable at the last time layer Displays a particular variable at the previous time layer Displays a particular variable at the next time layer Displays time layers of a particular variable consecutively and continuously Displays values of a particular variable along an arbitrary cross section Displays values of a particular variable along a certain part of a boundary Displays values of a particular variable along a sele
353. t and a Thickness on the right 130 The Edit Bar during the process of graphically defining a Solid by extruding a Base Surface Selection of a Surface left and definition of a Thickness Vector right 131 The 3D Layered Solid dialog window the General Geo Layers and Thickness Profiles Tabs viticdscsciseineseets tele connie sd eel cehaesedatisaccde ng aedeeciuatie tuece ieee ellie 133 The 3D Layered Solid dialog window the FE Mesh Tab for single and multiple ENAS EE onsick ea E dev eleaaeta nuesaaen Sounncbas and tae peadumaaeanaatentons 134 Examples of 3D General Solids Top formed by Planar Surfaces bottom formed by curved SUTPACES ssni ni E R EE E E EE OEE EES 137 Edit Bar during the process of graphically defining a Thickness Vector 140 The Thickness dialog windoW 5 0554 5 sedan sisiccaslessaiesyssatios vasa au yd uae yacnsyeayecauaeevcaeecuseans 140 A solid with several thickness Vectors coke een Sateen ea ewieds 141 FE Mesh for the solid in Figure 80 scscssccssssscsssnscsesesesesssesenccessaccesnaccecnaceseneece 141 Missing internal curves in the base surface c ceeeceeceeececesececeeececeeeeenaeerenaeeeeaaees 142 11 Figure 83 Figure 84 Figure 85 Figure 86 Figure 87 Figure 88 Figure 89 Figure 90 Figure 91 Figure 92 Figure 93 Figure 94 Figure 95 Figure 96 Figure 97 Figure 98 Figure 99 Figure 100 Figure 101 Figure 102 Figure 103
354. t how to make selections FE Mesh Sections and Help 240 Insert Object S Point Line Abscissa ET Line Polyline X Arc via 3 Points Arc via 2 Points and R Arc via Center R and Angle Circle via 3 Points X Circle via Center and Radi A Spline Surface via Rectangle t Surface via Boundaries ia Opening via Boundaries i Dimension A Comment Transform Object a a Translate 7 Rotate Al Mirror EL Intersect Lines Xe Insert Points on Line X SplitLine Help r How to Edit Domain Check Domain Definition gt Next FE Mesh Edit FE Mesh a H5 FE Mesh Generator E5 FE Mesh Parameters pe Insert Mesh Refinement 55 Generate FE Mesh 35 Delete FE Mesh 43 FE Mesh Statistics amp Remove Selected Elemen FE Mesh Advanced Options 2 Fundamental Triangulation Mesh Refinement amp Delaunay Retriangulation amp Convex Retriangulation Mesh Smoothing FE Mesh Sections 3 Cutwith Rectangle 4 Edit Sections EA New Section from View 4 Default Sections EA Display whole FE Mesh Hide whole FE Mesh Display Previous State W Toggle Visibility FE Mesh Selection Select Mesh Nodes CO Select Mesh Elements Help How to make FE Mesh gt Next Domain Properties Back Domain Definition Figure 155 Selected Edit Bars for Domain Geometry and FE Mesh 241 8 4 Too
355. t of local anisotropy Specifies the spatial distribution of the second component of local anisotropy Specifies the spatial distribution of the index that represents the local anisotropy tensor Specifies the spatial distribution of subregions for the mass balance calculations Specifies observation nodes for output of the pressure head water content temperature and concentration at each time step Deletes selected observation nodes Deletes all observation nodes Specifies nodal points representing tile drains Deletes selected tile drains Deletes all tile drains Specifies drain parameters Specifies nodal points representing flowing particles Deletes selected flowing particles Deletes all flowing particles Generates a stochastic distribution of scaling factors Makes the subregions for mass balance calculations similar to those for the soil materials Specifies that nonequilibrium concentrations i e kinetically sorbed concentrations or concentrations in the immobile water are a multiple of the liquid phase concentrations Specifies parameters for the spatial distribution of root water uptake Command used when defining properties on Geometric Objects Deletes all defined domain properties and assigns default values Specifies default domain properties that are constant for the same depths the Default Domain Properties dialog window Fig 115 Specifies the initial condition for water flow Specifies the ini
356. t will also allow users to redefine various objects of the x y graph One can for example change the text of both vertical and horizontal axis Axis gt Title captions and titles Title their fonts and colors one can copy the content of the graph to the clipboard Copy for later paste in various other windows applications e g MS Word PowerPoint or Excel or one can change the thickness and colors of displayed lines Many other modifications of the displayed x y graph are possible Data displayed in the x y graph can be exported into an ASCII file using the Export command The x y graph settings can be saved using the Save command Selected variable can be displayed either for all or for selected observation nodes Observation Nodes Chart Observation Nodes Horizontal Variable Time x Obs Node 2 Vertical Variable Pressure head Obs Node 3 i Obs Node 4 Obs Node 5 Observation Nodes Pressure Heads 200 100 D 100 200 300 400 50 100 150 200 250 Time days C Show All Figure 145 The x y graph dialog window displaying pressure heads in observation nodes 223 Table 24 Graph options in the HYDRUS interface Command Horizontal Axis Vertical Axis Observation Points Time Pressure Head Water Content Temperature Concentration x Sorbed Concentration x Pressure Heads Time Atmospheric Boundary Head Root Zone Head Variable Boundary Head 1 Constant Boundary Head Se
357. taken up unlimited passive root solute uptake When the concentration is higher than cRoot additional solute stays behind As the Active Nutrient Uptake is obtained from the difference between plant nutrient demand the Potential Solute Uptake Rate ML T needs to be specified and Passive Nutrient Uptake the presented model thus implies that reduced passive nutrient uptake is compensated for by active nutrient uptake Active nutrient uptake is simulated using Michaelis Menten kinetics the Michaelic Menten constant and a Minimum Concentration for Uptake need to be specified In addition the proposed root uptake model includes compensation for active nutrient uptake in a similar way as used for root water uptake using the Critical Stress Index Reduction in root water uptake will decrease passive nutrient uptake thereby increasing active nutrient uptake proportionally In other words total nutrient uptake is not affected by soil water stress as computed by the proportion of actual to potential root water uptake This is not realistic since one would expect that plant nutrient requirements will be reduced for water stressed plants For that reason the uptake model includes additional flexibility by reducing the potential nutrient demand Potential Solute Uptake Rate in proportion to the reduction of root water uptake see the last check box Reduce Potential Solute Uptake due to Reduced Water Uptake Active solute uptake is implemented
358. tangle Cut with Indexes Import FE Mesh Sections Cross Sections Edit Delete Selected Delete All Auto Adjust Work Plane Auxiliary Objects Dimensions Delete Selected Delete All Comments Edit Delete Selected Delete All Background Layers Edit Move Rotate initial conditions are assigned to Geometric Objects Transfer all properties e g materials initial conditions from Geometric Objects to FE Mesh Calls the FE Mesh Section dialog Fig 114 HYDRUS recognizes two different definitions of Sections one for geometric objects and one for the FE mesh A different dialog appears when called from the Domain Geometry part of the program In all other cases the FE mesh Section dialog appears Generates Geo Sections and FE Mesh Sections Creates a new section from currently selected objects FE Mesh Creates a new section from currently displayed objects FE Mesh Displays all objects or entire FE Mesh Displays a previously displayed view sections Hides selected elements Displays only currently selected objects FE Mesh Hides currently displayed objects FE Mesh and displays currently hidden objects FE Mesh Displays objects FE mesh nodes within a certain rectangle or rhomboid and hides all the others Displays objects with given indexes and hides all the others Import FE Mesh Sections Edits a cross section Deletes selected cross sections Deletes all cross sections Adjust Work Plane Deletes selected d
359. ted on FEM or the Transfer to FE Mesh Tata when a particular Property has already been edited on FEM commands located on the Edit Bar Fig 124 Here the assignment of materials can be further edited refined and finalized However these changes cannot be transferred back on the Geometric Objects After changes have been made on FEM and thus Properties assigned on FEM and Geo Objects no longer correspond the command Transfer to FE Mesh can be used to synchronize again the information in the two modes from Geometric Objects to FEM The Edit Bar commands Edit Properties on FE Mesh and Edit Properties on Geo Objects switches from one way of assigning properties on Geo Objects to another on FEM Similar approach and similar commands can be used to assign other Domain Properties and Initial and Boundary Conditions 6 5 2 Observation Nodes on Geometric Objects Observation Nodes are entered on Geometric Objects using either the Menu command Insert gt Domain Properties gt Observation Nodes or the New Observation Node command on the Edit Bar The New Observation Node command can be used in the Edit Properties on Geo Objects mode to define observation nodes only on Points defining the Geometry i e Points defining boundary curves Observation nodes for any other location have to be specified on the FE Mesh directly The same is true also for Drains and Flowing Particles 198 The Edit Observation Node window Fig 129 is displayed
360. tep of the running tool B Adjusting View When graphically entering objects one often needs to move or turn the scene or to enlarge or reduce a selected detail This can be done without interrupting the input of a particular object The fastest way is to press the center mouse button a wheel and then a dragging the scene with the mouse move b moving forward or backward an object by scrolling the wheel or c rotating the scene by simultaneously also pushing the right mouse button After releasing the center mouse button one can continue in the graphical input of an object Similar operations can also be performed using button on the View Toolbar ERRAR gear A majority of buttons on the View Toolbar do not interrupt the graphical input of an object i e after the adjustment of the View Window on can continue in the graphical input of an object C Snapping When entering Points graphically points created when entering curves or surfaces a process called Snapping is taking place This means that a cursor snaps to points of a Grid Fig 55 left or to existing points Snapping can be disabled using a button Snap to Grid on the Tools Toolbar Snapping on existing points or curves can not be disabled Snapping occurs when a center of a cursor comes close to an existing point and when this point is redrawn with a yellow color or any pre select color assuming that redrawing of preselected points is not switched off One can simultaneously ob
361. tep during calculations Four different time discretizations are introduced in HYDRUS 1 time discretizations associated with the numerical solution 2 time discretizations associated with implementation of boundary conditions 3 time discretizations associated with data points used in the inverse problem and 4 time discretizations which provide printed output of the simulation results e g nodal values of dependent variables water and solute mass balance components and other information about the flow regime Discretizations 2 3 and 4 are mutually independent they generally involve variable time steps as described in the input data file Time Variable Boundary Conditions Fig 37 and Output Information Fig 16 Discretization 1 starts with a prescribed initial time increment Ar This time increment is automatically adjusted at each time level according to the following rules a Discretization 1 must coincide with time values resulting from time discretizations 2 3 and 4 b Time increments cannot become less than a preselected minimum time step Afnin nor exceed a maximum time step Atmax 1 Atmin lt At lt Atinax c If during a particular time step the number of iterations necessary to reach convergence is lt 3 the time increment for the next time step is increased by multiplying Af with a predetermined constant gt 1 usually between 1 1 and 1 5 If the number of iterations is 27 At for the next time level is
362. th rate on Syy 1 d 0 9 0 3 Dans rate constant for lysis 1 d 0 15 0 05 Kans o2 saturation inhibition coefficient for So mg O L 1 Kans NHAN saturation inhibition coefficient for NH4 mg N L 0 5 Kans p saturation inhibition coefficient for P mg N L 0 01 Nitrite oxidising bacteria Nitrobacter spp HANb maximum aerobic growth rate on Syy 1 d 1 0 35 Dann rate constant for lysis 1 d 0 15 0 05 Kanv 02 saturation inhibition coefficient for So mg O L 0 1 K ANo No2N saturation inhibition coefficient for NO2 mg N L 0 1 K ANo NHAN saturation inhibition coefficient for NH4 nutrient mg N L 0 05 Kanosp saturation inhibition coefficient for P mg N L 0 01 90 Table 14 Kinetic parameters in the CWM1 biokinetic model Langergraber et al 2009 Parameter Description unit Value Hydrolysis for 20 C 10 C Ky hydrolysis rate constant 1 d 3 2 Ky saturation inhibition coefficient for hydrolysis g CODs g CODgm 0 1 0 22 NH correction factor for hydrolysis by fermenting bacteria 0 1 Heterotrophic bacteria aerobic growth and denitrification Ln maximum aerobic growth rate on Sp and S4 1 d 6 3 Ne correction factor for denitrification by XH 0 8 by rate constant for lysis 1 d 0 4 0 2 Kou saturation inhibition coefficient for So mg O L 0 2 Ksp saturation inhibition coefficient for Sp mg CODsr L 2 Ksa saturation inhibition coefficient for Sa mg CODs L 4 Kyo
363. the Tab Components of the Edit Surface dialog window Since Partial Surfaces are generated objects they cannot be deleted or their shape cannot be edited only the parental Surfaces can be edited When a parental Surface is divided into Components it still exists is listed in the Navigator but is not displayed in the View anymore only its Components can be displayed One can define for each Component its activity using commands Activate Partial Surface and Deactivate Partial Surface i e whether it should be a part of the domain and whether a FE Mesh should be generated on it or not In this way one can cut from the original Surface unneeded parts When an option Display components as independent surfaces is selected Components are displayed in the Navigator Data Tree as independent Surfaces and it is possible to select them graphically and use them for a definition of Solids A selected Component is displayed in a view in order to facilitate visual identification of Components 4 2 2 Steps to Define a Two Dimensional Domain 1 Definition of Boundary Curves of Particular Surfaces Boundary Curves are formed using basic geometric objects such as Points and Curves These objects can be specified in three different ways 1 Graphically One selects on the Edit Bar an appropriate tool and specifies new objects graphically in the View Window This is usually done by specifying coordinates of points while using the Grid Alignment or s
364. the domain where needed e g when it refines the grid Although quadrilateral or hegahedral elements may be generated by Genex T3D the computational module subdivides these elements into triangles or tetrahedrals respectively While the transition between domains with refined FE mesh and domains with global mesh size in MeshGen2D is relatively smooth and gradual see Figure 107 in Genex T3D the extent of this transition zone is defined exactly by users see Figures below Similarly as MeshGen2D the same FE Mesh Line Refinements can be assigned to multiple Points Lines Surfaces and Solids in the computational domain There are two ways how the FE Mesh Refinement can be assigned to a Point Figure 108 Users can use either Circular or Rectangular refinement For a Circular Refinement around a point a radial refinement area is defined around a node in all directions Users need to specify the Radius of the refinement area the Inner Targeted FE Size i c a FE size immediately around a point and the Outer Targeted FE Size i e a FE size at the outer end of the radial refinement area Fig 111 The Outer Targeted FE Size should be equal or slightly smaller than the Global Targeted FE Size When generating the FE mesh the mesh refinement is carried out gradually towards the center because the FE length at the periphery of the refinement area is usually identical with the global mesh width For larger differences between the inner and outer FE
365. through larger text files 7 2 1 Convert to ASCII The output files HOUT TH OUT CONCx OUT SORBx OUT TEMP OUT and V OUT provide binary output of specific variables The user interface can convert these binary files into the ASCII files H TXT TH TXT CONCx TXT SORBx TXT TEMP TXT and V TXT using the Convert to ASCII dialog window Fig 146 Results Other Information on the Data Tab of the Navigator Bar or Results gt Convert Output to ASCI The ASCII text files e g h txt th txt v txt simply provide Print Time followed by a sequential list of values of a particular variable These values are listed in the same order as Finite Element nodes Coordinates for each FE node can be found in the MeshTria txt file Convert to ASCII Convert to ASCII the following files K Cancel Pressure Heads h out Weater Contents th out elocities v out Concenrations conc out and sorb out Help Temperatures temp out Figure 146 The Convert to ASCII dialog window 226 8 Graphical User Interface Components 8 1 View Window 8 1 1 Scene and Viewing Commands We will use here the term Scene for the content of the View window Four types of commands are available to change the display of the Scene in the View window a Commands to define a required Display of the Scene Detailed information about particular commands is given in Section 8 4 In addition to those commands it is always p
366. tial condition for solute transport equilibrium concentrations Specifies the initial condition for solute transport nonequilibrium concentrations Specifies the initial condition for heat transport Imports the initial condition from previous simulations for water flow and solute and heat transport Command used when defining Initial Conditions on Geometric Objects Deletes all defined Initial Conditions and assigns default values 260 Boundary Conditions Water Flow Solute Transport Heat Transport Boundary Conditions Options Deletes All Boundary Conditions Specifies boundary conditions for water flow Specifies boundary conditions for solute transport Specifies boundary conditions for heat transport Specified additional system dependent water flow boundary conditions Clears all boundary conditions and assigns a No Flow boundary condition on all boundaries Edit Properties and Conditions on FE Mesh_ Selects that spatially variable properties e g materials initial conditions are assigned directly to the FE Mesh rather than to Geometric Objects Edit Properties and Conditions on Geometric Objects Selects that spatially variable properties e g materials Transfer all Properties to FE Mesh Sections Edit Sections Generate Sections New Section from Selection New Section from View Display Whole Domain Display Previous Partial View Hide Selection Display only Selection Display Reverse Cut with Rec
367. tially correlated Stochastic Parameters Hydraulic Conductivity Scaling Factor Standard Dev of log1 0i Correlation Length in x Correlation Length in z Log Normal Distribution Pressure Head Scaling Factor Standard Dev of logt Of Correlation Length in x Correlation Length in z Log Normal Distribution Water Content Scaling Factor Standard Dev of log Of Correlation Length in x Correlation Length in z Log Normal Distribution Figure 122 The Stochastic Parameters dialog window 192 6 5 Defining Properties on Geometric Objects As described above various spatially variable properties e g material distribution initial conditions etc can be specified in Version 2 0 of HYDRUS Standard and Professional not Lite either a directly on the Finite Element Mesh FEM as done in Version 1 0 or b on Geometric Objects e g boundary curves rectangles circles surfaces solids or Geo Sections only in Version 2 0 and the Professional Version To be able to define properties on Geometric Objects one needs to first enable this option Edit domain properties initial and boundary conditions on Geometric Objects in the Domain Type and Units dialog window see Figs 6 or 7 Which option is used depends on the menu command Edit gt Properties and Conditions on FE Mesh disabled when the FE Mesh does not exist A similar button switch is also av
368. ting is provided as an option in HYDRUS to minimize some of the problems with numerical oscillations when relatively steep concentration fronts are being simulated For this purpose the second flux term of advective dispersive equation is not weighted by regular linear basis functions but instead using nonlinear functions Yeh and Tripathi 1990 The weighing functions ensure that relatively more weight is placed on flow velocities of nodes located at the upstream side of an element Additional Artificial Dispersion may be added also to stabilize the numerical solution and to limit or avoid undesired oscillations in the Galerkin finite element results Artificial dispersion is added such that a Stability Criterion involving Pe Cr the product of the Peclet number and the Curant number Perrochet and Berod 1993 is satisfied The recommended value for Pe Cr is 2 0 c Solute Information Number of Solutes Number of solutes to be simulated simultaneously or involved in a decay chain reaction Pulse Duration Time duration of the concentration pulse Concentrations flux or resident along all boundaries for which no time variable boundary conditions are specified are then set equal to zero for times larger than the Pulse Duration When the Fumigant option is active this variable is used instead to define Time of Tarp Removal Mass Units Units to be printed to the output files or displayed in various graphs Mass units have no effect on th
369. tion 6 3 1 Time Variable Head Flux I BCs The options that are available on the first tab Time Variable Head Flux 1 BCs Fig 118 apply to the first Time Variable Head Flux boundary condition The following new options are available here a While in version 2 0 of HYDRUS 2D all boundary conditions i e fluxes or pressure heads changed in abrupt steps the new version allows boundary pressure heads to change smoothly with time Abrupt changes in the pressure heads lead to sudden changes in fluxes while smoothly changing pressure heads provide smoothly changing fluxes An example of such a boundary condition is the water level in a stream or furrow b While version 2 0 of HYDRUS 2D only allowed either time variable pressure heads or time variable fluxes on a particular part of the boundary the new version allows boundary conditions to change from variable pressure heads to a zero flux and vice versa This boundary condition can be used for example for a disc permeameter where the specified head changes to a zero flux during time periods when the permeameter is re supplied with water The zero flux is initiated by specifying a value larger than 999999 c When a time variable pressure head boundary condition is specified along a boundary then the specified value is assigned to the lowest nodal point of a particular boundary while pressure heads at other nodes are adjusted based on the z coordinate When this option is selected then nod
370. tion reactions In addition physical nonequilibrium solute transport can be accounted for by assuming a two region dual porosity type formulation which partitions the liquid phase into mobile and immobile regions Attachment detachment theory including filtration theory is additionally included to enable simulations of the transport of viruses colloids and or bacteria HYDRUS may be used to analyze water and solute movement in unsaturated partially saturated or fully saturated porous media The program can handle flow regions delineated by irregular boundaries The flow region itself may be composed of nonuniform soils having an arbitrary degree of local anisotropy Flow and transport can occur in the two dimensional vertical or horizontal plane a three dimensional region exhibiting radial symmetry about the vertical axis or a fully three dimensional domain The two dimensional part of this program also includes a Marquardt Levenberg type parameter optimization algorithm for inverse estimation of soil hydraulic and or solute transport and reaction parameters from measured transient or steady state data for two dimensional problems Details of the various processes and features included in HYDRUS are provided in the Technical Manual im nek et al 2011 The main program unit of the HYDRUS Graphical User Interface GUI defines the overall computational environment of the system This main module controls execution of the program and determ
371. tivate Activate by E mail Activate on line Request or Enter Activation Codes Internet Connection Required Deactivate by E mail Deactivate on line prere j Figure 165 The HYDRUS Authorization Status dialog window Tab Status For the commands in this dialog window to be active e g Activate by E mail or Activate on line HYDRUS needs to be run with administrator privileges That means that you need to be logged as an Administrator or as a user belonging to Administrators group when making changes to the authorization To run HYDRUS as administrator under Windows Vista or Windows 7 operating systems click on the HYDRUS icon on your desktop using the right mouse button and select Run as Administrator from the popup menu Warning displayed in Figure 166 is issued 276 when attempting to make changes to the Authorization Status while not running HYDRUS with administrator privileges a SS HYDRUS 2 xx HYDRUS activation requires administrator privileges You must be logged as an Administrator or as a user belonging to Administrators group when making changes to the authorization Under Windows Vista and Windows 7 you should run HYDRUS as administrator click on the HYDRUS icon on your desktop using the right mouse button and select Run as administrator Please restart HYDRUS with administrator priviledges or contact your system administrator Lo Figure
372. tively freely While the text above in Section 6 refers to the first approach specifying properties at FE Mesh the second approach on Geo Objects is briefly described below While this latter approach can be used for all Domain Properties and Initial and Boundary Conditions we will demonstrate its use below on Material Distribution for which it seems to be the most relevant There are multiple commands that are common for most properties when defining Domain Properties Boundary Conditions and Initial Conditions on Geometric Objects These commands are listed in the Commands part of the Edit Bar and are listed in Table 20 Table 20 Definition of commands used to manipulate Property Objects New Property Creates a new Property Object For some Properties there is a list of available options and user needs to select from this list e g water flow boundary conditions or can extend this list e g Materials For others user needs to define values e g scaling factors or functional forms e g initial conditions of new Property Objects Set Property Selects one particular Property from a list or Property Objects and assigns it to a selected Geo Object s Clear Property Clears a particular Property from selected Geometric Points This command is used only for Properties that do not have a default Property e g Nodal Recharge Observation Nodes Clear All Properties Clears all assigned Properties from geometric objects and as
373. tors define a linear plane with generally an inclined surface More than three thickness 141 vectors with different lengths then define the top surface that is formed by triangles whose coordinates are calculated from the thickness vectors using linear interpolation or extrapolation When breaks in the slope of the top surface are to be defined exactly then it is necessary to define internal curves in the base surface Figures 82 and 83 show the importance of having internal curves or not having them in the Y direction for proper definition of the solid compare Figures 80 and 82 Figures 81 and 83 Figure 82 Missing internal curves in the base surface Figure 83 Consequence of missing an internal curve in the base surface on the FE Mesh of the top surface Note Three Thickness Vectors needs to be specified to define a Domain with a linearly changing thickness As long as only two Thickness Vectors are specified the thickness of the Domain is constant and defined using the first Thickness Vector with lower index since three points are needed to define a plane 142 4 6 Intersections of Surface and Solids Intersections of Surfaces and Solids Fig 84 can be created using the following approaches A Intersection of Surfaces Select two or more Surfaces click with the right mouse button on these selected Surfaces and select the command Create Intersection When more types of different objects are selected e g
374. ture HYDRUS assumes that this dependency can be expressed by the Arrhenius equation Stumm and Morgan 1981 This equation can be expressed in the general form Br oo aex Rr where a and ary are values of the coefficient being considered at a reference absolute temperature T and absolute temperature T respectively R is the universal gas constant and E ML T M is the activation energy of the particular reaction or process being modeled The activation energy characterizing the temperature dependence of the solute transport and reaction parameters is entered in the dialog window shown in Figure 28 When the Fumigant option is active the fifth variable normally reserved for the Frendlich exponent is used to enter the activation energy for the resistance of surface tarp Temperature Dependent Solute Transport and Reaction Parameters Parameters SinkWaterl SinkSolid1 SinkGas1 SinkWaterl SinkSolid1 SinkGas1 51213 81171 51213 0 81171 51213 81171 Previous Figure 28 The Temperature Dependent Solute Transport and Reaction Parameters dialog window 71 3 14 Water Content Dependence of Solute Reaction Parameters The water content dependence of degradation coefficients is implemented using a modified equation of Walker 1974 uO u 0 min 3 r where 4 is the values of a particular coefficient rate constant at the reference water content 6 4 is the value of this coefficient at the
375. tus dialog window Fig 165 displays information about Authorization Status Last Activation and License Information such as License Number Computer ID Workplace and License Owner Authorization Status information includes information about a Status which can be either Not Authorized or Authorization OK 275 b Level of authorization which can be either 2D Lite 2D Standard 3D Lite 3D Standard or 3D Professional c whether or not the Authorization is Time Limited if yes then the Expiration Time is given and d whether or not the Network Installation is active if yes then the Number of Clients is given All this information is displayed as read only text that is filled in during the first activation of the software The button Send Authorization Report is used when resolving problems with software activation F HYDRUS 2 02 Authorization Status o pas Authorization Method Select available authorization method gt Hardware Key automatically at startup Software Key Status Add on Modules History of Activations Authorization Status Status Authorization OK Leve 3D Professional Time limited Authorization Network Installation Last Activation Activation Date 1 2 2011 Send Authorization Report Not available License Information License Number 1001 Workplace PCX Computer ID 106300092 Description Home PC License Owner PC Progress Activate or Deac
376. u saturation inhibition coefficient for Sno mg N L 0 5 Kyuu saturation inhibition coefficient for Syy nutrient mg N L 0 05 Kms saturation inhibition coefficient for Sms mg S L 140 Autotrophic bacteria Ln maximum aerobic growth rate on Syy 1 d 1 0 35 ba rate constant for lysis 1 d 0 15 0 05 Koa saturation inhibition coefficient for So mg O2 L 1 Kyua saturation inhibition coefficient for Sny mg N L 0 5 5 Kimsa saturation inhibition coefficient for Sms mg S L 140 Fermenting bacteria LFB maximum aerobic growth rate for Xps 1 d 3 1 5 Drg rate constant for lysis 1 d 0 02 Korp saturation inhibition coefficient for So mg O2 L 0 2 Kopp saturation inhibition coefficient for Sp mg CODsp L 28 Kyorp saturation inhibition coefficient for Sno mg N L 0 5 Kyure saturation inhibition coefficient for Syy nutrient mg N L 0 01 Kypsrp saturation inhibition coefficient for Sys mg S L 140 Acetotrophic methanogenic bacteria LAMB maximum aerobic growth rate on for Xap 1 d 0 085 DAMB rate constant for lysis 1 d 0 008 Koamp saturation inhibition coefficient for So mg O2 L 0 0002 Ksamp saturation inhibition coefficient for S mg CODs L 56 Kyoamp saturation inhibition coefficient for Sno mg N L 0 0005 KyNuaMsB saturation inhibition coefficient for Sny nutrient mg N L 0 01 Kyposamp saturation inhibition coefficient for Sys mg S L 140 Acetotrophic sulphate reducing bacteria LIASRB maximum aerobic growth rate for Xaspp
377. uation of the Wetted Area 187 The radius of the wetted area for drip irrigation for transient conditions can be calculated in Hydrus as follows The irrigation flux Q is applied to the single boundary node that represents the dripper with the Neumann flux boundary condition If the pressure head required to accommodate the specified flux Q is larger than zero the boundary condition in this particular node is changed into the Dirichlet head boundary condition with zero pressure head value and the actual infiltration flux Q through this node is calculated The excess flux Q Q is then applied to the neighboring node again with the specified Neumann boundary condition This procedure is iteratively repeated until the entire irrigation flux Q is accounted for and the radius of the wetted area is obtained Since the infiltration flux into the dry soil is larger for early times the wetted area continuously increases as irrigation proceeds This option is currently available only for two dimensional and axisymmetrical geometries Implementation User needs to specify the Time Variable Flux 1 boundary condition at the surface boundary The length of this boundary needs to be sufficient to accommodate the entire wetting zone The drip discharge flux Q needs to be entered in the Var FI 1 column of the Time Variable Boundary Conditions dialog window User also needs to specify from which node of the Time Variable Flux 1 boundary irr
378. ue limits transferred values will not exceed the specified minimum and maximum Minimimum Value 9 Maximum Value 10000 V Clipping box no transfer of values outside this box Xmin 199 111 im Xmax 466 762 m Ymin 263 435 m Ymax 640 187 m Zmin 8 75 m Zmax 33 25 m Figure 134 The Import of Values from Scattered Points dialog window When imported values possibly available only in some part of the transport domain are linearly interpolated extrapolated to the rest of the transport domain the calculated nodal values can be lower or higher when extrapolated than those measured imported If users want to prevent that they have several options how to proceed a They may specify additional import values for selected nodes in the transport domain or at the domain boundaries so that interpolation rather than extrapolation is used in 206 the entire transport domain Extrapolation is used in the part of the domain where no imported values are located b They may constrain interpolation extrapolation to only a certain part of the transport domain clipping box c They may specify what a minimum and maximum value could be Value Limits It is up to the users to select an optimal import and interpolation options suitable for their purpose depending also on an imported variable Note For the maximum accuracy in the transfer of measured values to the finite element nodes it is recomme
379. ulic Properties Model Soil Hydraulic Parameters Anisotropy Tensors Solute Transport Parameters General Information HP2 Components HP2 Definitions Solute Transport Parameters Solution Composition Solute Reaction Parameters Wetlands Parameters I Wetlands Parameters II Temperature Dependence Water Content Dependence Chemical Parameters Fumigant Application Heat Transport Parameters Root Water Uptake Root Water Uptake Models Pressure Head Reduction Osmotic Head Reduction Variable Boundary Condition Data for Inverse Solution FE Mesh Parameters Generate FE Mesh Delete FE Mesh Remove Selected FE Elements FE Mesh Statistics Advanced FE Mesh Generation Fundamental Triangulation Mesh Refinement Homogeneous Triangulation Check of Convexity Mesh Smoothing Select Mesh Nodes Select Mesh Elements Material Distribution Root Distribution Nodal Recharge Scaling Factor Hydraulic Conductivity 249 Initial Conditions Boundary Conditions Pressure Head Water Content Local Anisotropy Angle First Component Second Component Index Subregions Observation Nodes Edit in View Delete Clear All Drains Edit in View Delete Clear All Drain Parameters Flowing Particles Edit in View Delete Clear All Stochastic Distribution of S F Subregions Material Distribution Nonequilibrium Conc a Equil Conc Parameters for Root Distribution Delete All Domain Properties Default Domain Parameters Pressure Head Water Content Con
380. ult FE Mesh Sections the Mesh Section Tab of the FE Mesh Parameters dialog window Fig 105 or FE Mesh Sections for detailed description see Section 5 7 can be created by a user Default FE Mesh Sections depend on the geometry of the transport domain For examples default section include a Entire FE Mesh b Vertical horizontal shell and c Each horizontal vertical layer Mesh Sections can also be generated for each Geo Section see Section 8 1 8 The Mesh Sections are generated automatically when the FE Mesh is generated or anytime using the menu command Edit gt Sections gt Generate Sections note that the dialog window to Options for Generation of Geo Sections and FE Mesh Sections Fig 151 is similar to the Sections Tab of the FE Mesh Parameters window Fig 105 Main Stretching MG Options Options Sections Export Generate Mesh Sections FE Mesh Sections F Boundary Shell Mesh Layers 7 Mesh Sections for generated Geo Sections 7 Mesh Sections for user defined Geo Sections Previous Apply Default All Default Figure 105 The FE Mesh Parameters dialog window Mesh Section Tab 167 5 4 Finite Element Mesh Refinement The Finite Element Mesh Refinement is carried out in two steps 1 One must first define the desired type of FE Mesh Refinement using the dialog window shown in Figure 106 Mesh refinement can be defined around Points Lines
381. unter clockwise direction on closed curves Boundary nodes determine the local densities of the triangular mesh that is being generated for a given boundary nodal distribution and are part of the triangular mesh 175 Boundary Edges Boundary edges are abscissas discretizing boundary curves They connect generated boundary nodes are oriented in a counter clockwise direction and are located on the edge of the mesh Fixed Points Fixed points are points on boundary curves marked by red squares These points may be used to adjust the local density of boundary nodes using FE Mesh refinement By default fixed points are placed on all nodes of polylines and on all object boundary points describing the boundary but they can be also inserted or deleted at any other point on boundary curves Generation of the Unstructured Triangular Mesh The unstructured triangular mesh is generated by means of five operations 1 discretization of the flow domain into triangles with vertices at given boundary nodes Fundamental Triangulation 2 inserting new points in all triangles which do not fulfill a certain smoothness criterion Mesh Refinement 3 implementation of Delaunay s retriangulation for the purpose of eliminating all nodes surrounded by more than six triangles as well as to avoid extreme angles Remeshing 4 smoothing of the mesh by solving a set of coupled elliptic equations in a recursive manner Smoothing and 5 correction of possi
382. ution Displays or hides the Navigator window Displays or hides the Edit Bar Displays or hides Tabs in the View window Displays or hides the Status Bar Selects which toolbars are to be displayed the Toolbars dialog window Fig 156 Arranges toolbars Customizes toolbars the Customize Toolbars dialog window Fig Fig 157 Sets a default viewing direction in 3D and performs the View All command Zooms in on a certain part of the View window using a rectangle Changes a scroll position and a zoom factor so that all currently displayed objects are visible in the View Window This command does not change the viewing direction Shows the previous view on a certain part of the View window Sets the View windows so that dynamic actions can be carried out with a cursor Moving the cursor while holding the left mouse button allows the object to be displayed in a different part of the View window Pressing the Shift button on the keyboard allow zooming actions around the cursor Calls the View Stretching Factors dialog window Fig 148 and adjust stretching factors Sets perspective view Starts Autorotate function that will rotate the transport domain in the View window Cancels the Partial View and displays the entire transport domain Sets isometric view Sets the view of the transport domain in the X direction Sets the view of the transport domain in the Y direction Sets the view of the transport domain in the
383. verse estimation of solute transport parameter can be defined using different types of concentrations Available Concentration Types are a the resident concentration in the liquid phase b a log transformation of the resident concentration in the liquid phase c the outflow flux concentration d the solute concentration flux e the cumulative concentration solute flux and f the total resident concentration The total resident concentration includes concentrations in the sorbed and nonequilibrium phases The maximum number of iterations for the inverse solution is also specified in this dialog window If one selects zero number of iterations then only the direct simulation is carried out However users can still enter measured data in which case the code compares results of the direct simulation with the measured data Data for Inverse Solution OK Type Position Weight Cancel Help Add Line Delete Line on none wh a 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 C Show list boxes not recommended for large data files Figure 14 The Data for Inverse Solution dialog window In the table Data for Inverse Solution Fig 14 one specifies the measured data that will be analyzed during the parameter optimization process Many different types of data can be used to define the objective function that will be minimized for this purpose How the values in the X and Y columns are interpreted depends on the Type and Po
384. w If the option Changed Frames Only is on then changes in the View window are stored regardless of the actual time elapsed in redrawing the View For example if some changes in redrawing of view take place quickly followed by a pause and again fast changes in the resulting video all changes will be played back with a constant time delay The current version of HYDRUS does not have an option allowing to set a time interval between recorded frames It is entirely possible that one can edit Video recordings created by HYDRUS using some public domain programs for editing videos We currently do not have any experience with that and can not make any recommendations 299 9 10 About HYDRUS This window displays the program version the Program Tab authors of the HYDRUS application the Authors Tab and the License agreement the License Agreement Tab The Program Tab additionally displays other software products such as mesh generators that are used in HYDRUS About HY D R U S Program Authors License Agreement 2D 3D Version 2 x Program name HYDRUS Program version 2 01 0450 Release date 10 1 2011 WEB site www hydrus3D com Support support pc progress cz Copyright 2006 2011 PC Progress s r o All rights reserved This product uses GENEX Copyright c FEM Consulting s r o a T3D Copyright c Daniel Rypl CVUT Prague HY D R U Ss Program Authors License Agr
385. w FE Mesh Refinement No 1 FE mesh Refinement on ae sia oe Apply FE Mesh Refinement to ens Point Circular f Point Rectangular Line through FE Lenath O Surface O Solid Parameters Number of Global FE Size 50 cm Comment Current Global Targeted Size of Finite Elements 0 630 m Division FE Nodes 28 FE mesh Refinement on Line given by N points p N 17 Global FE Size 50 cm Comment 173 New FE Mesh Refinement No 1 Apply FE Mesh Refinement to Point Circular Point Rectangular Line through FE Length Line through Division 5 O Solid Parameters Targeted FE Size Current Global Targeted Size of Finite Elements 0 630 m FE mesh Refinement on Surface No 2 FE Size S 20cm gt tj Te Global FE Size 50 cm Comment New FE Mesh Refinement 1 Apply FE Mesh Refinement to O Point Circular Point Rectangular Line through FE Lenath Line through Division O Surface Said Parameters Targeted FE Size mi Current Global Targeted Size of Finite Elements 0 630 m FE mesh Refinement on Solid No 2 FE Size S 50cm S Global FE Size 100 cm Comment Apply Figure 111 The FE Mesh Refinement dialog window for the Genex T3D module with six different types of refineme
386. w is higher than the upper optimal iteration range the time step is multiplied by this number time step is decreased Recommended and default value is 0 7 Internal Interpolation Tables At the beginning of a numerical simulation HYDRUS generates for each soil type in the flow domain a table of water contents hydraulic conductivities and specific water capacities from the specified set of hydraulic parameters Values of the hydraulic properties are then computed during the iterative solution process using linear interpolation between entries in the table If the pressure head h at some node falls outside the prescribed interval ha hy the hydraulic characteristics at that node are evaluated directly from the hydraulic functions i e without interpolation The above interpolation technique was found to be much faster computationally than direct evaluation of the hydraulic functions over the entire range of pressure heads Interpolation using tables can be avoided by setting ha and hy both to zero Then the soil hydraulic properties are always evaluated directly from the hydraulic functions i e without interpolation Output graphs of the soil hydraulic properties will be given also for the interval ha hy Lower limit of the Absolute value of the lower limit L of the pressure head interval for tension interval which a table of hydraulic properties will be generated internally for each material Upper limit of the Absolute value
387. window Fig 35 Specifies time dependent boundary conditions for all transport processes the Time Variable Boundary Conditions dialog window Fig 37 Specifies data for the inverse solution their type location and associated weight the Data for Inverse Solution dialog window Fig 14 Selects the structured or unstructured finite element mesh generator the Finite Element Mesh Generator dialog window Fig Error Bookmark not defined Specifies either parameters of the Unstructured Finite Element Mesh Generator the FE Mesh Parameters dialog window Figs 98 through 104 or parameters of the structured mesh the Rectangular Domain Discretization dialog window Fig 96 or the Hexahedral Domain Discretization dialog window Fig 97 Generates unstructured finite element mesh Deletes unstructured finite element mesh Removes selected finite elements from the finite element mesh Note that this operation should not be performed when properties are specified on Geometric Objects Provides information about finite element mesh the FE Mesh Information dialog window Fig 113 Selects FE Mesh nodes This command is usually used to select nodes that are then either used to define the new FE Mesh Section or removed from the FE Mesh Selects FE Mesh elements to perform similar operations as for selected mesh nodes Performs triangulation of boundary nodes based on the Delaunay criterion Inserts a new point in the center of
388. y dripper is affected by many factors including the pressure in the cavity its size and geometry and the hydraulic properties of the surrounding soil Lazarovitch et al 2005 When a predetermined discharge of a subsurface source e g a subsurface emitter is larger than the soil infiltration capacity the pressure head in the source outlet increases and becomes positive The built up pressure may significantly reduce the source discharge rate A special system dependent boundary condition for flow from subsurface sources that uses the drip characteristic function was implemented in HYDRUS see the Technical manual This function has two variables i e the nominal discharge Optimal Flux in Fig 119 of the source for the reference inlet pressure hin usually being 10 m and the back pressure equal to zero and an empirical constant Exponent in Fig 119 that reflects the flow characteristics of the emitter Normally c 0 5 corresponds to a turbulent flow emitter and c 1 to a laminar one This option is currently available only for two dimensional and axisymmetrical geometries Implementation User needs to specify the Time Variable Flux 1 boundary condition along the dripper boundary and hin in the Var H 1 column of the Time Variable Boundary Conditions dialog window A positive pressure indicates an irrigation period and a negative pressure indicates a non irrigation period Surface Drip Irrigation Dynamic Eval
389. y SARSAN Ix E Furrow Results Pressure Head I DA Vow Options WW Rents Donan Geometry SD FE Mech Sectors E Coma Properties GG Inte Contin E Sardtary Condition Presuse Head jom corbahon 2 gt GD Concertiston 3 GD Floweng Parie r JiM G n Tne MryMax Godal n Space OE Numbering s Pressure Standard Scale OG Aatachary Otoci Custom Scale EG Rendering Model de Scale and Colors E Giagh type B uzing C Bi Cou Scale er Cortese Isoires Smooth cole tansitons when dang Syitem Dead Plane gt Z X RIR on Y 0000m Figure 143 The color smoothing 22l 7 1 4 Export Isolines The Export Isolines command File gt Export gt Export Isolines saves coordinates of all currently displayed isolines the Jsolines Graph Type has to be selected into a Project_Property_Isolines txt text file e g Furrow_Pressure_Head_Isolines txt Figure 144 displays an example of this file for the Furrow project In the text file a definition of each isolines is given first e g Isoline 1 Value 60 000 Segment 1 followed by the x and z coordinates of sequential points in which the isoline crosses edges of finite elements The Export Isolines command can be used for example to export coordinates of the groundwater table In such case a custom scale with one single value h 0 could be prepared and exported RISALA E Vk Yen ae Ey AA AN aA x GIN EA KNS N Sea SASARAN E o So o O Progra
390. y the Vector of Translation for the Translate or Copy operations or the Angle of Rotation for a Rotation or define the Mirroring Plane Axis for a Mirroring operation Translate Cop Vector of Translation Numbering di 0 000 Set first number for numbering of new objects that will be created during copying 0 000 Points 7 Automatic Z 0 000 Lines J Automatic Copy Surfaces Z Automatic Number of Copies EH Solids V Automatic Connections between Copies Lines Surfaces Solids Generate connecting objects between copies Apply Cancel Figure 56 The Translate Copy dialog window Rather than simply Translating or Rotating a given object one can choose to use this operation e g Translate Move or Rotate to create one or multiple copies of a given object by specifying the Number of Copies see Figs 56 and 57 left Once one or more copies of a given object are to be created one can also choose to Generate Connecting Objects Between Copies e g Fig 56 What types of connecting objects are to be created is selected in the Manipulation Options window Figs 59 HYDRUS can generate a lines between selected nodes and their copies b surfaces between selected lines and their copies and c solids between selected surfaces and their copies Lines can be either straight or curved when a copy is created using the Rotate operation 114 Rotate Rotation Copy Ang
391. zero for x gt x y gt y gt z respectively Vrugt et al 2002 and b x z and b x y z denote two and three dimensional spatial distribution of the potential root water uptake See Vrugt et al 2001 2002 for different configurations of the normalized spatial distribution of potential root water uptake rate The equations above are given and used in absolute coordinates i e they are independent of any actual selection in GUI The x and y coordinates are identical to x and y coordinates for the geometry of the transport domain The only exception is that the beginning of the z coordinate for the root distribution starts at the highest located node of the entire transport domain again independent of any actual selection 82 Root Distribution Parameters Vertical Distribution Maximum Rooting Depth Depth of Maximum Intensity Parameter Pz Horizontal Distribution R Specify Parameters for Horizontal Distribution Maximum Rooting Radius 90 Radius of Maximum Intensity 30 Parameter Px 1 Horizontal Distribution Y Specify Parameters for Horizontal Distribution Figure 36 The Root Distribution Parameters dialog window 83 3 21 Time Variable Boundary Conditions The Time Variable Boundary Conditions dialog window is shown in Figure 37 Time Variable Boundary Conditions Parameters OK Precip Evap Transp hCritA VarFll Var H 1 4 Cance

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