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1. Show Grid Rendering Mode gt 5 New Window Snap to Grid Graph Type gt E Arrange Symbols 1 Grid and Work Plane Display Options EP Main and Secondary Define Work Plane i Program Options E Tile Horizontally Coordinate System T Tile Vertically Color Scale T Cascade sa Translate T Close All T3 Rotate 1 0001 Domain Properties Material Distribution At Mirror wt Intersect Lines Split Lines gt Contents Insert Points on Line d Hydrus 3D License and Activation ke Check Geometry About Hydrus 3D A Figure 114 The HYDRUS Menus III Tools Options Windows and Help 172 Group A File B Edit Table 14 HYDRUS menu commands Menu New Open Close Save Save As Save All Import and 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 Delete All Domain Geometry Submenu Sub Submenu Import Hydrus 2D Project Import Input Data from IN Files Export Data for Hydrus Solver in Text Format Read Points from a Text File Import Geometry from a Text File Export Geometry from a Text File Export only Selected Objects Select by Rhomboid Select by Circle Select by Polygon Add to Selection Remove from Selection Standard Selection Mode Geometry Information Geometry Definition Points Lines Surface
2. S 5 00 em Current Global Targeted Size of Finite Elements 15 00 cm Comment Global FE Size 5 cm Figure 81 The New FE Mesh Refinement dialog window As an example Figure 58 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 of 50 cm and three FE Mesh Refinements Fig 58 top Refinement 1 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 58 bottom 125 eee rereneneres a Figure 82 Example of FE Mesh Refinements top and FE Mesh bottom 126 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 pr
3. Convert to ASCII the following files OK Cancel Pressure Heads h out mr Water Contents th out elocities v out Concenrations conc out and sorb out Temperatures temp out Figure 101 The Convert to ASCII dialog window 153 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 possible 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 resul
4. Move Copy Vector of Translation Numbering ax 000 fem az 0 00 em Set starting numbers for new objects that will be created during copying Points V Automatic Lines g Copy Surfaces V Automatic Number of Copies Solids M Automatic Apply Figure 45 The Move Copy dialog window Rotate Rotation Copy Angle 5 00 Number of Copies of Definition of the Axis of Rotation Point and Parallel Axis O2Points Pi Coordinates x x Z 1 Pont 2491 422 90 0 00 fom don Fa Numbering Mirror Definition of the Mirroring Plane Point and Parallel Plane O3Points Pic Yz W x ag 0 00 o ooo 1 Point Z 0 00 em Pick Copy ann Numbering C Make Copy Apply Figure 46 The Rotate left and Mirror right dialog windows 85 4 1 6 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
5. 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 Pressure Head Water Content Concentration Nonequilibrium Concentration Temperature Import Water Flow Solute Transport Heat Transport Boundary Conditions Options Generate FE Sections Edit Sections New Section from Selection New Section from View Display All Display Previous Hide Selection Display only Selection Display Reverse New Section by Rectangle New Section by Indexes Edit Delete Selected Delete All Auto Adjust Work Plane Dimensions Delete Selected Delete All Comments Edit Delete Selected Delete All Dynamic View Scroll Zoom Rotate View Stretching Perspective Auto Rotate 175 D Insert View in Direction List Boxes for Inverse Data Domain Geometry FE Mesh Refinement Domain Properties Initial Conditions Boundary Conditions Isometric In X direction In Y direction In Z direction Reverse X direction Reverse Y direction Reverse Z direction Points Lines Surfaces Openings Thicknesses Solids Graphically Dialog Material Distribution Root Distribution Nodal Recharge Scaling Factor Local Anisotropy Subregions Observation Nodes Drains Flowing Particles Pressure Head Water Content Concentration None
6. 64 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 30 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 450 in the root water uptake response 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 30 65 3 17 Root Distribution Parameters The spatial distribution of the roots can be specified using the Root Distribution Parameters dialog window Fig 31 The following two and three dimensional root distribution functions are implemented in HYDRUS Vrugt et al 2001 2002 z ek te VEREA EAMG Ln Xn Px ele Py oP A EAA wa EE 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 p py pz x L y L and z L are empirical parameters x y and z are in Fig 31 indicated as Depth of Maximum
7. Figure 88 The Temperature distribution dialog window The initial condition can be imported from the results of previous calculations 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 h3d 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 89 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 Warning Import of results of previous calculations as initial conditions for the new simulation can be done only from a project that has an identical FE Mesh discretization as the actual project 136 Import Initial Conditions Import data from Hydrus 3D project CAUSSLIHYDRUS3D 2D_Tests Furrow h3d Select quant
8. General Vector Y Previous Apply All Default Figure 77 The FE Mesh Parameters dialog window Tab Stretching 120 The Option 1 Tab Parameters for the unstructured triangular finite element generator are given in the Options 1 Tab of the FE Mesh Parameters dialog window Fig 78 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 an 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 domai
9. Key 2 and press Activate Now 4 Remember that your single user license is hardware dependent After upgrading your hardware BIOS hard drives you probably will have to ask for new activation codes In that case you are eligible to obtain those codes for free although subject to some limitations ask for more detail 5 Network installation A single user license only works for HYDRUS installed on a local drive Installation on a network drive requires a network license that allows you to run HYDRUS simultaneously on N usually N 20 client computers When installing HYDRUS on a network drive please remember that client computers must be authorized to access the HYDRUS installation directory and its subdirectories for writing It is also necessary to run the HYDRUS installation on each client computer so that all system files and ActiveX components are installed and registered on all client Windows systems 6 A network license requires activation on one client computer where HYDRUS is running on a network drive and a server where HYDRUS is running on a local drive Activation on the server is not required if HYDRUS is not used on this computer 194 Hydrus License and Activation Hydrus License Contact Information Level EEM PC Progress s r o ii Anglicka 28 120 00 Prague Options Czech Republic Tel FAX 420 222 514 225 2D Damains E mail hydrus pc progress cz Rectangular General Find your Reseller 3D Domai
10. Point a Beginning Point and an End Point Fig 62 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 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 103 Set new Thickness a Numbers for new Thickness E Point 4 Definition by Point and Length Point and Coord O Two Points O Three Points Vector Length L 100 00 cm C Reverse Points Vector Direction Perpendicular to the Base Surface O In x direction O In Y direction O In Z direction Help 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 61 The Edit Bar during the process of graphically defining a Thickness Vector A definit
11. 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 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 component 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
12. 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 87 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 will then be kept constant during the simulation Similar but simpler dialog windows are used to specify initial values of the temperature and the liquid and adsorbed concentrations e g Temperature Distribution dialog window Fig 88 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 135 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
13. as part of a solute decay chain Sink W0 Zero order rate constant for dissolved phase ML T SinkSO Zero order rate constant for solid phase 4 T SinkGO0 Zero order rate constant for gas phase y ML T 56 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 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 T for the second sorption sites First order entrainment detachment coefficient ka T 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 coefficien
14. 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 98 Edit Solid Edit Solid Genera Sub Layers Thickness Profies FE Mesh General SubLayers Thickness Pofles FE Mesh Solid No Number of Sub Layers n fa Sub Layers Constant Coume Thickness Solid Type 4 Layer Thickness T and Thickness Type Variable or Constant Ti Variable Base Surfaces 100 00 Layer 2 20000 M a Autodetect k adi 2 Layered j Thickness Vectors Autodetect T 500 cm Master Thickness Vector Base n Variable Comment Surfaces No 1 Thickness Length 500 cm Edit Solid General Sub Layers Thickness Profiles FE Mesh Thickness Profiles Profile Parameters 01 Default Profile No 1 Name Default Profile This Profile is used on Thickness Vectors No f Layer Thickness T Thickness Sum TS and Thickness Type Variable or Constant T cm TT cm Variable T 100 00 100 00 20000 300 0 M 200 00 soo M ier aoa a ee ee Figure 59 The Edit Solid dialog window the General Sub Layers and Thickness Pro
15. 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 window Fig 70 for this purpose 109 Cross Section Description L uL TRNA x Cross Section P Cross Section Definition Points definition line 3 Help 0 00 crm 000 fom 000 fom al 0 00 cm 0 00 em Direction Olnx Vector 0 00 cm direction ite ah vector intersection Ony 0 00 em Onz 000 er Figure 70 The Cross Section dialog window 4 6 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 di
16. 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 53 The Integrated Tab of the Edit Surface dialog window 92 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 geometrical 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 modeling of its shape see Figs 54 and 55 EA HYDRUS Test Domain Geometry TBR x C Eile Edit Yiew Insert Calculation Results Tools Options Window Help 3 0 Suas 22 aleli leee See Az Geometry aA FE Mesh Domain Pro d Initial Condit A Boundary C 000 Results For Help press F1 System Default Pi Figure 54 An examp
17. to edit pressure head initial conditions Sets the View window to View Edit Boundary Conditions mode to edit water flow boundary conditions 184 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 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 Insert Domain Geometry Points Graphically Dialog Lines Line Polyline Arc Circle Sets the View window to View Results mode to view pressure head distribution 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 110 Arranges toolbars Customizes toolbars the Customize Toolbars dialog window Fig Fig 111 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 w
18. x arbitrary shape FE Mesh density is Help j defined by the Global Targeted FE Size and by Mesh Refinement objects Cancel FE Mesh Refinements at Points FE Size 0 01 Z 5 ize m A Global Targeted FE Size 0 03 m Previous Figure 73 The Finite Element Mesh Generator dialog window One version of the dialog for the structured FE mesh is shown at the top and one for the unstructured mesh at the bottom of the window 116 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 coord
19. 00 Velocity y Display Values at Nodes 00 Velocity Vectors Help 0 Temperature gt Right click on the Color 900 Concentration 1 Scale displays options 00 Concentration 2 Back Boundary Conditions w Concentration 3 I Results Other Information B Edit Bar Sections 4 Geometry a FE Mesh Domain Proper Initial Conditions a Boundary Condi w Results 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 14 as well as a brief discussion of the action taken with particular commands Table 15 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 Geometry Information dialog 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
20. 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 Sand Theta s cm3 cm3 Silt Alpha 1 cm Clay n BD gr cm3 Ks cr day TH33 em3 cm3 TH1500 cm3 crn3 Predict Figure 20 The Rosetta Lite Neural Network Predictions dialog window 49 3 9 Anisotropy in the Hydraulic Conductivity For two dimensional problems users may need to specify the principal components of the anisotropy tensor K and K together with the angle w4 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 Kx ConAY and Kx ConAZ and six coefficients a that represent the cosine of angl
21. 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 000 2 100000e 000 3 200000e 000 Other notes 9 The minimum number of columns is 5 this corresponds to a single Sublayer 10 Z coordinates must be entered in the correct sequence i e from the bottom Base Surface up towards the end of the Thickness Vector 11 If sublayers 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 12 When the THICKNESS ARR3Z_ NLAYERS is used i e the input file includes data of thickness vectors with multiple sub 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 continu
22. 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 color points Displays the spatial distribution of a particular variable by means of color edges Displays Darcy velocity vectors 189 Display Options Edit Default Read Save As Program Options Windows New Window 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 Edits display options in the Display Options dialog window Fig 93 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 has two tabs one related to Graphics Fig 115 and one to Program itself Fig 116 Open a new View window 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 Clo
23. 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 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 properties 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 particu
24. Information Mass Balance Information Convert Output to ASCII Inverse Solution Results Fluxes across Mesh Lines Time Layer First Last Previous Next Animation Charts Cross Section Boundary Line Mesh Line Flowing Particles Draw Particles Positions 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 Graphical presentation of information abo
25. Intensity or Radius of Maximum Intensity parameters px py and p are assumed to be zero for x gt x y gt y 2z 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 66 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 ok Cancel Figure 31 The Root Distribution Parameters dialog window 67 3 18 Time Variable Boundary Conditions The Time Variable Boundary Conditions dialog window is shown in Figure 32 Time Varia
26. Number of Nodes 1D Elements 2D Elements 3D Elements FE Mesh Information Number of Program has created a default Nae set of FE Mesh sections You Ete can create your own sections to 1D Element simplify graphical input of data 2D Elements 3D Elements Previous Figure 84 The FE Mesh Information dialog window for a two dimensional problem top and a three dimensional problem bottom Figure 84 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 E ements the number of triangles on the bottom plane of the domain and the number of 3D E ements tetrahedrals in the entire transport domain 130 5 7 Finite Element Mesh Sections 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 thr
27. Objects Output data include various Results Data are organized in a tree like structure Figure 106 shows Data with expanded Domain Properties on the left and Results in the middle b A View Tab on the right of Figure 106 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 Isolines 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 160 Data Structure 3 Furrow 4 Domain Geometry Flow Parameters H FE Mesh S a Domain Properties Material Distribution 63 Nodal Recharge E Scali
28. Read Points from a Text File Import Geometry from a Text File Export Geometry from a Text File Export only Selected Objects Print Print Preview Print to the Clipboard Print Options Print Setup Project Information Project Manager Recent Files Exit Brief description of the command 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 Opens an existing project represented by the project_name h3d file using the Open dialog window which a user uses to browse for the HYDRUS project Closes an open project 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 Saves data of a particular project under a new project name using Save As dialog window Saves data of all projects Imports Hydrus 2D projects from Version 2 0 Import input data from in files that may have been modified manually outside of the HYDRUS GUI Export data for the HYDRUS solver into the working directory from which the computational module reads inputs and into which it writes outputs Reads single point coordinates from a text file Reads definition of the entire geometry from a text file Writes definition of the entire geometry to a text file Writes definition of the selected objects to a text file Prints th
29. 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 particular video format OpenGL acceleration should be disabled when problems occur when creating Video File Create Video File Video File C Flow4nimation avi Video Codec Type Microsoft MPEG 4 Video Codec V2 sv Quality 100 Recording Frequency Real Time Changed Frames Only Figure 121 The Create Video File dialog window 200 References 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 Wa
30. Standard Scale Custom Scale Edit Scale and Colors Color Smoothing 4 Isolines Color Contours y Color Points 4 Color Edges 4 Velocity Vectors Figure 108 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 Color Contours 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 94 Displays a selected variable using isolines Displays a selected variable using isobands color spectrum Displays a selected variable using color points Displays a selected variable using color edges Displays velocities using velocity vectors 164 Figure 109 shows two more Edit Bars i e those for Domain Geometry and
31. The Edit Bar is very dynamic since it changes depending upon the process being carried out Figure 107 shows the Edit Bars for different processes 1 e for the Material Distribution in the Domain Properties the Water Flow Boundary Conditions the Pressure Head Jnitial Conditions and the Water Content Results dz zixl T Boundary Condition gad Initial Conditions Material Distribution Water Flow a Pressure Head h cm Water Content th WB Material 1 C No Flux 1 000 0 429 E Material 2 F Constant Head E 10 000 0 412 ma 19 000 0 394 E Material 3 E Constant Flux Me ts noo E 376 Commands A Variable Head 1 s 37 000 0 359 223 Edit Materials Variable Head 2 46 000 m 2241 i E 55 000 0 323 C Values by Pointer E Variable Head 3 a E s 7 I Variable Head 4 ome 000 P mmm 200 mm 2 Ka How to set Domain Pr E Variable Flux 1 m 82 000 m 0 270 Ini it E variable Flux 2 91 000 0 252 Next Initial Conditions a ETT Back FE Mesh E Variable Flux 3 100 000 I Variable Flux 4 hee Mat ee i Min 100 000 Min 0 234 I Free Drainage E Deep Drainage Edit Commands 2 Time Layer E Seepage Faca Yf Set Values Time 0 0 00 days Atmospheric Boundary C Values by Pointer Numbering a Chart Tools Liu C Display Codes Cross Section Chart C Flow Animation C Codes by Pointer Boundary Line Chart Numbering Options x ie Took i cele Help pe Cross Section Chart Help a EA Li ikea E Bounda
32. The consistency of the geometry can be verified at any time using the command Check Geometry 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 4 2 2 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 point 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 err
33. Tools Toolbar 2 e ge 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 102 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 CARRAR EE are 62423 168 Rotate View Scroll View Zoom View Similar functions can 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 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
34. View Isometric In x direction In direction amp In z direction S Reverse x direction Numbering Numbering Options Full Rendering Autorotate Reverse direction show Work Plane Reverse Z direction 2 Set Grid and Work Plane yee Tijl Perspective S Coordinate System ae Display Options Figure 105 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 different 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 forh 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 and those for the F
35. analytical functions of Kosugi 1996 for twelve textural classes of the USDA soil textural triangle Textural class 0 0 a n K L L LL cm em 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 48 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 mschaap ussl ars usda gov Schaap et al 2001 Rosetta implements pedotransfer functions PTFs which predict van Genuchten s 1980 water retention parameters and the saturated hydraulic conductivity K 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 ER Rosetta Lite v
36. 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 57 left displays numbers for a Solid a Thickness Vector a Point and a Surface while during the second part it Fig 57 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 96 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 thickness 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 Sur
37. be modified or recalculated as needed 24 B Multiple HYDRUS 2D projects 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 HYDRUS 2D 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 h3d files Input data can be edited either using the HYDRUS graphical user interface this modifies directly the project_name h3d file or the input data can be modified manually In such case 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 h3d file using the command File gt Jmport 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 h3d When the project is closed the Working Directory is deleted Only when a
38. by specifying the number of nodes to be inserted on the line or distance of the point from the beginning of the line Fig 47 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 Paints Type of Points O Split Curve at Inserted Points Insert Parametric Paints a 7 N t Insert Intermediate Points ee al eae Numbering starts with Automatic Automatic Cancel Insert Points on Curve Line No Type of Points Split Curve at Inserted Points Insert Parametric Points New point A O Insert Intermediate Points Distance related to _ Length Diem GON era i 0 00 0 000 0 00 crn Line Start cm i 0 00 0 000 0 00 cm Line End D cm 0 00 ern Numbering starts with _ 0 00 cm No 0 00 cm Point Automattic 0 00 cm Line Automatic Figure 47 The Insert Point on Curve dialog window 86 4 2 Surface An object Surface refers to depending on the problem type and the selection made in the Geometry Information 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 defi
39. can be used to reduce the potential root water uptake to the actual water uptake rate Fig 29 Root water uptake with compensation can be simulated when the Critical Stress Index is smaller than one see the Technical Manual Simimek et al 2006 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 30 62 3 16 Root Water Uptake Parameters Parameters for the water and salinity stress response functions are specified in the Root Water Uptake Parameters dialog window Fig 29 and Fig 30 respectively Root Water Uptake Parameters Feddes Parameters PO POpt P2H P2L K Cancel Previous Previous Figure 29 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 29 left are described in detail in the HYDRUS technical manual Water uptake in this model is assumed to be z
40. 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 97 a Domain Geometry Set new Solid Brick a Numbers for new xx Solid Domain Geometr a 5 Thickness 1 Set new Solid Extruded a Point 37 Numbers for new Solid i Thickness Length Thickness 1 L 730 00 em Point g dL 10 00 em Surface to extrude Thickness Direction Surface 2 Perpendicular to the Surface Autodetect O InX direction Base Surfaces O In Y direction Thee O InZ direction as Help x Ee ass Ke Step 3 of 3 K Step 1 of 2 Set thickness of the new Select a Surface to extrude Solid K Press Esc or right mouse K Press Esc or right mouse button to end the tool button to end the tool Figure 58 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 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 59 that has four tabs General Sub Layers Thickness Profiles and FE Mesh The General Tab
41. inflow outflow rates to from that subregion together with the mean pressure head AMean mean temperature TMean and the mean concentration cMean over each subregion see Table 11 6 of the Technical Manual Absolute 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 Jnverse Solution Results on the Data Tab of the Navigator Bar 152 The text dialog displaying Mass Balance Information or Inverse Solution Results has also only a limited capacity If the file to be displayed is 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 is given Users in such case need 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 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 101 Results Other Information on the Data Tab of the Navigator Bar or Results gt Convert Output to ASCI Convert to ASCII
42. 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 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 FE Mesh Elements Surface Approx Mesh Refinement at Points Refinement on Lines Refinement on Surfaces Domain Properties Paints Handles aia ee Solid Thickness i g Flowing Particles O Dotted Boundary Conditions O Dashed Results Dash dotted Particle Trajectories Isolines Velocity Vectors OOO Transparent Auxiliary Objects O80 General L OOO Colors Line Type Numbering Figure 93 The Display Options dialog window 143 7 1 2 Edit Isoband Value and Color Spectra The Edit Isoband Value and Color Spectra dialog window Fig 94 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 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 an
43. mouse k Press Esc or right mouse button to end the tool button to end the tool Figure 67 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 107 4 6 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 68 Figure 58 shows an example of how the Furrow Label is used Edit Comment Text This is awell Options Offset a dx ly pixels C Frame dy pixels Figure 68 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 69 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 and color a
44. 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 2006 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 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 grid generators for relatively simple rectangular and hexahedral transport domains a grid generator for unstructured finite element m
45. 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 widespread 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 and XP environments The interface is connected directly to the computational codes The current version 1 0 of the HYDRUS graphical user interface represents a complete rewrite of the version 2 0 of HYDRUS 2D and expands its capabilities to three dimensional problems In addition to information given in this user manual extensive context sensitive on line help is made part of the graphical 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
46. 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 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 20 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 h3d that contains all input and output data when the Temporary 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 h3d file into a working subdirectory output data created by the calculation module are sent into th
47. 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 discretization 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 60 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 RSI relative size at the top and RS2 relative size at the bottom
48. selected from the List of Available Coordinate Systems dialog window Fig 120 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 120 bottom List of available Coordinate Systems Existing Coordinate Systems CS Type Name Description a Default Absolute coordinate system O Cartesian O Cylindric O Y Cylindric O Z Cylindric Spherical Polar New System New Coordinate System Description i Definition of the Coordinate System x em Y ern z cm CS Origin ooo 000 0 00 Pick Pointon X Axis 0 00 ooo ooo Pick Paint in Z Plane 0 00 0 00 0 00 Pick Pick All 3 Points Figure 120 The Coordinate Systems dialog windows 198 9 5 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 flu
49. 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 102 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 edited using the following operations delete copy Fig 45 move Fig 45 rotate Fig 46 left and mirror Fig 46 right Note that in addition to objects particular nodes of an object can belong to a selected set as well in which 72 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 37 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 11 Definition of terms related to geometry design
50. 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 90 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 87 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 command 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 do
51. 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 95 sums fia OA View Optors a O Doman Geonety O FE Meth Sectors os Doman Propetes Od iis Cortters OG Boundary Condtions W Ronk WD Premuse Head OW Wate Cortes OW Terperstue OW veost OW Corcerteston 1 OW Corcertisten OW Corcertaton 3 OW Flewng Pace DE Fe Meh BG Note AG Sutace Edger COD Varme Edger AG Sutace Facet COBB Nunberng DO Aday Obprcts oe Rendenng Model DW Giph Type Et Lights CGE Cok Scale BRM 42 821 62 340 75 0 O Efoma Qouble chck on the ooko panel to change colors Numter of Intermechate loire E zzu 20004 Jz 0 Remi Presmae Head h fom 72851 Wm 45813 dsa Emoty aa FaMaoMn zr i ja 4 ok 4 Tine Lytt Tene 2 10 days lt a Flow Anmnation When depen liine Chat Took When diseno Color Contours F CottSocion Chat E Banday Line Chat A Daplap Vates at Nodes Help gt Right chick on the Coker Scale dipl opion Back Boundary Conditions Figure 95 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 minimum and maximum values of a particular variable and then leaves the scale invaria
52. 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 25 2 Projects Geometry Information HYDRUS can solve water flow and solute and heat transport for two and three dimensional transport domains Geometry type is selected in the Geometry Information dialog Window Fig 6 and 7 In this dialog window users specify the Type of Geometry the Domain Definition the Length Units and the size of the Initial Project Group the approximate size of the transport domain Type of Geometry 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 a two or three dimensional transport domain 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 Geometry Information Type of Geometry Simple 3D hexahedral domain 2 Horizontal Plane defined by dimensions w x H x D 2D Vertical Plane 2D Axisymmetrical Vertical Flow 3D Layered Doma
53. 007 This report documents version 1 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 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 degradation 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
54. 103 that is called with the command View gt View Stretching View Stretching Factors Stretching Factors In x direction I 1 In Y direction 1l Calculate 1 Factors InZ direction 0 0217391 Adjust Grid Stretching 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 103 The View Stretching Factors dialog window Two options of View Stretching are available a Strict Stretching when all transport domain dimensions will be 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 156 8 1 4 Rendering Model Rendering serves to rapidly switching between displays of surfaces and solids One can se
55. 2 PH1 60 000 PH2 Standard Empty Standard Empty L 45 000 Fil Fill 30 000 Fill Mag Min x 15 000 Fill Mag Min Save 0 000 15 000 Palettes 30 000 Palettes 45000 E 60 000 In wo oa a lt l lt Gi 75 000 30 000 aaa J E Format When drawing Isolines 0 When drawing Isolines Double click on the color When drawing Color Contours 0 Double click on the color When drawing Color Contours o panel to change colors panel to change colors Cancel Cancel Number of Intermediate Isolines Number of Intermediate Isolines C E Format j i Figure 97 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 98 147 E HYDRUS Furrow HJO De Ok Yow jort Caaiton Bends ook Osters Window th gt ans ga z a a 4 E Furrow Results Pressure Head 14 View Opora S Doman Geomety SE FE Meth Sectors OF Doms Processes Custom Seale OG intial Contin 0 000 OG Bardey Conditions 0 D M Ret WW Pormes Head OW Water Cortert OW Tergerstze OW Voay OW Concentaten 1 OW Concertsten 2 OW Corcerteten 3
56. 9 Figure 80 Figure 81 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 96 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 98 The 3D Layered Solid dialog window the General Sub Layers and Thickness Profiles TAOS ge ost hie asd earned abe re vases dete eulass drives a ne wu amis Hepa dina ase mae vedas 99 The 3D Layered Solid dialog window the FE Mesh Tab for single and multiple EAA cis suastasseercedsbahsatiad be sdidas anda E E E T 100 Edit Bar during the process of graphically defining a Thickness Vector 104 The Thickness dialog windows cisecs ots det teeel aerate esued had Sond Fai sinaretet oer 104 A solid with several thickness vectors isis csssacieccadvssceaisanencessasonadsaniaceabanstaauanrituasanness 105 FE Mesh for the solid in Figure 63 5 sccjscias ivedsceds its cdetatedeatocas sete cons andaciusndews ted actstaseaiess 105 Missing internal curves in the base surface 2 29 cc xcesiiiecis st eeeeisved mars deen astedenasbense 106 Consequence of missing an internal curve in the base surface on the FE Mesh of the BOS SUPE ACE arnan a ecu te eaten ure a Seat cua euiad a cla el ad cum an alata alas 106 Edit Bar during the process of graphically defining a Dimension Selection of two definitio
57. C Screen Output V Press Enter atthe End Subregions for Mass Balances 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 information is to be printed at a regular Time Int
58. C00 Flown Paces DE Ft Mew AG Nodes 7 DI Sutace Edges 7 Crone Section Chast E Gann 4 te r E Boundary Line Chat y Daplay Vates af Nodes Hep amp Right chch on the Color Scale duplays options Back Bourctary Concitone Presne Head h feom Asda Obpect O Rendeng Model C75 Giph Type OT Liro OG Cote Scale Figure 98 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 99 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 148 id HYDRUS Furrow H30 Fle Eat Vew Iset Catulstion Ress Took Options Window Heb a alel4 QQ T aandaa rnw A View Opti
59. Cislerova 1988 Kosugi 1996 and Durner 1994 6 Qr and Qs denote the residual and saturated water contents respectively Ks Ks LT is the saturated hydraulic conductivity and is a pore connectivity parameter The parameters a Alpha L 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 4 Qm a water content larger or equal to 6 Ky Kk LT the unsaturated hydraulic conductivity at water content amp and amp Qk the water content associated with Ky Water Flow Parameters Material Properties for Water Flow Number of Materials 2 Cancel Qs 0 43 0 46 Soil Catalog Sit Water Flow Parameters Inverse Solution Material 1 Material Properties for Water Flow eo Number of Materials 1 a as Initial E stimate 0 008 0 35 Minimum Value 0 0 1 Maximum Value 0 0 6 Fitted Next Soil Catalog v Neural Network Prediction C Temperature Dependence Figure 19 The Water Flow Parameters dialog window for direct top and inverse bottom problems 45 Durner s 1994 model has three additional parameters wz w2 Alpha2 L and n2 n2 where w 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
60. 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 gas phases are to be multiplied by a tortuosity factor according to the formulation of Millington and Quirk 1991 Check this box if the solute transport and reaction parameters are assumed to be temperature dependent 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 Check this box if the Wetland module is to be used This module is described in detail by Langergraber and im nek 2005 The Wetland module for two dimensional problems only was developed to model biochemical transformation and degradation processes in subsurface flow constructed wetlands The module considers the following components dissolved oxygen organic matter 3 fractions of chemical oxygen demand COD readily and slowly biodegradable and inert nitrogen compounds ammonia nitrite nitrate and dinitrogen inorganic phosphorus and heterotrophic and autotrophic microorganisms Organ
61. Dimensions Lx _ 1000 09 fem Lz 200 00 cm Slope a Dimensions Lx 1000 00 Ly i 1000 00 lz 200 00 Slope o ogor mee s ooe Figure 11 The Hexahedral Domain Definition dialog window In the Geometry Information 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 29 There are three types of three dimensional transport domains Solids see also Section 4 4 depending upon the selection made in the Geometry Information dialog window Fig 6 and 7 e 3D Layered Hexahedral This type of solid has a Hexahedral Shape and is defined by its basic dimensions The base can have a certain slope in the X and Y dimensions Fig 9 e 3D Layered General This type of solid is defined by the Base Surface see Section 4 2 and one or more Thickness Vectors see Section 4 5 e 3D General This type of solid is defined using a set of surfaces that form its boundaries This selection is not possible in the current version of HYDRUS 30 3 Flow Parameters 3 1 Main Processes In the Ma
62. E Mesh 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 simplest command is the New Section from View command which creates a newly named section from currently displayed objects in the View window The New Section from Selection command creates a newly named section from currently selected objects or the FE Mesh The Display All and Display whole FE mesh commands causes the entire computational domain or FE Mesh to be displayed 159 8 2 Navigator Bars The Navigator Bar Fig 106 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 Geometry Flow Parameters FE Mesh Domain Properties Initial and Boundary Conditions and Auxiliary
63. FE Mesh The Insert Object of the Domain Geometry Edit Bar allows users to Insert Objects with which a 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 73 FE Mesh Parameters Figs 76 through 79 Insert Mesh Refinement Fig 81 Delete All Refinements Generate FE Mesh Delete FE Mesh and FE Mesh Information Fig 84 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 select how to make selections FE Mesh Sections and Help 165 Insert Object Point Line Abscissa ET Line Polyline amp Arc via 3 Points Arc via 2 Points and R X9 Arc via Center R and Angle Circle via 3 Points Circle via Center and Radi amp Spline i Surface via Rectan
64. HYDRUS 2D 3D Hydrus 3p FURROW DER Eile Edit Yiew Insert Calculation Results Tools Options Window Help Deuas ie RX amp REE 5 EB Dike Rea u3 Concentration Project Data W FURROW M Project Information i Domain Geometry i Flow and Transport Paramete H i FE Mesh S Domain Properties Material Distribution EE Nodal Recharge Gi Scaling Factors Gi SF Pressure Head A SF Hydraulic Condu A SF Water Content ae Gi Anisotropy A Anisotropy Ange aer ite ad A Anisotropy Ist Com A Anisotropy 2nd Con Time Layer Subregions booo i Observation Nodes y esi gt Time 19 65 00 days E Flowing Particles lt H Initial Conditions E FURROW Results Pressure Head Pressure Head h cm 72 851 59 332 45 813 32 294 18 775 5 255 8 264 21 783 35 302 48 821 C Flow Animation Chart Tools ressure Feat Fil Cross Section Chart 900 water Content Ea Boundary Line Chart 00 velocity Sa Display Values at Nodes LH Velocity Vectors Help 000 Temperature Right click on the Color 00 Concentration 1 Scale displays options Concentration 2 Back Boundary Conditions Concentration 3 Results Other Information W Edit Bar Domain Proper F Initial Condition For Help press F1 Software Package for Simulating the Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated
65. K 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 133 Default Domain Properties Properties of Horizontal Layers zlem Code Mater Roots Axz Bxz Dxz Temp Cancel 200 00 20 190 00 20 180 00 20 170 00 20 160 00 20 150 00 20 140 00 20 130 00 20 120 00 20 110 00 20 100 00 20 90 00 20 80 00 20 70 00 20 60 00 20 50 00 20 40 00 20 OH One won Help lo 7 MS Excel Import Export Copy Sel on nn e wh Copy All w pear O Edit in Resizeable Window amt ft a ae ne wh az 9 9 9 9 9 9 9 9 9 9 9 9 9909 o ie 9 0 0910 00 00 0 090 09 99 90 909 9 9 0 0 0 0 0 o lt ai 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 gt aiir o e e and Heat Transport for changed Codes Linear Interpolation of Pressure Heads between the first and last layer Figure 86 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 Va
66. 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 68 Templ Temp2 Concl Conc2 Conc3 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 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 The first 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 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 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 32 can be
67. Media User Manual Version 1 02 March 2007 PC Progress Prague Czech Republic 2007 J im nek and M ejna All rights reserved The HYDRUS Software Package for Simulating the Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated Media User Manual Version 1 02 J im nek M ejna and M Th van Genuchten March 2007 University of California Riverside Riverside CA PC Progress Prague Czech Republic George E Brown Jr Salinity Laboratory Riverside CA 2007 J im nek and M ejna All rights reserved Table of Contents Abstract as erica ennaa ead encan cesses tows tadada aneti Guan coun eta eee paa autos 17 Introduction to the HYDRUS Graphical User Interface 0 0 cccecccccseessssceeeesesseeeeeeseeseenes 17 1 Project Manager and Data Management 0 0 0 ccccccccccssesccseeseeseeseeecesessesececseseeseeecseeaeenes 21 2 Projects Geometry Information 0 000ccccecccceescecesscecssececeseeecsseeecseeecseeecseeeeseeeenseeees 26 3 Flow PAV AmMmeter nci n aa a a aasiadueaaisae ep E 31 Dede Main Processes zitis arire alah idles Dasha ale at a E E S A a ER 31 3 2 Inverse Solution es ineat aie a e a a a aa a ai a 32 3 3 Tim Jnformation nrinn ipres EE E E EE E E E aa REER 36 3 4 Output Information osssosssseesseesseseesseessesseesesseeseesresseeseeserssesresrrsstessessesstossessrssresseesees 38 3 5 Merati n Criterid isiin
68. NEMIEK 000 H3D Exit Ctrl F4 Ctrl Z Ctrl C Find Delete All Domain Geometry Flow and Transport Parameters FE Mesh Domain Properties Initial condition Boundary Conditions Sections Cross Sections Auxiliary Objects bd v v 4 Geometry 6 EE Mesh E Domain Properties g Initial Conditions Boundary Conditions 00 Results fe Navigator Gal Edit bar Status bar 3 Toolbars 3 Arrange toolbars 37 Customize toolbars A Standard view Zoom by Rectangle GA view all FP Previous view Se Dynamic view Scroll Zoom Rotate GE View Stretching rf oe View in Direction gt Figure 112 The HYDRUS Menus I File Edit and View 171 OSAA Calculation Results TREMMEE Results Tools Options DAPET Tools Options Window Domain Geometry gt E5 FE Mesh Parameters Display Quantity gt i i gt A FE Mesh Refinement 55 Generate FE Mesh Mny 7 Domain Properties gt 25 Delete FE Mesh Initial condition gt 43 FE Mesh Statistics ees Boundary Conditions gt g Soll Hydraulic Properties Cross Sections gt mme EEO S Xi i gt Advanced FE Mesh Generation wien mamai eae 3 Run HYDRUS 3 Run T Auxliary Objects gt Convert Output to ASCI Time Layer Charts Flowing Particles Figure 113 The HYDRUS Menus II Insert Calculations and Results Options Window PE Options Developers Windo Help
69. 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 polylines 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 in
70. 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 79 The FE Mesh Parameters dialog window Tab Options 2 123 The Mesh Section Tab The program can generate default FE Mesh Section the Mesh Section Tab of the FE Mesh Parameters dialog window Fig 80 or FE Mesh Section can be created by a user Default FE Mesh Sections depend on the geometry of the transport domain For examples for the three dimensional domains default section include a Entire FE Mesh b Vertical horizontal shell and c Each horizontal vertical layer FE Mesh Parameters Main Stretching Options 1 Options 2 Mesh Sections Generate Mesh Sections The program can generate default Cancel FE Mesh Sections You can create v Automatic own Sections with the Cut with Rectangle tool 7 Mesh Sub Domains ek Previous Apply All Default FE Mesh Parameters 7 The program can generate default FE Mesh Sections ou can create own Sections with the Cut with Rectangle tool Mesh Layers Mesh Shell Sub Layers Columns C Intersections of Columns and Sub Layers i Previous Apply mR Eek All Default Figure 80 The FE Mesh Parameters dialog window Mesh Sec
71. Rendering part of the View Tab of the Navigator Bar ceseeseeeeteeeeeeee 157 The Pop up Menu from the View Window cceeceessesscesecssecsseeseeeeeessesseeaeeaee 159 Selected Navigator Bars Data Tabs on the left and in the middle the View Tab ON theright essre iinr eE EE anette coat eueay EA ER Selected Edit Bars from left to right for Material Distribution in Domain Properties Water Flow Boundary Conditions Pressure Head Initial Conditions and Water Content R sults mea r a eite toes a eia atapa at eiea taiese tate gues 162 The Color Scale Display Options mene osc sass ecsshedeerdascises Gears eaesantieeaniens 166 Selected Edit Bars for Domain Geometry and FE Mesh 0 ccceeceeseeseeeeteeees 166 The Toolbars dialog window os ticcncst sete ie Se4rkcavsevanddecie Ons cavhals Mock aeanion 167 The Customize Toolbars dialog Window cccccesscesseesteceeeceeeeeeseecsaeenteeneeeenseees 167 12 Figure 112 Figure 113 Figure 114 Figure 115 Figure 116 Figure 117 Figure 118 Figure 119 Figure 120 Figure 121 The HYDRUS Menus I File Edit and View cccccccscceseceeseeesceceeceteeeeeeenseees 171 The HYDRUS Menus II Insert Calculations and Results cceeeeseeeseeetees 172 The HYDRUS Menus II Tools Options Windows and Help eeeeeeee 172 The Program Options dialog window the Graphics Tab ccceseseereeeeeeeeenee 191 The Program Options dialog wi
72. 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 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 103 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 Displays a menu with nine commands for editing sections Create New Section from Selection Create New Section from Current View Display All Display Previous Display only Sele
73. a Solid in the horizontal direction Fig 59 It is possible in the Edit Solid dialog to define number of Sublayers 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 as described below A thickness of a Sublayer is calculated as follows e Thicknesses of Sublayers given in the Table are calculated on the Master Thickness Vector e The sum of Thicknesses of all Sublayers 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 Sublayers automatically A Solid can have more Thickness Vectors of different lengths so that specified Thicknesses of Sublayers can not be maintained The program then does the following For Sub Layers with the Constant Thickness Type the specified thickness is maintained at all Thickness Vectors i e over the entire computational domain For Sub Layers with the Variable Thickness Type their thicknesses are linearly increased or decreased so that the sum of Thicknesses of all Sublayers corresponds with the length of a particular Thickness Vector 4 4 3 Individual specification of different Thicknesses of Sublayers at different Thickness Vectors In the preceding paragraph we have described how to define Thicknesses of Sub Layers on the Master Thickness Vector using a table Fig 59 This table represents the so called Profile i e a part
74. 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 138 Boundary Condition Options Boundary Conditions Options for Time Variable Head 1 C interpolate variable pressure head boundary conditions in time C Switch the boundary condition from variable pressure head to zero flux when GWL gt 999999 Switch the boundary condition from time variable pressure head to zero flux when the specified nodal pressure head is negative Switch the boundary condition from time variable head to atmospheric when the specified nodal pressure head is negative Switch the boundary condition from time variable head to seepage face when the specified nodal pressure head is negative Treat the time variable flux boundary condition as atmospheric i e with limited pressure heads C Apply atmospheric boundary conditions to nonactive seepage face Other Boundary Conditions Options Figure 90 The Boundary Condition Options dialog window 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 w
75. above the graph a pop up menu will appear that 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 Vertical Variable Time Pressure head Obs Node 2 Obs Node 3 Obs Node 4 Obs Node 5 Observation Nodes Pressure Heads 200 100 0 100 200 300 400 100 150 200 250 Time days C Show All Figure 100 The x y graph dialog window displaying pressure heads in observation nodes 150 Table 13 Graph options in the HYDRUS interface Command Observation Points Time Pressure Heads Time Water Boundary Fluxes Time Cumulative Water Boundary Fluxes Time Solute Fluxes Time Horizontal Axis 151 Vertical Axis Pressure Head Water Content Temperature Conce
76. additional parameters sw QsW the saturated water content of the main wetting branch a AlphaW L the shape parameter of the main wetting branch and K KsW LT the saturated hydraulic conductivity associated with the main wetting branch in case hysteresis also occurs in the conductivity function Temperature Dependence Check this box 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 parameters were taken from Carsel and Parrish 1988 Table 7 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 the catalog for the Kosugi s model were obtained by fitting retention curves generated using the Carsel and Parish 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 Cla
77. ants 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 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 139 Stochastic Dist
78. art 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 93 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 displayed 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 142 7 1 1 Display Options The Display Options dialog window Fig 93 allows users to select a how different objects from the Category
79. ary Fluxes Cumulative Fluxes Solute Fluxes First Last Previous Next Animation Cross Section Boundary Line Mesh Line Draw Particles Positions Draw Particles Trajectories 177 G Tools H Options I Windows J Help 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 Intersect Lines Split Lines Graphically n Points Distance Insert Points on Line Graphically n Points Distance Check Geometry Repair Geometry Generate Domain Surfaces Create Video File Rendering Mode Full Model Transparent Model Wire Model Graph Type Izolines Color Contours Color Points Color Edges Velocity Vectors Display Options Edit Default Read Save As Program Options 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 Hydrus Online 178 Troubleshooting Hydrus License and Activation About Hydrus 179 Table 15 Brief description of HY DRUS menu commands Group Command A File New Open Close Save Save As Save All Import and Export Import Hydrus 2D Project Import Input Data from IN Files Export Data for Hydrus Solver
80. ary 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 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 Examples of simple rectangular and general two dimensional geometries are shown in Figure 8 An example of a simple hexahedral three dimensional geometry is given in Figure 9 27 NNN NY ERRERA Figure 8 Examples of rectangular top and general bottom two dimensional geometries Figure 9 Example of a hexahedral three dimensional geometry 28 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
81. ation codes are inserted during the first attempt HYDRUS issues a warning After the second attempt with wrong activation codes the Request Code 1 is changed and new activation codes need to be requested We recommend using standard functions Copy amp Paste when inserting activation codes to minimize risk of inserting wrong numbers 9 2 2 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 Reinstallation to another computer a b c d Before any hardware change reinstallation of the Windows OS or moving HYDRUS license to another computer deactivate HYDRUS on the original computer Go to the Hydrus Activation dialog and press the Deactivate HY DRUS button Send a copy of the file that is created during the deactivation to us or your HYDRUS distributor After you finish HYDRUS installation on the new computer you will have to activate it again 196 9 3 Print Options Dialog Window The Print Options dialog window contains three tabs Fig 119 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 Pict
82. ation 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 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 criterion is not reached i e some changes would still occuer 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 wo
83. bjects 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 7 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 7 2 Relations among Objects More complex objects are defined 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 7 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 a
84. ble Boundary Conditions Parameters OK Precip Evap Transp hCritA Yar FIt Var H 1 Re Cancel 0 0 16 15000 0 0 0 18 15000 0 02 0 13 15000 0 0 2 15000 0 0 28 15000 0 18 15000 0 08 15000 0 14 15000 0 11 15000 0 11 15000 0 11 15000 0 11 15000 Linear interpolation of time between the initial and final time 1 Surface area associated with transpiration Help Add Line Delete Line o ora d m AR o 2 En 0O00 0 0 0090 0 0 0 0 0 0 0 0 0 0 0 0 0 nm lt YVoooodo cd cod cod cod cod os Figure 32 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 Precip Precipitation rate LT 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 Fll 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 flux boundary condition is specified Same for Var F12 Var F13 or Var Fl4 Var H 1 Groundwater level
85. ble 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 35 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 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 37 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 next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 36 left The Edit Bar will als
86. boundaries for which no time variable boundary conditions are specified are then set equal to zero for times larger than the Pulse Duration Mass Units Units to be printed to the output files or displayed in various graphs Mass units have no effect on the calculations 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 Geometry Information 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 L the 52 Stability Criterion Use Tortuosity Factor Temperature Dependence Attachment Detachment Filtration Theory Wetland Module d Iteration Criteria length unit defining geometry and fluxes e g m Similarly the solute mass c OV 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
87. cal 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 0 O a n K LL LL em cm d Sand 0 053 0 375 0 035 3 18 643 Loamy Sand 0 049 0 390 0 035 1 75 105 Sandy Loam 0 039 0 387 0 027 1 45 38 2 Loam 0 061 0 399 0 011 1 47 12 0 Silt 0 050 0 489 0 007 1 68 43 7 Silty Loam 0 065 0 439 0 005 1 66 18 3 Sandy Clay Loam 0 063 0 384 0 021 1 33 13 2 Clay Loam 0 079 0 442 0 016 1 41 8 18 Silty Clay Loam 0 090 0 482 0 008 1 52 11 1 Sandy Clay 0 117 0 385 0 033 1 21 11 4 Silty Clay 0 111 0 481 0 016 1 32 9 61 Clay 0 098 0 459 0 015 1 25 14 8 47 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 Carsel and Parish 1988 Textural class 0 0 a n K L L gt L L gt cm cm d Sand 0 020 0 417 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
88. cheme 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 Weighting 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
89. cified in the FE Mesh Parameters dialog window Figs 76 through 79 This dialog window has five Tabs 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 76 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 77 to make the mesh anisotropic specifying the Maximum Number of Nodes on Boundary Curve on the Options 1 Tab Fig 78 and Minimum Number of Nodes on Boundary Curve on the Options 2 Tab Fig 79 and using Finite Element Mesh Refinement Fig 81 While the Page 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 a user can specify on the Main Tab the No of Horizontal Layers only 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 It is recommended to use Triangular Prisms rather than Tetrahedrals since then the number of finite elemen
90. close curve The Edit Bar displayed during the operation will list Boundary Curves defining the Surface Fig 48 left A surface can be edited using the Edit Surface dialog window Fig 48 right which specifies surface type the number of boundary curves defining the surface its number and had a box for possible comments or a description A surface must be created before one can do finite element discretization 87 Edit Surface General Integrated Surface No LE Jer Surface Type Set new Surface pa Number for new Surface B Boundary Curves List of Boundary Curves r 1 4 for example 1 9 3 7 Stop Help a Ke Pick a boundary curve of the new Surface Ke Press Esc or right mouse Cancel button to end the tool Figure 48 The Edit Bar during the process of defining graphically a surface left and the General tab of the Edit Surface dialog window right A base surface is formed by a planar surface of arbitrary shape The base surface can contain openings internal curves and internal points Fig 49 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 49 A solid showing the base surface 88 If the solid needs to be divided into vertical columns then these columns must be defined using internal c
91. csseeecsseeeesseeeeseeeesseeees 72 4l Bo ndary Objects nonesis oct mia a uh sl arent tome a ante ali oe chanics goad 72 AACN POMS E E E lied ceabet atau cia tes secriae staeatatouel as 75 41 2 Lines and Polplines nerriet aa a aa ea aes 71 l3 AAO CUT LGN sees ehh i tae A a a a N ada a E 79 4 1 4 Curves ROS DIOS toss vols AG Sea cede ules Naludees a a a a a den oan ate 82 4 1 5 Move Copy Rotate and Mirror Operations ccccccccccccesceetseteteeeteteteeessees 85 4 1 6 Additional OP TOM ONS cre Got ehanineic ue tieccietysdea dea hentai aie cate ales mite 86 42i OULU LE eset el aoe Sagi Paths ete cla nl Sees tugd Schaar E E dS Etnies tel ene fle 87 4 2 1 Steps to Define a Two Dimensional DOMAIN ccccccceecceesceeste eens ents tet eetseees 90 4 2 2 Several notes on rules for correct definition of the Geometry 0c cccee 91 4 2355 Internal OBES Ge caer raa deta suis a acaa hoes a conan bh aula chant cee 92 439 MOOI ON rane e a testes ae Sateen yc Secale ciate telnet Seta aden aa adit cad ts Sain ade SE 90 FA Solids sivas icaitat BicBenkivn a aceasta phen ead PO Oe 96 4 4 1 Division ofa Solid into Columns lt 1 nnsiscdeicssseiite seated tasseoeacdaatdancsneddelvodads 101 4 4 2 Division of a Solid into Sublayers cccccccccesceeceesetenseeesecuseceeseesssecaeenteeeaees 101 4 4 3 Individual specification of different Thicknesses of Sublayers at different Thiekness Vectors cernas a ai eed eats 101 4 4 4 S
92. ction Display Reverse Edit Section Graph Type Commands Tsolines Displays a menu with five commands Displays the spatial distribution of a certain variable by means of isolines 169 Color Contours Color Points Color Edges Velocity Vectors Color Scale Options Color Smoothing Surface Lighting Displays the spatial distribution of a certain variable by means of color contours 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 Al ea View Edit Domain Geometry View Edit FE Mesh View Edit Domain Properties a 4 Fs i 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 Conditions 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 Re
93. d 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 format The E format is then used also on the Edit Bar and for printing only for a particular variable Edit Isoband Values and Color Spectra Scales 100 000 Standard 143 261 potait Empty Eill 186 521 229 782 E se Fill Max Min 273 043 Save 316 304 359 564 402825 Palettes Default 489 347 Save 532 607 575 868 i J E Format Number of Intermediate Isolines LEE thee When drawing Isolines Mm Double click on the color panel When drawing Color Contours to change colors Cancel Figure 94 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 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 144 intermediate numbers by interpolation A specified Number of Intermediate Isolines can be drawn between
94. d button the right mouse button see the Help part of the Edit Bar or clicking the Stop button on the Edit Bar xl a Domain Geometry Set new Spline Numbers for new Curve E Point 24 Coordinates ba 525 37 cm Z 42 54 cm Ref Coord System O Current CS Grid Origin Last Point Spline Type Spline OB Spline Bezier Curve Stop Help a Ke Step 4 of N Set next point of the new Spline K Press Esc or right mouse button to end the tool Figure 43 The Edit Bar during the process of defining graphically a spline 83 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 step of the running tool B Adjusting View When graphically ent
95. dialog window ccccesseeteeeeteees 71 A base surface showing several basic geometric Objects cccceeeceeeseeeteesteeeteeeeees 75 The Edit Bar during the process of defining graphically a new point left and a new line fighi ee esas deel atch eg ana nes ab Davin Tat Biass e a E A a dates 76 The Edit Point dialog window as2 90t3 60 pgascens necks eit acaba iene terse 76 Different ways of adding Parametric Points ON a CUIVE eeeeeeceeeceeenteeseeeeeeeeeeaees 78 The Edit Curve dialog witdOw wis cgsstcastacictinsa neo ties da nasi eeiaana as 79 The Edit Bar during the process of defining graphically a radius for a new arc left or a MEW CIC les TIIE sic cseo2i suet chcesnagss beard a a sass anehoactiaka A Gah aww E aN 80 The New Line Arc dialog wide wi ce sscctescc icra makdadaeashinedlntealae nm aeeedeeass 81 The New Line Circle dialog window 0 ccccccessceesseesseceseeeeeeenseecsaecnseeneeeenseeesaeenes 82 Edit Bar during the process of defining graphically a spline c ce eceeeeeeeeereeeteees 83 Snap to a point left and snap to a curve right cc ceeeecceseseesteceeeceeeeeeseeeseceteeeseee 84 The Move Copy dialog Windows cccscccsscesecseseeeceeseeceseesseeeeseecsaecnseeeeeeeeseeeaeenes 85 The Rotate left and Mirror right dialog windows cccecsceesseceteceteeeeeeeeseeeaeenes 85 The Insert Point on Curve dialog Window 0 ccccccsesesesesesseseseseseesceesenecesesese
96. dient Background visually more effective background is displayed which may be useful for presentations and minimum time for one frame during flow animation Program Options OpenGL Graphics Program Options Files and Directories Options OpenGL Hardware Acceleration Note Changes to the settings become active only after the program has been ended and restarted Performance Optimization Stable Max Speed Otimization is to be set to Stable if problems with graphic occur Simplified display in Move modus Move Zoom Rotate The simplified display will be activated when there are less than 5a refreshments per second d Pre selection Mark object while hovering above it with cursor Display values properties at pre selected objects C Gradient Background Flow Animation Minimum Time for One Frame 500 gt ms Figure 115 The Program Options dialog window the Graphics Tab 191 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 On the left side of the Program Options Tab Options one can a sel
97. dow Tab Options 2 ccceeseeeseeeteeeteeeeees 123 The FE Mesh Parameters dialog window Mesh Section Tab for two top and three dimensional bottom applications cceccceescessceesseceteceeeceeeeeeseeceseceeeeeeeeseaeenseees 124 The New FE Mesh Refinement dialog window cccccessceeseeesceeteeeeeeeeeeeeeeenseees 125 11 Figure 82 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 Figure 104 Figure 105 Figure 106 Figure 107 Figure 108 Figure 109 Figure 110 Figure 111 Example of FE Mesh Refinements top and FE Mesh bottom cceeeeseerees 98 Example of mesh stretching using a stretching factor of 3 in the y direction 129 The FE Mesh Information dialog window for a two dimensional problem top and a thre dimensional problem bottom 2ccscnacksatineidcuia cael cate acsa days 130 The FE Mesh Sections dialog Window sccssccsscsssecsssescssnesssessecsssacssanessasenacess 132 The Default Domain Properties dialog Window ccccccescceeeeeeeeseeeeteceteeeeeeenaeees 134 The Water Flow Initial Condition dialog window cccccceeseesceeseceteeeteeeeeeenseees 135 The Temperature distribution dialog WindOW ccccccesceesceeeeesceceeceeeeeee
98. ds j Flow and Transport Parameters Gj FE Mesh Domain Properties Initial Conditions Boundary Conditions Auxiliary Objects Results Graphical Display Coordinate System Color Scale Translate Rotate Mirror Sat Intersect Lines Split Lines Insert Points on Line Check Geometry Repair Geometry Create Video File n Points Distance Insert Object Point Y Line Abscissa EL Line Polyline x Are via 3 Points amp Y Arc via 2 Points and A 3 Arc via Center A and X Circle via 3 Points X Circle via Center and X Spline iG Surface via Rectangle iQ Surface via Boundaries a Opening via Boundaries i Solid Brick Solid Extruded Edit Lines Delete Lines Results Other Information Bp Thickness Vector i Dimension yA Comment Split Lines Graphically Insert Parametric Points n Points Transform Object eS Translate TR Rotate Ab Mirror Insert Points on Line a Spit Line 3 Tools Y 577 93 cm Reverse Orientation Distance FE Mesh Refinements Fi A Geometry A fie Data 60 View amp Sections Inserts new points on the curve via graphics itions a Bouni 000 Results Plane XY X 267 84 cm EA Domain Proper Initial Ci Z 0 00 cm System Default Figure 38 Different ways of adding Parametric Points on a curve 4 1 2 Lines and Polylines Li
99. e HYDRUS will import first only thickness vectors without sub layers Then define a 3D Layered Solid using imported points and import the same file again Sub 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 Sub layers will be added to the Solid 115 5 Finite Element Mesh 5 1 Finite Element Mesh Generator The Finite Element Mesh Generator dialog window Fig 73 is used whether to select a structured finite element mesh for relatively simple rectangular or hexahedral domain or a more general unstructured finite element mesh The dialog provides a brief description of each mesh generator and a simple bitmap with an explanation of the main terms involved While the structured finite element generator can be used only for simple rectangular of hexahedral domains the unstructured finite element generator is used for more complicated geometries FE Mesh Generator FE Mesh Generation Method Generator Description Structured Structured mesh for rectangular or Meshgen hexahedral domain Mesh is generated Cancel according to user defined horizontal and vertical discretization Horizontal Discretization Vertical Discretization Next FE Mesh Generator FE Mesh Generation Method OK Generator Description O Structure Triangular mesh for any 2D domain of
100. e 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 subregion and the
101. e 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 HYDRUS 2D version 2 x projects to HYDRUS Calculate Calculates selected HYDRUS projects This command allows users to calculate multiple selected projects simultaneously 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 k
102. e Transport First Type Third Type Volatile Type Heat Transport First Type Third Type Cross Sections Graphically Dialog Mesh Line Graphically Dialog Auxiliary Objects Dimension Comment Bitmap 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 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 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 cro
103. e 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 78 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 39 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 39 left in the New Line dialog window the Edit Curve dialog window has also the FE Mesh Tab Fig 39 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 i Edit Curve General FE Mesh General FE Mesh Curve No Are No 1 FE mesh Refinement Curve Type FE Mesh Refinement Polyline List of Points 3 4 Comment Global FE Size om Figure 39 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 in 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 b
104. e columns Particular columns in the input file have the following meaning 114 Coe et GON aA X coordinate Y coordinate Z coordinate of the Definition Point of the Thickness Vector Anchor Point see Figure 62 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 inclined Z coordinate of the lower point of the first sublayer of the Thickness Vector a point denoted N1 in Figure 62 of the User Manual When P N1 this coordinates is the same as the 3 coordinate Z coordinate of the upper point of the first sublayer of the Thickness Vector Z coordinate of the upper point of the second sublayer of the Thickness Vector Z coordinate of the upper point of the last sublayer 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 sub 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
105. e content of the View window Previews the content of the View window before printing 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 119 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 their 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 180 Edit Undo Redo Copy Paste Select Select by Rhomboid Select by Circle Select by Polygon Add to Selection Remove from Selection Standart Selection Mode Properties Find Delete Delete All Domain Geometry Geometry Information Geometry Definition Points Line Surfaces Openings Thickness Vectors Solids Flow Parameters Main Processes Inverse Solution Time Information Output Information Water Flow Parameters Iteration Criteria Hydraulic Properties Model Soil Hydraulic Parameters Revers
106. e 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 Position values Weight is the weight associated with a particular data point The following information can be included into the objective function 33 Table 2 Data Types for the objective function Inverse Problem 0 Cumulative boundary fluxes across a specified boundary 1 Pressure head measurements at selected observation point s 7 9 Prior knowledge of parameter o oS 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 34 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 Averaged water content of the entire flow domain 2 0 Concentrations temperatures Obser
107. e ignored as Comments 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 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 Sublayers with variable thicknesses The number of Sublayers 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 fiv
108. e 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 applications respectively Mater Material number Roots Root distribution AXzZ 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 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 O
109. e 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 Jnsert gt Domain Geometry gt Opening gt Graphically from the menu or alternatively the command Opening by 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 or more boundary objects forming a closed curve The Edit Bar displayed during the operation will list Boundary Curves defining the Opening similar to Fig 48 left Alternatively an opening can be created using the New Opening dialog window Fig 56 by clicking on the command Jnsert gt Domain Geometry gt Opening gt Dialog from the menu An opening can be edited using the Edit Curve dialog window Fig 39 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 a Boundary Curves 1234 Comment Opening representing well a co Figure 56 The New Opening dialog window 95 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 a
110. e package is activated using the HYDRUS License and Activation dialog window Fig 118 that is called using the command Help gt Hydrus License and Activation The HYDRUS License and Activation dialog window contains information about current Hydrus License Not Activated 2D Lite 2D Standard 3D Lite 3D Standard 3D Professional or Network Contact Information an option to Find your Reseller this command launches Internet Explorer Browser and opens the HYDRUS web page with a list of resellers License Request Information Request Codes 1 and 2 to be emailed to the Hydrus reseller or distributor place to enter the Activation Codes Activate HYDRUS Enter Activation Codes and information on How to Activate Contact Information and License Request Information can be copied to the clipboard using commands Copy and Copy to the Clipboard The HYDRUS can be activated as follows 1 Select a product that you want to activate The program will generate License Request Information involving two codes specific for your computer and the selected product 2 Copy and save the generated license request information We recommend using the button Copy and the function Paste for this purpose If you do not intend to purchase Hydrus on line you can close the Hydrus License and Activation dialog 3 Contact a software vendor and provide the license request information After purchasing you receive one or two activation codes Enter those in Key 1 and
111. e same folder When saving a project output files created by the computational modules are also included into the project_name h3d 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 116 W 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 Direct1 CA USSL HYDRUS3D Projects Direct1 Tutorials C ussl Hydrus3D Tutorials Remove Set Current Figure 2 The project Manager with the Project Groups tab 21 Project Manager Project Groups Projects Current Project Group Options Name 3D_Tests Show Project Preview Description Three Dimensional Examples Show Hydrus 2D Projects Directory C ussl Hydrus3D Projects 3D_Tests Name Ext Descripti
112. ea acorn eS 155 81 3 CLEMO Factors sete at Saat Soles Falah hae kel dees od Sel Folch aa tad oie aus 156 81 4 Rendering Model asirar eA tessa deus E EE aay es das 157 8 1 5 Selection and Edit Commands 4 icciscsiacrscieiniaderseissestecetisssieddacedein Geaesesaneetess 157 86s FP p p Men s Halt corre chanel oconsitet naka seats hdc tae a tas tae 158 elites Dras and Dropia Todt Sate ade es Casas Meads MC Seti lad calla A TE Ns tetas 159 r e sSCCHOMS E ete sch tel 2s ha Ge pha Seek Meads SLM TE 159 8 2 Navigator Bars auior CRITE CoE RP Sene E E ko ENT SUT eB Nar a CORT ITET Arey 160 ey TER OS gies E San acd dae ech A A AE 162 S4 Toolbars enn o EE ka Nal a ae aa es aa 167 8 3 HYDRUS MENUS a ta ns See EE cata Nees reece aR Ea aTi 171 Miscellaneous Information 0 0 ccc eceeceeecceseceseeeesseeseeesecaeceaecaeeeseveceseeesaeceaeenaeeaeeeneees 191 Dads Program Options eer in Masti E se Ooi a Gs E ce R itl 191 9 2 HYDRUS License and ACHVAN OM ed cots 6s ei5 Gag asec RGUTA OIG 194 92 1 Reguest CODES sax decades Sack aa p r nee tadas Sax Sans tee ati seas 195 9 2 2 Reinstallation Moving to another Computer cccccecceecceesteeeteeeteteteeenseees 196 OS SETAE OD OUS E EE E E E E E EA ten dea cee 197 94 C rdinate Systems onsi ie a E A E A T E leh nals TOE 198 9 5 DOS Window During Calculations os cststssdesbresasasrandaetaranahaas ixheits diaeva tabaenncianaieas inane 199 96 VIREO LUGS caida suai gids fe ons ihds
113. ect a time interval for Auto save b specify Memory size for the Undo buffer and c specify the Maximum number of FE Mesh On the right side of the Program Options Tab Options one can a specify whether or not the program Reloads last opened projects at startup 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 and d specify whether the results are to be kept in an external directory By default keep results in external directory Program Options Graphics Program Options Files and Directories Options Auto save input data to gt min Reload last opened projects a temporary file every v at startup C Save FE Mesh in text format for Memory size for the a calculation Undo butfer 512 kB Enter 0 if you don t want to run auto save C Save Domain Properties in text Recommended max number of finite format for calculation es gO By default keep results in external 2D Projects 100000 directory for new projects elements for 3D Projects 500000 Figure 116 The Program Options dialog window the Program Options Tab 192 In the Program Files and Directories Tab Options one can specify the various HYDRUS files and the Configuration file for display options e Directory for HYDRUS Settings and Authori
114. ed interval ha hb 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 hb 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 hb Lower limit of the Absolute value of the lower limit L of the pressure head tension interval interval for which a table of hydraulic properties will be generated internally for each material Upper limit of the Upper value of the lower limit L of the pressure head interval tension interval for 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 42 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 Soi
115. 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 h3d file using the command File gt Jmport and Export gt Import Input Data from JIn 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 69 3 19 Constructed Wetlands Parameters for constructed wetlands are entered in the Constructed Wetland Model Parameters I and II dialog windows Fig 33 and 34 respectively This module is described in detail by Langergraber and im nek 2005 The Wetland module two dimensional was developed to model biochemical transformation and degradation processes in subsurface flow constructed wetlands The module considers the following components dissolved oxygen organic matter 3 fractions of chemical oxygen demand COD readily and slowly biodegradable and inert nitrogen compounds ammonia nitrite nitrate and dinitrogen inorganic phosphorus and heterotrophic and autotrophic m
116. ee dimensional problems one section by default is formed by the Whole FE Mesh Section DO_000 in Fig 85 whereas each horizontal vertical for some applications layer forms one additional section Sections ML _001 through ML 010 Mesh Layer in Fig 85 while the last section is made up by the vertical surface Section ML_000 Shell Fig 85 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 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 Edit Bar or using Edit gt Sections gt Edit Sections 131 FE Mesh Sections Sections Selected Sections DO_000 Whole FE Mesh Display ML_O00 Shell ML_001 Mesh Layer Hide ML_O002 Mesh Layer Sod ML_003 Mesh La
117. eeeeeeeeeeesseeeeeeeees 56 The Temperature Dependent Solute Transport and Reaction Parameters dialog PUTIN OW oa Sacha sa esa Ne i ea aia Roe net aa aS a cn tat 59 The Heat Transport Parameters dialog WindOW cccsccessceeseeeteeeeseceeeeeeeeeeseeesseenes 60 The Root Water Uptake Model dialog window 0 c cccsccesseesseeeteceeeeeseeeeseeesseeneenees 62 The Root Water Uptake Parameters dialog window for the stress response function of Feddes et al 1978 left and van Genuchten 1985 right ccceesceesseeeteeeteeeeeee 63 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 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 VOSS ASIC coins nna sata pee ante dent Sia esi Nedeat Maa das deans A eae teens 64 The Root Distribution Parameters dialog WindOW cc ccccessseceteceeeeeeteeeeeeeeseeesaeenes 67 The Time Variable Boundary Conditions dialog Window ccceseeseesteereeeeeeeeeeeees 68 The Constructed Wetland Model Parameter I dialog window c cccscesceesteeeteeees 70 The Constructed Wetland Model Parameter II
118. eeeseeetaeens 136 The Import Initial Condition dialog windoW 0 cccccccescceseeeeeeeeseeceseceeecnteeseeeenaees 137 The Boundary Condition Options dialog Window ccesccesseeeeeesseceteceeeeeeeeensees 139 The Stochastic Distribution of Scaling Factors dialog window cccccccceeseereees 140 The Stochastic Parameters dialog window csc ccsve ssesaici a seicasddecas ead astans nue 141 The Display Options dialog window cccccessceesceeseeececeseceeeeeeeeeeseecaeeneeneeeenseees 143 The Edit Isoband Value and Color Spectra dialog Window cccccceseeeeeeeeeeeeteees 144 The use of intermediate isolines 34 5553 Geeta ales areata tna lat adit hank eae 145 The Color dialog window 25 Foc oc acctean cede tes we acectacy odes caterer vs Sates weaaiaceerecteas aac ceaees a deodes 146 Adjusting scale in the Edit Isoband Value and Color Spectra dialog window 147 he useof the CUstoinn SCAle seco caw ciin ouii niie nnna a repel eae 148 TV CACOROE SPOOL MIB zaure teh odiaran ish fos a ads cbos asian ane Sty abe cdvs noma ie Uncut vaneones 149 The Convert to ASCII dialog window 2 cassosyaieineu ieee Graceantiotin 153 x y graph dialog window displaying pressure heads in observation nodes 150 The Grid and Work Plane dialog Window 0 cccceccceesseesseceseceeeeeeseeceseceteeeteeenseees 155 The View Stretching Factors dialog Window cccccccccssscessceeseeeseecsseceseeesseeeseees 156 The
119. efined 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 41 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 42 left while coordinates of points defining the circle its center and radius are entered in the Circle Tab Fig 42 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 coordinates are to be changed 81 New line New line General Circle General Circle Curve No C
120. enuchten 1980 for twelve textural classes of the USDA textural triangle as obtained with the Rosetta Lite program Schaap et al 2001 m7 Gor dexceads vaasadsct odoin ysasanashavatiars dead tevedaens toad te 47 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 Parish 1988 raa cava otinaes sit a aces eas ter ries a E do Tea O E seme stas Mla enone 48 Soil hydraulic parameters for the analytical functions of Kosugi 1996 for twelve textural classes of the USDA soil textural triangle cece eeceesseeeteceteeeeeeeeeeeneees 48 Definition of terms related to geometry design eeescccececeseceeeeeeeceeeeeeeeeeeeeeseeesseens 73 Definition of terms related to boundary discretization cccccsceceseceseeeeeeeeteeeeseeees 127 Graph options in the HYDRUS interface 00 0 ceseceeteceeeeeeeeeeaeecaeeeeeeneeeenseees 151 HY DRUS menu commands x5 03 50ciusi sdescgis spucatiaksginasabehacdusksasveags dnccd abs tuowesannacaeah oeeeenanids 173 Brief description of HYDRUS menu command6 eee eeeeeeeeeceteceeeereeeseeeeeeeeeaees 180 15 16 Abstract im nek J ejna M 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 Media User Manual Version 1 0 PC Progress Prague Czech Republic 2
121. ept 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 23 Project Information Name Furrow Description MEAE Working Directory Temporary is deleted after closing the project Permanent resultfiles are keptin this directory Directory CAussl Hydrus3D Hydrus3D Furrow Project Group Name 2D_Tests 3 Description Two Dimensional Examples Directory C usshHydrus3D Projects 2D_Tests Figure 4 The Project Information dialog window New Project Group Project Group Name 3D_tests Description Examples of three dimensional problems Directory CAussl Hydrus3D 3D_Tests Figure 5 General description of the HYDRUS Project Group Projects created by the previous version 2 0 of HYDRUS 2D can be imported into the current version of HYDRUS using two ways 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
122. ering 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 EKARA eka 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 44 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 observe on the Edit Bar that an index of a preselected point and its c
123. ero 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 POpt P2H P2L P3 r2H Value of the pressure head L below which roots start to extract water from the soil Value of the pressure head L below which roots extract water at the maximum possible rate Value of the limiting pressure head L below which roots cannot longer extract water at the maximum rate assuming a potential transpiration rate of 72H As P2H but for a potential transpiration rate of r2L Value of the pressure head L below which root water uptake ceases usually taken at the wilting point Potential transpiration rate LT currently set at 0 5 cm day 63 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 f
124. erval 38 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 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 39 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 and 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 unt
125. es between the ith principal direction of the tensor K and the j axis of the global coordinate system i 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 Aniz Conx Con y Con z Cos x CosfY y CosfZ 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 50 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 Space 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 Solute Transport Time Weighting Scheme Space Weighting Scheme Galerkin Finite Elements Crank Nicholson Scheme Upstream Weighting FE Implicit Scheme GFE with Artificial Dispersion Solute Information Number of Solutes 1 Use Tortuosity Factor ss Temperature Dependence of Transport and Pulse Duration 1 Reaction Parameters L C ttachment Detachment Concept Mass Units mmol virus bacteria transport Stability Criterion 2 Iteration Criteria for Nonlinear Adsorption only Absolute Concentration Tolerance Relative Concentratin Tolerance 0 f j Ma
126. es 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 163 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 94 Right clicking results in the display of the pop up menu Fig 108 that allows users to choose different display options such as Color Smoothing Isolines and Isobands These options are defined in more detail below Min Max Global in Time Min Max Global in Space
127. es 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 qvadrilateral 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 Geometry Information 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 Edits selected points Edits selected lines using the Edit Curve dialog window Fig 39 Edits selected surfaces Edits selected openings Edits selected thickness vectors Edits solids 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
128. eseeesesenenseaes 86 Edit Bar during the process of defining graphically a surface left and the General tab of the Edit Surface dialog window right cccccecccsscesssecseeceseceeeeeeseeceeeceeeeeeeenseees 88 A solid showing the base surtate csccncessssctsvera Givi acvisdacde nie lveneies esa wee 88 Solid showing separate vertical columns 0 cccceeceeesceesseceteceseeeeeceeseeceaecneeeeeeenaaes 89 A solid with its base surface in the XZ plane and thickness vectors in the Y direction EE dba es Rae ash aura E NE ENEE 89 FE Mesh for a solid with its base surface in the XZ plane and thickness vectors in the Ne SPURS OUIOT ts ig cause tics eta eianaledeb r seas onda cate aa e A reese capa aa ie eai 90 The Integrated Tab of the Edit Surface dialog Window eccescceseeeteeteeeteeeeeeseeeaees 92 An example of internal Objects 2v 0isecancesats excised cate da ieee sieee san eae ae 93 An example of an Upper Surface definition using Internal Curves and Thickness VEC ODOT ca eats eek tent iat tae ees ll neni Stel E ai Se ant tanta 5 ae 94 The New Opening dialog Window wccscicecvssinensicssuseus tc dines toddasdasdeeacissskdenoucsuesartabdacsdet 95 10 Figure 57 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 7
129. eshes 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 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 17 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 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 18 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
130. face 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 A simple Hexahedral Solid can be created graphically using the menu command Jnsert 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 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 displayed next to the cursor and on the Edit Bar which will automatically change to the one displayed in Figure 58 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 58 right for the definition of the Thickness Vector The selection can be made on the Edit Bar that also displays the
131. files Tabs 99 Edit Solid General Sub Layers Thickness Profiles FE Mesh Set Relative Size of FE distance between mesh layers at the top and bottom of the domain RS1 1 Generate Distribution RS2 1 RS 0 3 Edit Solid General Sub Layers Thickness Profiles FE Mesh FE Mesh Layers N 2q Set vertical Mesh Density in Layers FE Mesh Density in Sub Layers RS Relative Size of Mesh Elements On Thick Vect Denese eee relative thickness of mesh layers No 1 m Pik Figure 60 The Edit Solid dialog window the FE Mesh Tab for a single and multiple layers 100 4 4 1 Division of a Solid into Columns Notice that the Base Surface must be defined using several Surfaces see Fig 49 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 Division of a Solid into Sublayers Sublayers are used to divide
132. g 23 Specifies solute transport parameters the Solute Transport Parameters dialog window Fig 24 Specifies solute reaction parameters the Solute Reaction Parameters dialog window Fig 25 Specifies parameters defining the temperature dependence of reaction and transport parameters the Temperature Dependent Solute Transport and Reaction Parameters dialog window shown in Figure 26 Specifies heat transport parameters the Heat Transport dialog window Fig 27 Selects the root water uptake stress response models for both salinity and water stress the Root Water Uptake Model dialog window Fig 28 Specifies parameters in the root water uptake water stress response model the Root Water Uptake Parameters dialog window Fig 29 Specifies parameters in the root water uptake salinity stress response model the Root Water Uptake Parameters dialog window Fig 30 Specifies time dependent boundary conditions for all transport processes the Time Variable Boundary Conditions dialog window Fig 32 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 73 Specifies either parameters of the Unstructured Finite Element Mesh Generator the FE Mesh Parameters dialog window Figs 76 through 79 or parameters of the
133. g 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 possible 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 t
134. g the menu command 137 Edit gt Boundary Conditions gt Boundary Conditions Options or from the Edit Bar for Water Flow Boundary Conditions version using the BDRC Options command The following new options are available in HYDRUS a b c d e g h While in version 2 0 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 While version 2 0 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 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 nodes wi
135. gle iQ Surface via Boundaries id Opening via Boundaries is Dimension 4 Comment Transform Object a Translate T3 Rotate AK Mirror wt Intersect Lines Xe Insert Points on Line Split Line Help How to Edit Domain Ke Check Domain Definition gt Next FE Mesh 3 Tools 212 Edit FE Mesh 5 FE Mesh Generator E5 FE Mesh Parameters amp Insert Mesh Refinement 55 Generate FE Mesh 5 Delete FE Mesh FE Mesh Statistics amp Remove Selected Elemen FE Mesh Advanced Options Fundamental Triangulation Mesh Refinement amp Delaunay Retriangulation amp Convex Retriangulation amp Mesh Smoothing FE Mesh Sections 3 Cutwith Rectangle 4 Edit Sections EA New Section from View 4 Default Sections EA Display whole FE Mesh amp Hide whole FE Mesh Display Previous State 8 Toggle Visibility FE Mesh Selection Select Mesh Nodes C Select Mesh Elements Help k How to make FE Mesh Next Domain Properties Back Domain Definition 166 Figure 109 Selected Edit Bars for Domain Geometry and FE Mesh 8 4 Toolbars 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 110 Users can also create their own
136. h Point No Point Type Point No E 9 FE mesh Refinement S at Point S 2 cm y Coordinates FE Mesh Refinement Coordinate system Cartesian Reference Point No 0 P XY Z Coordinate X Coordinate Z Global FE Size 5 cm Comment Figure 37 The Edit Point dialog window 76 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 e Cartesian e Cartesian e X cylindrical e Polar e Y cylindrical e Z cylindrical e Spherical 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 Standard These are regular points defined using two or three coordinates e Parametric These points are located on a curve and their location is calculated usi
137. h 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 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
138. he 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 78 its anisotropy Figs 77 and 83 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 When 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 128 2 g T 28 OE VAAN i p Spg ONIY TE A eke f TAH ae ai Be ee A ts gas gi CNA sae 38 CALAN MONO gi 6 Ny WW CERAM a A gas g UO A HORAN OR pee 32 A NARRATION S24 3 NAKANO KAUN Peek of VINYARD DUN NOR ee TTE LO ONA AN DNNN aig SH Eha RE A AVVN E K onin sE amp 8 EIIN NN TE t HE Aa P NK mu a beh fa NOG Fig 83 Example of mesh stretching using a stretching factor of 3 in the y direction 129 5 6 Finite Element Mesh Statistics FE Mesh Information
139. he 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 E 7 EEE Ee EN Custom colors JIB BEES T E Sog pgp eal 240 ColorlSolid Lum 119 Blue 0 Define Custom Color Figure 96 The Color dialog window 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 e Empty Deletes all values used with commands Fill and Fill Max Min 146 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 e 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 Scale see Figure 97 Edit Isoband Values and Color Spectra Edit Isoband Values and Color Spectra Scales e Scales 75 000 PH1 PH
140. ic nitrogen and organic phosphorus are modeled as part of the COD Heterotrophic bacteria are assumed to be responsible for hydrolysis mineralization of organic matter aerobic growth and denitrification anoxic growth while Autotrophic bacteria are responsible for nitrification 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 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 53 conjugate gradient method After inversion the coefficients are re evaluated using the initial solution and the new equations 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 prob
141. ic Nissan pate ae sheng Bead ie sea Re aes 200 References 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 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 ccccceeseeeeeeereeeteees 20 The project Manager with the Project Groups tab ecccecceeceeeeeetseeeeceteeeeeeeeaeees 21 The Project Manager with the Projects tab 0 i0suieanchteni heesevlisasie eens 22 The Project Information dialog window ccccsscessceescesnceesseceeeeseeeessecneeeeeeeeseeesaeees 24 General description of the HYDRUS Project Groups ccecceecceesceeeseeeeeeteeeeeenseees 24 The Geometry Information dialog window with 3D preview scesesceeeceteeeeeeees 26 The Geometry Information dialog window with 2D axisymmetrical preview 27 Examples of rectangular top and general bottom two dimensional geometries 28 Example of a hexahedral three dimensional geometry cccceecceesseesseceeeeeeeeeteeeeneees 28 The Rectangular Domain Definition dialog Window eeceeseecesecesecneceeetneeeneeeeees 29 The Hexahedral Domain Definition dialog window cccccceesseeeteceeeeeeeeeeseeeseenes 29 The Mai
142. ically 185 Spline Surfaces Openings Thicknesses Solids 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 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 Inserts a spline either graphically or numerically the Edit Curve dialog window without the FE Mesh tab Fig 39 Inserts a 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 new FE mesh refinement graphically the FE Mesh refinement dialog window Fig 81 Defines new FE mesh refinement graphically the FE Mesh refinement dialog window Fig 81 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
143. icro organisms Organic nitrogen and organic phosphorus are modeled as part of the COD Heterotrophic bacteria are assumed to be responsible for hydrolysis mineralization of organic matter aerobic growth and denitrification anoxic growth while autotrophic bacteria are responsible for nitrification Solute Transport Constructed Wetland Model Parameters Hydrolysis oo 8 Hydrolysis Rate Constant 01 Sat Inh Coeff for Hydrolysis Heterotrophic Organisms Mineralization 0 1 Max Aerobic Growth Rate Sat Inh Coeff for Substr 0 0025 eee 05 Sat Inh Coeff for NH4 0 2 Sat Inh Coeff for 02 Sat Inh Coeff for P Heterotrophic Organisms Denitrification 0 08 Max Denitrification Rate 05 Sat Inh Coeff for NO2 0 2 Sat Inh Coeff for 02 C Sat Inh Coeff for Substr 05 Sat Inh Coeff forN03 005 Sat inh Coeff for NH4 0 01 Sat Inh Coeff for P Previous Autotrophic Bacteria Nitrosonomas 0 015 Max Aerobic Growth Rate Sat Inh Coeff for NH4 0 0015 1 Rate Constant for Lysis ae Sat Inh Coeff for P Sat Inh Coeff for 02 Autotrophic Bacteria Nitrobacter 0 0167 Max Aerobic Growth Rate 0 1 Sat Inh Coeff for NO2 0 0015 Rate Constant for Lysis 205 Sat Inh Coeff for NH4 0 1 Sat Inh Coeff for 02 0 01 Sat Inh Coeff for P Figure 33 The Constructed Wetland Model Parameter I dialog window 70 Constructed Wetland Model Parameters II 28000 o oa jv a
144. icular 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 Figure 10 shows a dialog for the creation of Special Profiles There is always a Default 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 101 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 62 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 Sublayers on all Thickness Vectors by changing a single Profile 4 4 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 i
145. il 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 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 Upper Limit of the Tension Interval Initial Condition In the Pressure Head O In the Water Content 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 head precision tolerances 40 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 Water Conte
146. imation 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 selected 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 OK Soil Hydraulic Parameters Solute Transport Parameters Help Concentration Type Resident Concentrations Log Re
147. in Definition Hexahedral parametric O General Units Length cm v Initial Workspace x Y Min 0 00 0 00 Max 1000 00 1000 00 C Set View Stretching Factors Automatically C Display Workspace Outline Figure 6 The Geometry Information dialog window with 3D preview 26 Geometry Information Type of Geometry Simple 2D rectangular domain 2D Horizontal Plane defined by dimensions W x H ee 2D Vertical Plane 2 Help 3D Layered Domain Definition Rectangular parametric General Units Length cm v Initial Workspace x Z Min 0 00 0 00 cm Max 1000 00 200 00 fem C Set View Stretching Factors Automatically C Display Workspace Outline Figure 7 The Geometry Information dialog window with 2D axisymmetrical preview Domain Definition This section allows a user to choose between a simple geometry having a structured finite element mesh or a more general geometry having an unstructured finite element mesh Only simple geometries may be used depending on the authorization Simple 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 be straight Nodes along the upper boundary line may in that case have variable x and z coordinates However the lower bound
148. in Processes dialog window Fig 12 users specify the processes to be simulated i e water flow multiple solute transport heat transport and or root water uptake 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 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 first 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 For two dimensional problems a user can also select if a Direct or Inverse problem is to be solved Inverse problems involve the estimation of selected parameters from available experimental data Main Processes Simulate K Water Flow Solute Transport Heat Transport Cancel Previous Figure 12 The Main Processes dialog window 31 3 2 Inverse Solution HYDRUS implement a Marquardt Levenberg type parameter est
149. inates Fig 74 The relative size of finite elements on the vertical side can be 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 Rectangular Domain Discretization Horizontal Discretization in Direction Count 11 1 3 4 5 _ xem 0 00 200 00 300 00 400 00 dz cm 0 00 0 00 0 00 0 00 Generate Vertical Coordinates Set relative size of finite elements 1 2 a 4 5 6 7 8 9 Previous Figure 74 The Rectangular Domain Discretization dialog window 117 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 Discre
150. indow 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 103 and adjust stretching factors Sets perspective view Starts Autorotate function that will rotate the transport domain in the View window 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 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 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 37 Inserts a line either graphically or numerically the Edit Curve dialog window without the FE Mesh tab Fig 39 Inserts a polyline either graphically or numerically the Edit Curve dialog window without the FE Mesh tab Fig 39 Inserts an arc either graphically or numerically Inserts a circle either graphically or numer
151. ion of the Thickness Vector i e its Boundary Points is given and can be edited in the Thickness dialog window Fig 62 New thickness Thickness No 2 at Point No Bai 1 Boundary Points No To Thickness me SE N N2 E v Comment Figure 62 The Thickness dialog window 104 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 1 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 63 Figure 63 A solid with several thickness vectors N N X S A 7 H 7 4 N N N 2 2 7 2 4 Figure 64 FE Mesh f
152. ircle No z Curve Type Definition Points E AE List of Points r New 1 3 New i Pick all Circle Center Circle Parameters x 50 00 em r 50 25 em i 5 00 cm z 0 00 om Comment Figure 42 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 generally have to lie in the same plane Howeve
153. ities to import Pressure Head v Temperature v Concentration 1 V Concentration 2 Concentration 3 select Time Layer O The Last Final Time Layer Time Layer No imme 24 100 00 days Figure 89 The Import Initial Condition dialog window 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 click 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 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 Simunek et al 2006 Alternatively users can first select boundary nodes and then assign desired boundary conditions by clicking at a particular boundary condition at the Edit Bar 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 90 that is called usin
154. l Graph Type Isolines Color Contours Color Points Color Edges Velocity Vectors 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 102 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 94 Moves or copies a selected object Rotates a selected object Mirrors a selected object Finds the intercept of two lines and insert an interception point on the lines 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 full object
155. l Hydraulic Model Hydraulic Model van Genuchten Mualem C with Air Entry Value of 2 cm O Modified van Genuchten Brooks Corey O Kosugi log normal Dual porosity Durmer dual van Genuchten Mualem Dual porosity mobile immobile water c mass transfer O Dual porosity mobile immobile head mass transfer Hysteresis No Hysteresis O Hysteresis in Retention Curve Hysteresis in Retention Curve and Conductivity Hysteresis in retention curve no pumping Bob Lenhard 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 Genuchten 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 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 43 Hysteresis When
156. lar variable at selected observation points as well as 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 simulation by means of contour maps isolines spectral maps and velocity vectors and or by animation using both contour and spectral maps 19 E Hydrus 3D FURROW File Edit View Insert Calculation Results Tools Options Window Help D suas Fie a a e gE REAAG E Dike Res u3 Concentration Project Data 0 Results W FURROW U Project Information Pressure Head h cm Domain Geometry 72 851 G Flow and Transport Paramete 59 332 i FE Mesh os S Domain Properties 18 775 G Material Distribution 5 255 EE Nodal Recharge 8 264 5 S Scaling Factors 21 783 A SF Pressure Head 35 302 l SF Hydraulic Condu 48 821 GG SF Water Content on S Anisotropy Anisotropy Angle ie sd Anisotropy 1st Com Anisotropy 2nd Con Time Layer Subregions Observation Nodes A Geometry E FE Mesh Domain Proper Ga Initial Conditions Boundary Cond W Resuts Time 19 65 00 days v E Flowing Particles H Initial Conditions E FURROW Results Pressure Head zz Sg lt Flow Animation Chart Tools 7 Fessure Tien Ti Cross Section Chart 000 Water Content E Boundary Line Chart
157. le of internal objects 93 EA HYDRUS Test Domain Geometry TBR C Fie Edit view Insert Calculation Results Tools Options Window Help y Ueke m F Aeae EE in Pro Initial Condit Boundary C MO Results For Help press F1 System Default Pi Figure 55 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 tolerance usually 0 1 mm 94 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 positiv
158. lect 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 Ee Rendering Model wie SO Full S E Surfaces Outline O Transparent Filled S E Solids Outline amp Transparent Filled E He Graph Type H E gt Lighting a mA Color Scale a Data Go View amp Sections Figure 104 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 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 statu
159. lems involving transient water flow or b restarted with a reduced time step for steady state flow problems 54 3 11 Solute Transport Parameters Soil and Solute Specific Transport Parameters are specified in the Solute Transport Parameters dialog window Fig 24 Solute Transport Parameters Soil Specific Parameters Solute Specific Parameters mo Bulk D Disp L Disp T Fract Thlmob Sal Difus W Difus G _ Cancel 1 5 0 5 0 1 0 1 0 0 1 5 0 5 0 1 0 Nest i Figure 24 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 p ML Longitudinal 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 dia
160. lid 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 dimensional computational domain that is formed by the base surface and thickness vectors 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 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 Sublayers Such domain is then called the 3D Layered domain Although such 74 domains can not be fully general they allow definition of a majority of realistic 3D problems Computation domain can be formed using several surfaces that can touch each other but can not overlap Fig 35 It is possi
161. log window are specified for each solute Diffus W Diffus G Molecular diffusion coefficient in free water D LT Molecular diffusion coefficient in soil air Da L T 55 3 12 Solute Reaction Parameters The Solute Reaction Parameters and concentrations for Boundary Conditions are specified in the Solute Reaction Parameters dialog window Fig 25 Each solute has its own Solute Reaction Parameters dialog window Reaction Parameters for Solute 1 Boundary Conditions OK cBnd cBnd2 cBnd3 cBnd4 cRoot 3 cWell cBnd c amp tm Cancel 1 0 0 0 0 0 0 0 Help Reaction Parameters Henry SinkL1 SinkS1 Previous Figure 25 The Solute Reaction Parameters dialog window The following Solute Reaction Parameters are specified for each soil material Kd Adsorption isotherm coefficient k M L Nu Adsorption isotherm coefficient 7 M L Beta Adsorption isotherm exponent Henry Equilibrium distribution constant between liquid and gaseous phases ke SinkL1 First order rate constant for dissolved phase 44 T SinkS1 First order rate constant for solid phase 44 T SinkG1 First order rate constant for gas phase 4e T1 SinkL1 First order rate constant for dissolved phase 4 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 4e T
162. lude various Labels or define permanent Cross Sections or Mesh Lines 4 6 1 Dimensions Dimensions can be added to describe spatial properties of the computational domain in the View window using the Insert 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 58 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 67 left After the second point is selected a cursor in the View window and the Edit Bar Fig 67 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 67 right xi zix a Domain Geometry Domain Geometry Set new Dimension a z z Number for new Set new Dimension a 5 Dimension Number for new Dimension Dimension Type Definition Points Length Odx Point 1 1 Paint 2 0 Odz l Stop Stop Help R Help a Ke Step 2 of 3 Ke Step 3 of 3 Set second point of the new Set position of the new Dimension Dimension Ke Press Esc or right
163. lues at the Edit Bar on the right side of the view window the Water Flow Initial Condition dialog window Fig 87 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 equilibrium with the pressure head of the lowest point in the selected region Equilibrium from the lowest located nodal point and c a Linear distribution with depth When options a or b are selected only one value of the pressure head needs to be specified For option c one needs to provide values of the pressure head or water content for the top and bottom of the selected domain 134 Water Flow Initial Condition Distribution Values in selected nodes Same value for all nodes Selected Nodes 400 Minimum value 100 Linear distribution with depth Maximum value 100 Pressure Head Other Options Top Water Content Value Figure 87 The Water Flow Initial Condition dialog window To simplify definition of the initial condition for problems that involve slopes an option is provided to have pressure heads decrease in the x
164. m being solved Problems with high pressure gradients e g infiltration into an initially dry soil and for soils with highly nonlinear soil hydraulic properties require relatively small initial time steps The initial time step is used at the beginning of the simulation or whenever boundary conditions are substantially changed e g the water flux changes by 25 or more Minimum Time Step Minimum permitted value of the time increment dtmin 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 Maximum Time Step Maximum permitted value of the time increment dtmax T The maximum time step can be a relatively large number the optimal time step is selected by the program unless small time steps are required for example to simulate temperatures during one day Boundary Conditions Time Variable Boundary Condition The number of time dependent 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 37 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 OK V T Level Information Every n time steps Interval Output Help Count 3 Cancel
165. meters Information needed for defining heat transport problem is entered in the Heat Transport dialog window Fig 27 In this window users specify Heat Transport Parameters and temperatures for the Boundary Conditions Heat Transport Parameters 2 Boundary Conditions OK TBound1 TBound2 TBound3 TBound4 TBound5 TWell Cancel 1 0 0 0 0 0 Help Heat Transport Parameters 1 Temperature Amplitude Set Default Volume sowed Heat Capacities Time interval for one temp cycle Thermal Conductivity Loam L Heat Transport Parameters 2 Disp L Disp T f b1 b2 1 1 56728E 016 2 53474E 016 Previous Figure 27 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 6 Org M Volume fraction of organic matter 6 Disp L Longitudinal thermal dispersivity Az L Disp T Longitudinal thermal dispersivity Ar L b1 Coefficient b in the expression for the thermal conductivity function W L K b2 Coefficient bz 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 C J L K Co Volumetric heat capacity of organic matter C J L7 K 60 Cw Volumetric heat capacity of the liquid phase C J L K Boundary C
166. n an a wo if z o z Figure 34 The Constructed Wetland Model Parameter II dialog window 71 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 element mesh Alternatively a more general 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 or the base plane base surface of the three dimensional domain In both 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 nonintersecti
167. n Processes dialog window nc dessicrssccdsacissaideseacdeieds iadrianasdiadakdasmivatdanetans 31 The Inverse Solution dialog Window ccesccescsessceesseesseceeeeeeeeeeseecsaecnseeeeeeeeseeesaeenes 32 The Data for Inverse Solution dialog Window ssessessssssessessessessseeseseesseeseeserssesse 33 The Time Information dialog Window ccccccecessessessessesseseeseeseeseesecseceesecseeseeeeeeaeeaees 36 The Output Information dialog Window ccccceceeesseseesseseeseeseeeeseesecseceesecseeseeeeseeaees 38 The Iteration Criteria dialog window ssi sisasatiesaccssscdeatavanedacssetesaasttvussaotaagnatantandadasas dods 40 The Soil Hydraulic Model dialog Window cccccccceseceseceeeceeeeeeseceteeeeecenseeenseeesaeens 43 The Water Flow Parameters dialog window for direct top and inverse bottom TSENG a occa AAE E A Soe Catia Nos E eco aac ees RaC ae earned 45 The Rosetta Lite Neural Network Predictions dialog window cceseeseeetees 49 The Edit Local Anisotropy dialog window for two dimensional applications 50 The Tensors of the Anisotropy dialog WindOW c cccssccsseceeseeeseeeeseceteeeeeeeeseeeseenes 50 The Solute Transport dialog Window cccscccscsssscessseeeseceseeseeeeeseecsaecneeeeeeenseeeaeenes 51 The Solute Transport Parameters dialog windoW ccccsceeeseeesseeeteceteeeeeeesseeeaeenes 55 The Solute Reaction Parameters dialog window ccccecsseeseeetecee
168. n 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 76 or to increase the Smoothing Factor in the FE Mesh Quality group discussed below FE Mesh Parameters Main Stretching Options 1 Options 2 Mesh Sections FE mesh Limits 1200 Max number of nodes on boundary curves Max number of FE mesh nodes 2D mesh 100000 FE mesh Quality Max number of overall remeshing iterations Number of intensive smoothing steps z Previous Number of internal iterations for intensive smoothing ha Be Apply Number of internal iterations for standard smoothing Smoothing factor gt 1 All Default Figure 78 The FE Mesh Parameters dialog window Tab Options 1 121 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 gener
169. n points the distance of which is to be labeled left and the dimension type Carana MEE dre Seda teewe Sad cadet lesen ded loca wasps au desi caaaieotata tate EA 107 The Edit Comment dialog window caaiadiecinnas eee ue ei ees 108 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 109 The Cross Section dialog windowW soa c64 oes scares cyse less cySeanen sa bens ne ecacs coriereasMaededtonea teed ce 110 The Mesh Line dialog watid Wei assets ais tiaieiaiecausk vende Becta taiedaieca bh eeceadh eae 111 The Fluxes across Mesh Line dialog window c c cccssccessceeeeeeseeeneeceseeneeeeeeeenseees 112 The Finite Element Mesh Generator dialog window One version of the dialog for the structured FE mesh is shown at the top and one for the unstructured mesh at the bottomof the window x55 esas ee a E a et apt aaa eas ated va 116 The Rectangular Domain Discretization dialog Window e cssceeseeeeeeeeeeteeeeeenee 117 The Hexahedral Domain Discretization dialog WiINdOW c ccccccesseceteeeteeeeeeeneeees 118 The FE Mesh Parameters dialog window Tab Main ccccccsessseeeteeeeeeeeeeeeeeees 119 The FE Mesh Parameters dialog window Tab Stretching 0 0 0 0 ccceeceeseeseeeeteees 120 The FE Mesh Parameters dialog window Tab Options 1 cceeceeeceeseeteeeteees 121 The FE Mesh Parameters dialog win
170. n the FE Mesh Refinement is defined for both a point and a line then the FE Mesh Refinement specified for the lower level objects i 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 12 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 counter clockwise direction on closed curves Boundary nodes determine the local densities of the triangular mesh that is 127 being generated for a given boundary nodal distribution and are part of the triangular mesh 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 describin
171. nce 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 Range convergence 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 Multiplication Factor convergence for 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 Multiplication Factor convergence for water flow 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 prescrib
172. nd 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 8 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_WORD followed by coordinates of points defining given object Two or three coordinates for two and three dimensional problems of a single point are given on a single line Numbers can be delimited using a space a semicolon or a tabulator 113 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 ar
173. nd offset are displayed at the Edit Bar Fig 69 right 4 6 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 Jnsert 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 One can then simply trace the bitmap to specify the computational domain 108 Domain Geometry Domain Geometry Set new Comment cas Set new Comment za Number for new Number for new Comment Comment ill Text Text Text Text my Lr Frame C Frame Position Offset x 862 69 om dx 40 pix he dy 130 pix Z 173 88 em Step 10 pix Stop Stop Help x Help x Ke Step 1 of 2 Ke Step 2 of 2 Set position of the new Set offset of the new ornment Comment K Press Esc or right mouse K Press Esc or right mouse button to end the tool button to end the tool Figure 69 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 4 6 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
174. nd 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 102 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 Work Plane Origin Point No Grid Options Grid Type Number of Grid Points M Snap Cartesian l M Show O Polar Direction1 30 30 Direction 2 30 30 C Dynamic update Grid Point Spacing Distance b 50 00 cm Distance h 50 00 cm Rotation p oom 0 Figure 102 The Grid and Work Plane dialog window 155 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
175. ndow the Program Options Tab eeeeeeee 192 The Program Options dialog window the Files and Directories Tab 4 193 The HYDRUS License and Activation dialog WindOW ccccesseceteeeteeeeteeeteees 195 The General Picture and Legend tabs of the Print Options dialog window 197 The Coordinate Systems dialog WindOWS cccceeseesseeeteceeeceeeeeeseecaeeeteeeeeeenseees 198 The Create Video File dialog window sca assess cette Jaca adiasania ein 200 13 14 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 List of Tables Commands in the Project Mana Ser lt uvecvedaiesaceessbodeaceat jascants aseseneac eae ease acer 23 Data types for the objective function Inverse Problem eeceseeeceeteeereeeeeeteeenee 34 Definition of the column X in Fig 14 based on Data Type Inverse Problem 34 Definition of the column Y in Fig 14 based on Data Type Inverse Problem 35 Time Information variables a a E E a E a AORT E 37 Time Step Control variableSnsczienehis iieri ie oa a e E EEE isnt 42 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 Parish 1988 ziru EE O EO eae eae 47 Soil hydraulic parameters for the analytical functions of van G
176. ne the Base Surface for Solid 3D Layered domains e 3D General The term Surface serves to define boundary surfaces of a general 3D solid This type of solids is however not yet available in the current version of HYDRUS 3D Standard More detailed information can be found at Solid General At present the only available type of a Surface is a Planar Surface This type of the Surface is defined by its boundary curves that must all lie in the same plane and can not cross each other 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 Surface by Rectangle and Surface by 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 36 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
177. nes 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 39 When entering a new line graphically users can select the command Jnsert 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 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 36 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 second one while the last point of the first line will be the beginning point of the second line Each abscissa is considered to b
178. ng Factors amp Anisotropy Al Angle A 1st Component A 2nd Component A Subregions EE Observation Nodes e Flowing Particles H Initial Conditions E Boundary Conditions E Auxiliary Objects E Results Graphical Display Results Other Information lt m EJ Sections fe Data soa Bs Data Structure 3 Furrow Domain Geometry Flow Parameters FE Mesh Domain Properties Initial Conditions Boundary Conditions Auxiliary Objects See Results Graphical Display 000 Pressure Head 000 water Content 000 velocity 000 velocity vectors 000 Temperature 000 Concentration 1 000 Concentration 2 00 Concentration 3 Results Other Information BB lt M E Domain Geometry FE Mesh Sections HO Domain Properties Initial Conditions GQ Pressure Head Temperature gi Concentration 1 Concentration 2 ga Concentration 3 d Boundary Conditions 000 Results amp FE Mesh OEZ Numbering Elg Ausiliary Objects Rendering E4 Graph Type E gt Lighting a GB Color Scale H D 0 E Ege Data 6 View Figure 106 Selected Navigator Bars Data Tabs on the left and in the middle the View Tab on the right 161 8 3 Edit Bars The 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
179. ng 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 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 37 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 38 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 TT id HYDRUS sssss Domain Geometry m Fie Edit View Insert Calculation Results BESS Options Developers Deuas re TOR Window Help B x KEELEKE yg lalaaaaym ax oA Domain Geometry al A Show Grid i Snap to Grid 2 Grid and Work Plane Define Work Plane Project Data WW sssss U Project Information Domain Geometry a Geometry Information Points Lines Surfaces Openings Thicknesses Soli
180. ng 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 102 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 Jnsert 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 Geometry 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
181. ns License Request Information Hexahedral General Layered Request Code 1 328418869 Network Request Code 2 10184485 Network License Hydrus version Beta 05 Level to activate 3D Standard Number of Clients Network License No Display Your Current License Deactivate HYDRUS Copy to the Clipboard Activate HYDRUS Enter Activation Codes Activate Now How to Activate Figure 118 The HYDRUS License and Activation dialog window 9 2 1 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 can not be used repeatedly even for the same computer 2 Request Code 2 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 195 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 two attempts available to activate HYDRUS with particular request and activation codes If wrong activ
182. nserts 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 operation 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 Sublayers A Solid can be vertically divided into Sublayers 102 4 5 Thicknesses 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 62 There are several ways in which a Thickness Vector can be specified graphically and these are displayed at the Edit Bar Fig 61 which appears once a command for defining a Thickness Vector is selected a b c d Point and Length A user specifies the lengt
183. nt Mesh Statistics topic sss Picts nis chad sia een oud ands an ie andd eevee and bananas vies 130 5 7 Finite Element Mesh SCCHONS 2sccccdtesscsedaceg Sabi acaseies te tssaciesst asennad eee Rages 131 6 Domain Properties Initial and Boundary Conditions 0 0 ccccccccccceseeeeseeeesteeees 133 9 6 1 Default Domain Properties arses cate cs Gate thee caida ccuuathadess acai ntus crated acaccclanleceetaanths 133 62 Inita Conditions siaa aa at el MGA A Sak a eal BON Tate ed cota 134 GS Boundary Conditions sasis siriani an A aE E A cesar A EATE 137 6 4 Domain Properties messiccana a a E EE EER 139 Graphical Outp t ensanse n eke Sh CAA AEE A is 142 7 1 Results Graphical Display s nossessonseenessseessesesseessessessressessresresseeseesesseeseseessesse 142 Teki Display OptOnS cesinta AEE E A E AA 143 7 1 2 Edit Isoband Value and Color Spectra soosoosneonenneseesseeseeseeeseesessessseesee 144 7 2 Results Other Information sossessessseseeseesssessesessssessessrssressessresresseeseesresseeseesersseesse 150 Take Mee Convert to AS CU eere ee a R e E e AATE RRE EE 153 Graphical User Interface Components cccccccccessccesscecesececsseeecsseeecseceeseeeesseeees 154 Sl Kiew Wind Wrecn tniii a de leave vases AAE a E a AT E E ai 154 8 1 1 Scene and Viewing Commands s sssssessssessesessssessessrssressessrsseesseeseesresseeseese 154 8 1 2 Grid and Work PIA Ccecsaoy cine naan cases aucee ove des
184. nt 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 lcm Information specified in the Time Step Control part of the dialog window is related to the automatic adjustment of the time step 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 de
185. nt 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 145 After clicking on the color panel with the left mouse button the Color dialog window Fig 96 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 temperatures Since the Standard Palette can not be changed once any color is changed t
186. ntration x Sorbed Concentration x Atmospheric Boundary Head Root Zone Head Variable Boundary Head 1 Constant Boundary Head Seepage 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 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 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 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 Flux Cumulative Variabl
187. o 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 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 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 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 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 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
188. o show which point its number is being defined and what reference coordinate system the current coordinate system or 75 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 xl a Domain Geometry Set new Line 2s xl Numbers for new a Domain Geometry Curve id Set new Point a Point J Number for new Point S Coordinates x 319 40 em Coordinates f Z 520 15 cm ba 568 66 cm Z 335 08 cm Ref Coord System O Current CS Ref Coord System Grid Origin O Curent CS O Last Point Grid Origin LL Apo Help a Help a re Step 1 of 2 EA Samen bork eo point of the new k Press Esc or right mouse s anon torered ine teal Ke Press Esc or right mouse button to end the tool Figure 36 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 37 In addition to the General Tab Fig 37 left in the New Point dialog window the Edit Point dialog window has also the FE Mesh Tab Fig 37 right Coordinates of a point and its number are entered in the General Tab while the FE Mesh Refinement at a given point can be defined in the FE Mesh Tab Edit Point bed Edit Point General FE Mesh General FE Mes
189. ocess 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 76 through 79 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 76 the Main Tab and 2 refining the FE Mesh the FE Mesh refinement dialog window Fig 81 1 A global Targeted FE Size Fig 76 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 51 or FE Mesh Refinement Figs 37 35 and 81 FE Mesh Refinement can be implemented for various geometrical objects including Points Lines or Surfaces Fig 81 When several FE Mesh Refinements overlap in one location such as whe
190. ochastic Parameters dialog window 141 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 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 color points color edges spectral maps and or velocity vectors Graph Type at the View Tab of the 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 94 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 Ch
191. on Processes Res MB Modified O0T est2 Grass Field Problem Hupselse Beek 1982 WSHR 10 2 2006 3D Flow and transport through a dike with a seer d 6 24 2006 Multiple hysteretic loops Lenhard et al 1991 6 24 2006 Column test One dimensional infiltration test 6 24 2006 Grass Field Problem Hupselse Beek 1982 6 24 2006 Comparison with the 2 D analytical solution 6 24 2006 Solute transport with nitrification chain 6 24 2006 Solute transport with nonlinear cation adsorpti 2 15 2006 Solute transport with kinetic linear cation adsc 6 24 2006 Solute transport with first order attachment 6 24 2006 Contaminant transport from a waste disposal s 6 24 2006 ce MH KH MS Reo Project Name Dike Description Flow and transport through a dike with a seepage face root uptake Program Name Hydrus Project Type 3D Processes Water Flow Solute Transport Root Water Uptake Results Yes File Size 13 8 MB Modified 6 24 2006 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 Group has its own name description and pathway Figs 2 and 5 A Project Group can be any existing accessible subdi
192. onditions 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 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 T T Acos 2n 2 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 Defaul
193. ons M Rents A Damani H FE ETT Presuue Head h femi O A Doman Propertes O d ira Conditions a Boundary Condition W Reri O Fresne Head GD wae Cortert 9 OD Terceatue gt BD Veloety gt Concertiation 1 OW Concertiation 2 GD Concertiation 3 OW Poweg Paces MB FEH t Ji MAM G n Tine MiryMax Godal in Space 7 Standard Scale By hary Obyrets Qustom Scale Rendering Model Yo Graph Type T Lighters Bi Cov ae Cat Scale and Cols Smooth cole transition when daeng color contours Sytem Delad Pre gt Z X VRoma Y 000m Figure 99 The color smoothing 149 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 100 Figure 100 shows the x y graph dialog window that displays pressure heads in observation nodes Table 13 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 13 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
194. oordinates are displayed in edit controls These controls are disabled since displayed values can not be changed Snapping on curves Fig 44 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 44 Snap to a point left and snap to a curve right 84 4 1 5 Move Copy Rotate and Mirror Operations All boundary objects can be manipulated using the Move Copy Rotate or Mirror operations in the Move Copy Fig 45 Rotate Fig 46 left and Mirror Fig 46 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 specify the Vector of Translation for the Move or Copy operations or the Angle of Rotation for a Rotation or define the Mirroring Plane Axis for a Mirroring operation
195. or 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 29 right are as follows P50 The coefficient 450 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 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 Threshold Slope Conversion to pressure osmotic head Conversion to pressure osmotic head Osm Coeff Osm Coeff Database Ta Figure 30 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 30 left are as follows Threshold Value of the minimum osmotic head L the salinity threshold above which root water uptake occurs without a reduction
196. or 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 91 4 A point can not lie on a curve without being its definition point 5 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 their integration 7 Surfaces can not partially cover each other see also 6 Points located outside of Surfaces are ignored when generating FE Mesh 4 2 3 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
197. or the solid in Figure 63 The height of a solid is constant when less than three thickness vectors are used Three thickness vectors define a linear plane with generally an inclined surface More than three thickness 105 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 65 and 66 show the importance of having internal curves or not having them in the Y direction for proper definition of the solid compare Figures 63 and 65 Figures 64 and 66 Figure 65 Missing internal curves in the base surface Figure 66 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 106 4 6 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 computational domain inc
198. port Specifies boundary conditions for heat transport Specified additional system dependent water flow boundary conditions Generates default FE Sections Calls the FE Mesh Section dialog Fig 85 HYDRUS recognizes two different definitions of Sections one for geometrical 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 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 Edits a cross section Deletes selected cross sections Deletes all cross sections Adjust Work Plane Deletes selected dimensions Deletes all dimensions Edits a comment Deletes selected comments Deletes all comments 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
199. quilibrium Concentration Temperature Import Water Flow 176 Graphically Dialog Read from File Line Polyline Arc Circle Spline Graphically Graphically Rectangle Dialog Graphically Dialog Graphically Dialog Graphically Graphically Brick Dialog Hydraulic Conductivity Pressure Head Water Content Angle First Component Second Component Index No Flux Constant Head Constant Flux Seepage Face Variable Head 1 4 Variable Flux 1 4 Free Drainage Deep Drainage E Calculation F Results Cross Sections Mesh Line Auxiliary Objects 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 Run Time Information Mass Balance Information Convert Output to ASCII Inverse Solution Results Fluxes across Mesh Lines Time Layer Charts Flowing Particles Delete Results Atmospheric Boundary Solute Transport First Type Third Type Volatile Type Heat Transport First Type Third Type Graphically Dialog Graphically Dialog Dimension Comment Bitmap Fundamental Triangulation Mesh Refinement Retriangulation Check of Convexity Mesh Smoothing Pressure Heads Water Content Concentration Nonequilibrium Concentration Temperature Velocity Pressure Heads Bound
200. r 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 82 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 43 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 spline is ended by pressing the Esc keyboar
201. re three types of Solids depending upon the selection made in the Geometry Information 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 that form its boundaries This selection is not possible in the current version of HYDRUS xi a Domain Geometry Set new Solid Extruded a Numbers for new zixl Solid Domain Geometry E Thickness 1 Set new Solid Extruded a i Numbers for new Pont Solid Thickness Length Thickness 1 L 590 00 cm Point 9 dL 10 00 cm Surface to extrude Thickness Direction Surface 2 Perpendicular to the Surface Autodetect O In direction 7 Base Surfaces O In Y direction V Thick Vectors O InZ direction e Help a Hel a x Ke Step 2 of 2 Step 1 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 57 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
202. rectory 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 22 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 h3d 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 h3d file In addition to a Name and a brief Description of a Project the Project Manager also displays dimensions for a particular problem Type 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 th
203. ribution of Scaling Factors dialog window Fig 91 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 Hydraulic Conductivity Scaling Factor Pressure Head Scaling Factor C Water Content Scaling Factor Other Options Recalculate Parameters Figure 91 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 92 In this dialog users need to specify whether the scaling 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 spatially correlated 140 Stochastic Parameters Standard Dev of log10 y Correlation Length in x Correlation Length in z Log Normal Distribution Correlation Length in x ff Correlation Length in z os Log Normal Distribution Standard Dev oflog106 Correlation Length in x fs Correlation Length in z bs Log Normal Distribution Figure 92 The St
204. rrochet 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 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 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 Jacques 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 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 Media Version 1 0 Technical Manual PC Progress Prague Czech Republic 2006 Stumm W and J J Morgan Aquatic Chemistry An Introduction Emphasizing Chemical Eq
205. ry Line Chart K How to set Boundary i AST X Display Values at Nod gt Next Calculation Res Ke How to set Initial ali TP Back Initial Conditions Next Boundary Condi Poo Back Domain Propert Right click on the Color Scale displays options Back Boundary Cond RW Tools 3 Tools Figure 107 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 162 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 which 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
206. s Openings Thickness Vectors Solids 173 Flow Parameters FE Mesh Domain Properties Main Processes Inverse Solution Time Information Output Information Water Flow Parameters Iteration Criteria Hydraulic Properties Model Soil Hydraulic Parameters Anisotropy Tensors Solute Transport Parameters General Information Solute Transport Parameters Solute Reaction Parameters Temperature Dependence 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 Generator 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 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 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 Default Domain Parameters 174 C View Initial Conditions Boundary Conditions Sections Cross Sections Auxiliary Objects Bitmaps
207. s 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 157 Apart from selecting objects graphically they can also be selected using their Indices or by means of Sections Double clicking on selected objects or simultaneous holding the Altt 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 sensi
208. scribed in the input data file Time Variable Boundary Conditions Fig 32 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 discretizations 2 3 and 4 b Time increments cannot become less than a preselected minimum time step Atnin NOT exceed a maximum time step Atay 1 Atmin lt At lt Atmax 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 At with a predetermined constant gt 1 usually between 1 1 and 1 5 If the number of iterations is gt 7 At for the next time level is 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 A 3 and the iterative process restarted We note that the selection of optimal time steps At during execution is also influenced by the adopted solution scheme for solute transport 41 Table 6 Time Step Control variables Lower Optimal Iteration When the number of iterations necessary to reach Range converge
209. ses 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 118 Displays the version and authors of the HYDRUS application 190 9 Miscellaneous Information The Program Options dialog window has three tabs one related to Graphics Fig 115 one to 9 1 Program Options Program Options Fig 116 and one to Program Files and Directories Fig 117 On the left side of the Graphics Tab 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 On the right side of the Graphics Tab Options one can select a b c d e Simplified display in Move modus 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 a different background Gra
210. sident Concentrations flow Concentrations 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 32 The objective function for the inverse 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 w N 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 C Show list boxes not recommended for larg
211. sired 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 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 90 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 internal 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 selecing from the popup menu the Create Opening command Additional information can be found at Openings 5 Geometrie Check
212. 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 Specifies default domain properties that are constant for the same depths the Default Domain Properties dialog window Fig 86 Specifies the initial condition for water flow Specifies the initial condition for solute transport equilibrium concentrations 183 Nonequilibrium Concentration Temperature Import Boundary Conditions Water Flow Solute Transport Heat Transport Boundary Conditions Options Sections Generate FE Sections Edit Sections New Section from Selection New Section from View Display All Display Previous Hide Selection Display only Selection Display Reverse Cut with amp Rectangle Cut with amp Indexes Cross Sections Edit Delete Selected Delete All Auto Adjust Work Plane Auxiliary Objects Dimensions Delete Selected Delete All Comments Edit Delete Selected Delete All View Geometry FE Mesh Domain Properties Initial Conditions Boundary Conditions 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 Specifies boundary conditions for water flow Specifies boundary conditions for solute trans
213. splay selected variables along defined Mesh Lines Similarly to Cross Sections the locations of Mesh Lines are saved and can be recalled at any time 110 Mesh Line Description 1 Meshline to calculate flux Mesh Nodes for example 1 2 3 4 573 423 302 204 139 248 427 389 311 588 377 102 386 239 172 C Alow arbitrary indexes not only adjacent nodes Fluxes Calculate Fluxes across this Mesh Line Figure 71 The Mesh Line dialog window A description of the Mesh Line is given in the Mesh Line dialog window Fig 71 which contains the Mesh Line number its description a list of nodes defining the Mesh Line and whether or not the computational module should 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 72 after using the Results gt Fluxes across Mesh Lines command This dialog displays actual and cumulative water and solute fluxes across individual Mesh Lines 111 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 o FA a E D _ h B 5 te B 100 150 200 250 Time days Figure 72 The Fluxes across Mesh Line dialog window 112 4 7 Other Notes on O
214. ss section graphically Inserts a cross section using the dialog window Inserts a mesh line graphically Inserts a mesh line using the dialog window Inserts auxiliary object dimensions Inserts auxiliary object comment Inserts auxiliary object bitmap Specifies either parameters of the Unstructured Finite Element Mesh Generator the FE Mesh Parameters dialog window Figs 76 through 79 or parameters of the structured mesh the Rectangular Domain Discretization dialog window Fig 74 or the Hexahedral Domain Discretization dialog window Fig 75 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 84 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 according to Delaunay criterion Corrects possible errors which may appear during smoothing and retriangulating 187 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 Run Time
215. structured mesh the Rectangular Domain Discretization dialog window Fig 74 or the Hexahedral Domain Discretization dialog window Fig 75 Generates unstructured finite element mesh Deletes unstructured finite element mesh Removes selected finite elements from the finite element mesh Provides information about finite element mesh the FE Mesh Information dialog window Fig 84 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 according to Delaunay criterion 182 Check of Convexity Mesh Smoothing Domain Properties 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 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 Default Domain Parameters Initial Conditions Pressure Head Water Content Concentration 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
216. sults mode to view the pressure head distribution Time 1 0 20 days vi gt Wem 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 for which results are available 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 170 8 5 HYDRUS Menus The main window of HYDRUS contains a menu that has ten submenus i e File Edit View Fig 112 Insert Calculations Results Fig 113 Tools Options Windows and Help Fig 114 Table 14 lists the main groups the main menu items as well as the main submenu and sub submenu commands Table 15 then provides brief descriptions of all menu commands iy Edit View Insert Calculation i Edit View Insert Calculation Result Insert Calculation Results Tools Of IO New Open i Close fel Save G Save As Gil Save All Save Special Import and Export Print Ctrl P Print Preview Print to the Clipboard Print Options Printer Setup Ctrl C Project Information Project Manager 1 C USSL 3D_Tests Test2 H3D 2 C USSL Furrow H3D 3 C USSL 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 AN
217. t 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 values 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 1 and JmK 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 61 3 15 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 28 Root Water Uptake Model Water Uptake Reduction Model Feddes O S Shape Critical Stress Index 1 Solute Stress Model O No Solute Stress O Additive Model Threshold Model S Shape Model Previous Figure 28 The Root Water Uptake Model dialog window 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
218. t ka T for the first sorption sites When Filtration Theory Fig 23 is used to calculate the attachment coefficient then the following parameters must be entered instead D_Soil D_Virus SMax2 Stick Eff2 DetachSolid2 SMax1 Stick Eff1 DetachSolid1 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 1 Sticking efficiency a for the second sorption sites First order entrainment detachment coefficient ka T for the second sorption sites Parameter in the blocking function for the first sorption sites Sticking efficiency a for the first sorption sites First order entrainment detachment coefficient ka T for the first sorption sites Boundary Conditions Concentrations for time independent Boundary Conditions are also specified in this dialog window 57 cBnd1 cRoot cWell cBnd7 cAtm d Value of the concentration for the first time independent boundary condition ML Set equal to zero if no time independent boundary condition is specified The same for cBnd2 through cBnd4 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 zer
219. teehee adalat as i a eid ties a ee does Sek 40 3 6 Soil Hydraulie Mod l rsson rians eii aA EET AERE RTA AREE Taa 43 3 7 Water Flow Parameters oosseeeneseeesseseesseseesessesersessereesseseestssesresesseseesseseesesseseesessese 45 38 Ne ral Network Predictions coating en a ei cre E ase 49 3 9 Anisotropy in the Hydraulic Conductivity ccccccccescceseceesceesseeeseceeceseeeeaceeseseeeneeeeeaeees 50 3 10 Solute Transport arans anaie a a sa ne ands E A R ein a Bia 51 3 11 Solute Transport Parameters s sesesssesseseesseseesessseessesessressessrssressessessressesstssresseesee 55 3 12 Solute Reaction Parameters eae iiss oka caies sakes aecdia ys devas ta ekanivas cess oat atentaes Saad ettantan Sas 56 3 13 Temperature Dependence of Solute Transport PAVAMEHELS ccccccesccesseteteeeteeeteettees 59 Sel Heat Transport Parameters bicseitis area edusiraeaoviniadsesduteamaardunend AEO E EE E EEEa 60 3 15 Root Water Uptake Model wiicles ce sagers sa tdadt cad acesateses ta oh sg Bases veda vac ease 62 3 16 Root Water Uptake Parameters aes isi hai iat pad Nei euia ta lsyasied Bei an tees 63 3 17 Root Distribution Parameters see Rte Gain oath tea ea tnatua ea eema aah ac cat ata 66 3 18 Time Variable Boundary Conditions vssscisccassesdesadens ansceis ideas dia seig iadins ahaa van ha 68 3 19 Constructed Wetlands urs piriana A A EE ATAS ARTS A ARTEA EEG 70 4 Geometry of the Transport Domain 00 ccc cccccccesscecesececsseee
220. teps to Define a 3D Layered Domain ossssssossessseeseeseesseesseserssressessresees 102 A ES E e Nae cat Base a e aa 103 4 6 Auxiliary Objects i R a E A E A A 107 Lol Dimensions Ae acdal tits etda a e i Fie lag aa ae n aaan 107 462a Babelse etei i A a a E N E ER het 108 4 6 3 Bitmaps Texture J eresas a EAE E A EREE 109 LOA UG POSS NCCIMIONG anant e a E eel A a A 109 amp 6 5 Mesh Lin S no ncirinorinerenranei csc aio nate ded SA AHR se 110 4T Other INGLES ON OD CCS unice oeiia a a E E EEEE ares elas vee 113 4 7 1 Object Numbering sisson cicaes aches scaaheeq sas steandy tun eteomelecasttuesdiesentetetudanaeeme nea 113 4 7 2 Relations among Objects wccsidissiesssbaga hetero cate aah Ra asics oss 113 4 7 3 References among Objects and Convention for Writing a List of Indices 113 4 8 Import Geometry from a Text File pessscccssczsacuaseceunsbaeichiohe eee nade dieuaaee wees 113 37 Finite Element Mesh ecrire a a ARTA E E R ee 116 5 1 Finite Element Mesh Gener arar sic iscg ait asaahicashsastvassaaeideaaniwanadvasiacesiandina uqanieia tana 116 5 2 Structured Finite Element Mesh Generator c ccccccssccssecssesseeeneeeccesecesecnseeeseneeeeensees 117 5 3 Unstructured Finite Element Mesh Parameters soosoo 119 5 4 Finite Element Mesh Refinement aise csdeteascnsast suse ok sq Suasec vs toad ae etes eee rastetga tice totes 125 5 5 Unstructured Finite Element Mesh Generator MeshGen2D nosos 127 5 6 Finite Eleme
221. ter 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 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 Kosugi K Lognormal distribution model for unsaturated soil hydraulic properties Water Resour Res 32 9 2697 2703 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 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 for 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 Millington R J and J M Quirk Permeability of porous solids Trans Faraday Soc 57 1200 1207 1961 201 Pe
222. tersect the outside boundary of the computational domain at its definition points An internal 173 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 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 35 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 The base surface is a two dimensional surface that can be extended into a three dimensional so
223. th 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 This is similar to c except that an atmospheric boundary condition is assigned to nodes with negative calculated pressure heads This is similar to c except that a seepage face boundary condition is assigned to nodes with negative calculated pressure heads 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 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 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 temperature 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
224. 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 problem is not further shown here 58 3 13 Temperature Dependence of Solute Reaction Parameters Several of the diffusion Dw Dg zero order production Ye first order degradation 44 Lis lg Llw Hs and fg and adsorption ks ke P 7 coefficients may be strongly dependent upon temperature 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 Er ra a a ep ET where a and ar 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 26 Temperature Dependent Solute Transport and Reaction Parameters Parameters Sinkater1 SinkSolid1 SinkGas1 SinkWater1 SinkSolid1 SinkGas1 51213 81171 51213 81171 51213 81171 Previous Figure 26 The Temperature Dependent Solute Transport and Reaction Parameters dialog window 59 3 14 Heat Transport Para
225. the time discretization information the Time Information dialog window Fig 15 Specifies print options The Output Information dialog window Fig 16 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 hysteresis 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 19 181 Anisotropy Tensors Solute Transport Parameters General Information Solute Transport Parameters Solute Reaction Parameters Temperature Dependence 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 Advanced FE Mesh Generation Fundamental Triangulation Mesh Refinement Retriangulation 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 Fi
226. 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 employed 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 44 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 1 e Brooks and Corey 1964 van Genuchten 1980 Vogel and
227. tion Tab for two top and three dimensional bottom applications 124 5 4 Finite Element Mesh Refinement The Finite Element Mesh Refinement is carried out in two steps l One must first define the desired type of FE Mesh Refinement using the dialog window shown in Figure 81 Mesh refinement can be defined around Points Lines Number of Points on the Line or Surfaces 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 37 or the Edit Curve dialog window Fig 39 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 New FE Mesh Refinement FE mesh Refinement Apply FE Mesh Refinement to oo Point PRO POOKY Line FE Size Line Number of Points Surface Finite Element Size
228. tion by R 130 00 cm Radius dR 10 00 fom O Angle a 5 00 7 O Height L el Hep a 2 of 2 7 tep 2 of 2 Ke Step 3 of 3 F EEOAE Set radius of the Circle R K Press Esc or right mouse K Press Esc or right mouse Button trend helical button to end the tool Figure 40 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 41 left in the New Line dialog window the Edit Line dialog window has also the Are Tab Fig 41 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 41 The Edit Curve dialog window Fig 41 has an additional FE Mesh Tab similarly as for a line in Fig 39 not shown here where a user can refine the FE Mesh along a given arc 80 New line New line Es arene General Arc General Arc Curve No Arc No E Curve Type Definition Points List of Points al i Adjustable Point When changing Arc parameters adjust point Comment Arc Center Arc Parameters x 50 00 cm r 50 25 cm T 5 00 cm Kg 50 25 cm z ooo em 180 00 Figure 41 The New Line Arc dialog window An object circle is always d
229. tive 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 105 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 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 102 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 93 158
230. tization 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 75 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 Hexahedral Domain Space Discretization Horizontal Discretization in 2 3 4 5 x em 250 00 50000 75000 1000 00 dz om 0 00 0 00 0 00 0 00 il 1 2 3 4 5 6 y cm 0 00 100 00 200 00 30000 40000 500 00 dz cm 0 00 0 00 0 00 0 00 0 00 0 00 my Generate Vertical Coordinates Count 51 Set relative size of finite elements TEES O O wD Aea w Nel Previous Figure 75 The Hexahedral Domain Discretization dialog window 118 5 3 Unstructured Finite Element Mesh Parameters Parameters for generating the Unstructured Finite Element Mesh are spe
231. toolbars and customize them in various ways using the Customize dialog window Fig 111 Toolbars Toolbars Tools View GUI Time Layer Toolbar name Standard Show Tooltips C Large Buttons Figure 110 The Toolbars dialog window Customize Toolbars Commands Categories Buttons es vYUROU ES Edit VEGA oS View i a a a S 9 RDB Tools ws ABEARER Window Calculation Select a category then click a button to see its description Drag the button to any toolbar Description Figure 111 The Customize Toolbars dialog window 167 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 Ds New Project Creates a new project Open a Project Opens an existing project represented by the project_name h3d 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 and 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
232. ts 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 geometrical 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 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 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 154 screen and the printer Users can create a
233. ts is three times smaller and thus the calculations are faster FE Mesh Parameters Man Stretching Options 1 Options 2 Mesh Sections oo Targeted FE Size Cancel C Automatic TS 10 00 cm Targeted FE Size TS 0 10m gt 4 Number of Mesh Layers NL 20 Type of 3D Elements Apply Apply Tetrahedral C Deta Triangular Prism All Default Figure 76 The FE Mesh Parameters dialog window Tab Main 119 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 77 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 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 The Stretching Direction is defined by a vector with two coordinates Vx and Vz for vertical two dimensional domains For three dimensional problems this vector requires three components Vx Vy and Vz FE Mesh Parameters Main Stretching Options 1 Options 2 Mesh Sections Stretching Factor Fs Mesh stretched in Fs 1 No Stretchi x direction with factor o Stretching Fs 3 0 Stretching Direction OY 62
234. uilibria 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 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 van Genuchten M Th Convective dispersive transport of 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 202 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 GEOCHEM ical equilibria in reactive multicomponent systems Environs Sci Div Publ No 3170 Oak Ridge National Lab Oak Ridge TN 1990 203
235. uld 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 122 The Option 2 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 2 Tab Fig 81 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 1 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
236. ure Tab users further select Print Quality 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 General Picture Legend General Picture Legend Print Page Orientation Print Quality Colors and Frame Portrait Lines and Text Black Landscape All Colored Page Margins 02 Draw Frame M Legend O User Defined Left 20 00 mm Text Size Symbol Size and Line Width Top 20 00 mm Proportional to Picture Size Proportional to Picture Size Right 20 00 mm Constant Constant 4 gt 44 gt 14d 4d Bottom 20 00 mm Factor 1 00 Factor Default Default Print Options General Picture Legend Legend Rows Row Text Content i M Project000 Project Info v v FE Mesh Picture Desc w 2 3 Text Size Height 4 00 gt mm dx 0 00 S mm dy 3 00 3 mm Font Default OK Cancel Help Figure 119 The General Picture and Legend tabs of the Print Options dialog window 197 9 4 Coordinate systems The Coordinate System to be used for the transport domain definition can be
237. urves in the base surface The FE mesh then follows exactly the specified shape of these internal curves Fig 50 Figure 50 Solid showing separate vertical columns 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 51 and 52 show an example of a solid that has a base surface in the XZ plane and thickness vectors in the Y direction Figure 51 A solid with its base surface in the XZ plane and thickness vectors in the Y direction 89 Figure 52 FE Mesh for a solid with its base surface in the XZ plane and thickness vectors in the Y direction 4 2 1 Steps to Define a Two Dimensional Domain 1 Definition of Boundary Curves of Particular Surfaces Boundary Curves are formed using basic geometrical 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 snapping 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 de
238. ut the number of iterations time step and Peclet and Courant numbers Displays mass balance information and mean profile properties 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 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 selected mesh line Draws positions of flowing particles 188 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 Intersect Lines Split Lines Insert Points on Line Check Geometry Repair Geometry Generate Domain Surfaces Create Video File Options Rendering Mode Full Model Transparent Model Wire Mode
239. vation node number Concentrations for the second solute 4 Negative observation node number Hydraulic conductivity 6 Material number 1 constant pressure head or 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 35 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 Time Information Time Units Time Discretization O Seconds Initial Time O Minutes Final Time O Hours Initial Time Step Days Minimum Time Step Maximum Time Step Boundary Conditions Time Variable Boundary Conditions Number of Time Variable Boundary Records 1 aa Previous Figure 15 The Time Information dialog window 36 Table 5 Time Information variables Time Units Time units T to be used throughout the application 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 dt T The initial time step should be a function of the type of proble
240. 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 spatial distribution of the second component of local anisotropy for two dimensional applications Specifies the spatial distribution of anisotropy tensors for three dimensional applications 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 Specifies 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 186 Seepage Face Variable Head 1 4 Variable Flux 1 4 Free Drainage Deep Drainage Atmospheric Boundary Solut
241. x across the boundary having a constant flux or pressure head 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 199 9 6 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 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
242. ximum Number of Iteration il Previous 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 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 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 0 leads to a diagonal matrix G which is much easier to solve but generally requires much smaller time steps 51 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 S
243. y Loam Sandy Clay Silty Clay Clay Neural Network Prediction The program uses pedotransfer functions PTFs based on neural networks to predict van Genuchten s 1980 water retention parameters and the saturated hydraulic conductivity K based on textural information see Section 3 8 below 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 46 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 Parish 1988 Textural class 0 0 a n K L L gt L L gt cm cm d Sand 0 045 0 430 0 145 2 68 712 8 Loamy Sand 0 057 0 410 0 124 2 28 350 2 Sandy Loam 0 065 0 410 0 075 1 89 106 1 Loam 0 078 0 430 0 036 1 56 24 96 Silt 0 034 0 460 0 016 1 37 6 00 Silty Loam 0 067 0 450 0 020 1 41 10 80 Sandy Clay Loam 0 100 0 390 0 059 1 48 31 44 Clay Loam 0 095 0 410 0 019 1 31 6 24 Silty Clay Loam 0 089 0 430 0 010 1 23 1 68 Sandy Clay 0 100 0 380 0 027 1 23 2 88 Silty Clay 0 070 0 360 0 005 1 09 0 48 Clay 0 068 0 380 0 008 1 09 4 80 Table 8 Soil hydraulic parameters for the analyti
244. y 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 41 When entering a new arc or circle graphically a user must select the command Jnsert 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 part of the Domain Geometry version of the Tool Bar at the right side of the View Window and then enters are 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 40 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 79 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 g J xl Point l 14 Domain Geometry Set new Circle a Parameters Numbers for new R 80 00 cm Curve E BJ dR 10 00 cem Point 18 Reverse Orient Parameters Defini
245. yer atthe ML_004 Mesh Layer UnSelect ML_O05 Mesh Layer ML_O06 Mesh Layer _Rename ML_O0 Mesh Layer ML_008 Mesh Layer ML_009 Mesh Layer Move Up ML_010 Mesh Layer Delete Move Down Create New Section From Selection From Current View Default Sections Show All Hide All Only Selection Hide Selection Reverse Figure 85 The FE Mesh Sections dialog window 132 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 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 86 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 ar
246. zation Files e Working Directory for Temporary Files Default Directory for HYDRUS Projects Program Options E E E emee Graphics Program Options Files and Directories Files and Directories Directory for HYDRUS Settings and Authorization files its and Settings 4ll Users 4pplication Data PC Progress HYDAUS 1 xx Setting Working directory for Temporary files C Documents and Settings 4ll Users Documents PC Progress HYDRUS Texa T Default directory for HYDRUS Projects C Documents and Settings All Users Documents PC Progress HYDRUS 1 xx F Configuration file for Display Options C Documents and Settings VAll Users pplication Data PC Progress HYDRUS 1 Figure 117 The Program Options dialog window the Program Directories Tab 193 9 2 HYDRUS License and Activation HYDRUS is protected by a software lock that is based on information about the hardware on which it is run 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 The activation process consists of generating two request codes that need to be sent to the HYDRUS distributor He She then generates for these two request codes corresponding activation codes and sends them back to HYDRUS users Different HYDRUS functions will be activated after inserting activation codes depending upon the type of purchased license The HYDRUS softwar

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