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The HP2 Program for HYDRUS (2D/3D) - PC

1. Variable Aux 2 Fux ecco W E SSS SSS SS SS SEs SSAA ee SS 7 Venable Head 4 Variable Head 1 SAR REAR SS SASSER a NINN NS N NA AN S 9993 PAANAAAS SAREE On the Navigator Bar click on Solute Transport Assign Third Type BC with the following pointers as shown below Solute Transport Boundary Condition Painter to the vector of boundary conditions 3 o4 4 amp 4 B4 944i l E a uec cue eii E i eem em ee e MR SESE SESE ESSE ES ESSN M s Se eee ra 5 REESE RSE 5 SIRI mS Mr SERRA SS NM NS e SE SS lip ASNI ai cse turo a RRR ROR RARE Run Calculations Click the Calculate Current Project command ii on the Toolbar or Calculation gt Calculate Current Project Execution time on 3 GHz PC 468 s 4 5 3 Output The steady state pressure heads and velocity fields are depicted in Figure 26 Uranium concentration profiles are shown in Figure 27 pH calcite and gypsum profiles are shown in Figure 28 73 1200 000 1065 037 330 074 795 110 660 147 525 184 390 221 120 235 0 000 149 632 284 595 70 195 63 813 57 432 51 051 44 669 38 288 31 907 25 525 19 144 12 763 6 381 0 000 Figure 26 The steady state pressure head cm top and flux cm d bottom profiles for the Tailing Pile Leaching example 0 00000e
2. NIS PIN NSIS SS SRA RRR RAISERS RARER Initial Conditions Click on the Initial Conditions under the View Window On the Navigator Bar click on Pressure Head Select the entire transport domain 71 From the Edit Bar select the command Set Pressure Head IC Set Pressure Head IC or Insert gt Initial Condition gt Pressure Head Water Content In the Water Flow Initial Condition window Check Equilibrium from the lowest located nodal point Check Slope in X direction Set the slope to 4 4 Set Bottom Pressure Head Value to 1 200 cm Water Flow Initial Condition Distribution Jj Same value for all nodes Equilibrium from the lowest located nodal point 2 Linear distribution with depth 44 Slope in t direction 0 Pressure Head 1546 26 Bottom Pressure Head Value 1200 em On the Navigator Bar click on Solution Composition Assigned the Solution Compositions as follows Values in selected nodes Mo of sel Nodes 852 Minimum value 1546 26 hd aximum value 1200 Other Options Constant Internal Pressure Head Sink Source Time v aniable Interial Pressure Head Sink Source values in var HAJ Time t anable Internal Flux 5ink Saurce values in Var Fld Cancel Boundary Conditions Click on the Boundary Conditions under the View Window 72 On the Navigator Bar click on Water Flow Assign BC as follows
3. Cai mne Ci 4 2 OU X 249 9B59 Button OK Button Next Time Variable Boundary Conditions Edit gt Flow and Transport Parameters Variable Boundary Conditions Fill in the time and the solution composition numbers for the top boundary Time cValuel 8 3001 18 3002 38 3001 60 3003 Observation Nodes Click on the Domain Properties Tab under the View Window On the Navigator Bar click on Domain Properties Observation Nodes or Insert gt Domain Properties gt Observation Nodes Click on the Insert Observation Node Insert Observation Node command on the Edit Bar and insert observation nodes on the left column at depths of 2 4 6 and 8 cm Run Calculations 38 Click the Calculate Current Project command pes on the Toolbar or Calculation gt Calculate Current Project Execution time on 3 GHz PC 7 s 4 2 3 Output Figure 16 gives the K concentration at different depths in the profile Figure 17 shows the outflow concentration The first pulse is identical to the single pulse project Then additional solute pulses of different solution compositions will restart the cation exchange process depending on the incoming solution composition Observation Nodes K 0 0012 0 0010 0 0008 0 0006 0 0004 0 0002 HHE A DU 20 30 40 0 10 Conc mol ma Time hours Figure 16 Time series of K concentrations at four depths for the multiple pulse cation exchange example
4. Heat Transport Root water Uptake Inverse Solution Required Add on Modules 8 HPZ Figure The Main Processes dialog window 1 2 1 2 Solute Transport General Information When the HP2 module is used basic information needed for defining solute transport problem is entered in the Solute Transport dialog window displayed in Figure 2 Once the HP2 module is selected in the Main Processes window large parts of the Solute Transport dialog window are disabled since they are not relevant to HP2 However a user can still select the Space and Time Weighting Schemes and the Stability Criterion which constraints the temporal discretization see the HYDRUS Technical Manual A user has to specify the Number of Solutes 1 6 main HP2 components and can select the tortuosity model either Millington and Quirk T 1961 or Moldrup 11997 2000 models can be used Note that also Mass Units are disabled since concentrations are entered using PHREEQC conventions 1 e many different types of units can be used such as mol l mmol L mg L ug L ppm etc and results are reported in mol L with the assumption that 1 L water kg water Time Weighting Scheme Space Weighting Scheme Explicit Scheme amp Galerkin Finite Elements Cancel Crank Nicholson Scheme ance 3 Upstream Weighting FE 5 Implicit Scheme Jj GFE with Artificial Dispersion Help Salute Information Number of Salutes B Mass Units 1000 Stabil
5. Additions to Thermodynamic Database 15 2 1 4 2 Definitions of Solution Compositions ecce 16 LA 55 Geochemical Model ess tuoi dta cetus dean aene bud eum Rast enun dad 17 DAE 0 E 17 2015 DOMETT POTE POLONI TE OT S dan visar vo RR 20 2 1 6 Solute Reaction 21 2 1 7 Initial and Boundary Conditions Sana sess 20 216 dJIBZ PRAT ang PUNCH CONTOS vrer pt 20 225 JPOSUPEOCOSSIDP nn 25 221 Results Graphical Display a ada ed e FORD 25 2 2 2 JResults Other 25 3 Example Problems epis ete iattatudicq atten um Dated iet tad Matta 21 4 Step by Step Instructions for Selected Examples nan nnne nene ese ee ee nene eneve eee 29 41 Example 1 Transport and Cation Exchange Single Pulse 20 Ade PROD VON i ERR NER AN E Med 30 rcc 30 aS EE OI DU P Tro TEE 36 4 2 Example 2 Transport and Cation Exchange Multiple Pulses 37 IJWODIEnJelumiitOn saute aab a m RE 37 5 e 37 NT U nuuc D MCI OTT TET CEPT TT BOT PRO eT TELM UE A 39 4 3 Example 3 Transport and Dissolution of Gypsum and Calcite 40 Z3 Froplem A 40 ASL tuta teli N te Ead 40 OU o Tm TS 44 4 4 Example 4 Furrow Irrigation with Cation 48 Problem DONO dec ERE Maec duum Rt 49 dba D e e mu ed un ix mato cuis 50 dka OUUU aa a a a 56 4 5 Example 5 Leaching of th
6. Iteration Criteria Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Iteration Criteria Leave default values Button Next Water Flow Soil Hydraulic Model Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Hydraulic Properties Model Leave default values as follows Radio button van Genuchten Mualem Button Next Water Flow Soil Hydraulic Parameters Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Soil Hydraulic Parameters Catalog of Soil Hydraulic Properties Loam Qs 0 35 Ks 10 cm d Button Next 41 Solute Transport General Info Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt General Information Number 01 Solutes 6 Select HP2 HYDRUS PHREEQC Button Next Solute Transport HP1 Components and Database Pathway Database Pathway Leave the default PHREEQC database and default path Six Components Total_O Total_H Ca C 4 Cl S 6 Note Redox sensitive components should be entered with the secondary master species 1 e with their valence state between brackets The primary master species of a redox sensitive component 1 e the element name without a valence state is not recognized as a component to be transported Therefore the primary master species C cannot be entered here one has to enter either C 4 or C 4 Also S is not allowed one has to enter either S 6 or S 2 Note that the HYDRUS GUI wil
7. Sa JES calcite 0 3 92E 5 O2 g 0 68 reactive_transport dimension 2 Button OK Additional Output Define the additional output to be written to selected output files selected_output totals Ca Mg C1 S C equilibrium phases gypsum calcite Button OK Button Next Solute Transport Solute Transport Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Transport Parameters Bulk D 1 8 g cm Longitudinal Dispersivity Disp L 1 cm Transverse Dispersivity Disp T 0 1 cm Molecular Diffusion Coefficient for Liquid Phase Diffus W 0 Button Next Solute Transport Reaction Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Reaction Parameters Boundary Condition cBnd1 3001 the solution composition number for the upper boundary condition 43 Button Next Rectangular Domain Spatial Discretization Edit gt FE Mesh gt FE Mesh Parameters Horizontal Discretization in X Count 1 Entries in the x column 0 1 Horizontal Discretization in Z Count 101 Default Entries in the z column Button Next Default Domain Properties Edit gt Domain Properties gt Default Domain Properties Set Code on the first and last row to 1 Set the initial pressure head h for all nodes equal to zero Set the temperature Temp to 25 Set the solution concentration sc to 1001 Button Next Observation Nodes Click on the Domain Prop
8. example only the outflow concentrations of Cl Ca Na and K are of interest 4 1 2 Input Project Manager File gt Project Manager Button New New Project or File gt New Name 2D CEC 1 Description Transport and Cation Exchange single pulse Working Directory Temporary exists only when the project is open Button Next Domain Type and Units Edit gt Domain Geometry gt Domain Type and Units Type of Geometry 2D Simple 2D Domain Options 2D Vertical Plane XZ Units cm Initial Workspace X Min 0 X Max 1 Z Min 0 Z Max 8 cm Button Next 30 Regular Domain Definition Edit gt Domain Geometry gt Simple Domain Dimensions Lx 1 cm Lz 8 cm Slope a 0 Button Next Main Processes Edit gt Flow and Transport Parameters gt Main Processes Uncheck Water Flow Note this is a steady state water flow Check Solute Transport Button Next Time Information Edit gt Flow and Transport Parameters gt Time Information Time Units Seconds Final Time 86400 s Initial Time Step 180 s Minimum Time Step 180 s Maximum Time Step 180 s Note we use the constant time step to have the same conditions as in the original comparable PHREEQC calculations in general there is no need to have constant time steps in HP2 Button Next Output Information Edit gt Flow and Transport Parameters gt Output Information Print Options Check T Level Information Check Screen Output Check Press Enter at t
9. 00 5 00000e 05 1 00000804 1 50000e 04 2 00000e 04 2 50000e 04 3 00000e04 3 50000004 A4000005 04 4 50000e 04 5 000006 04 Figure 27 Uranium concentration profiles at time O top 250 middle and 500 bottom d for Tailing Pile Leaching example 74 JUN Figure 28 pH top calcite mol L middle and gypsum mol L bottom profiles after 1000 4 for the Tailing Pile Leaching example 76 References Jacques D and J Sim nek User Manual of the Multicomponent Variably Saturated Flow and Transport Model HP1 Description Verification and Examples Version 1 0 SCK CEN BLG 998 Waste and Disposal SCK CEN Mol Belgium 79 pp 2005 Jacques D J Sim nek D Mallants and M Th van Genuchten Operator splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles J Contam Hydrology 88 197 218 2006 Jacques D J Sim nek D Mallants and M Th van Genuchten Modeling coupled hydrological and chemical processes Long term uranium transport following mineral phosphorus fertilization Vadose Zone Journal 7 2 698 711 2008 Jacques D J Sim nek D Mallants and M Th van Genuchten Modelling coupled water flow solute transport and geochemical reactions affection heavy metal migration in a Podzol soil Geoderma 145 449 461 2008 Jacques D J Simunek D Mallants and M Th van Genuchten Modelling the f
10. SIS ISIN NIS SERE SRST AAA EAA TANNA aw BSISISISIS NN BSRSRRIS SSRN SAAS ASSESS SERERE INAS SSNANIN NAAN ASNN gs 100 cm SIAN AAAS SS ANNE HASSE SERS SSS ANIA j ANN ANS AA URNA AS WAAAY ANAT NM XSAN NIS 100 cm Figure 20 Schematic representation and finite element mesh of the flow domain for the furrow irrigation system for example 4 49 The calculation was run at a constant temperature of 25 C The bulk density of the soil was taken as 1 4g cm and molecular diffusion as 2 cm day Longitudinal and transverse dispersivities were equal to 2 and 0 2 cm respectively The solution composition of the water initially present in the soil profile is that of the following highly sodic water Cay 1 0 Mg7 0 0 14915 0 K7 0 0 SOg7 3 5 Cl120 0 mmol Lt The cation exchange capacity is equal to 7 143 mmol kg 10 mmol dm and is divided between exchangeable calcium and sodium it is equilibrated with the solution The solution composition of the irrigation water was almost gypsum saturated Car 16 3 Mg7 0 0 Najz4 4 K120 0 Cly25 0 SO41216 0 mmolL As a consequence of the reactions of the irrigation water with the exchanger composition cation exchange was the dominant chemical processes in the soil profile Cation exchange is treated as an instantaneous process in the model 4 4 2 Input Project Manager File
11. closed form equation for predicting the hydraulic conductivity of unsaturated soils Soil Sci Soc Am J 44 892 898 1980 Yeh G T and V 5 Tripathi A critical evaluation of recent developments in hydrogeochemical transport models of reactive multichemical components Water Resour Res 25 93 108 1989 Yeh G T and V S Tripathi A model for simulating transport of reactive multispecies components Model development and demonstration Water Resour Res 27 3075 3094 1991 78
12. complex Verification examples that are described below in this report and that can also be downloaded from the HYDRUS website SS steady state water flow T transient water flow 27 28 4 Step by Step Instructions for Selected HP2 Examples The purpose of these examples is to documents how to use the version 1 0 of HP2 The following tutorials are described in this report Example 1 Transport and Cation Exchange Single Pulse Example 2 Transport and Cation Exchange Multiple Pulses Example 3 Transport and Dissolution of Gypsum and Calcite Example 4 Furrow Irrigation with cation Exchange Example 5 Leaching of the Uranium Tailings pe ee While the first three examples involve one dimensional steady state water flow examples 4 and 5 involve transient two dimensional water flow Cation exchange is the main chemical process in examples 1 2 and 4 Precipitation dissolution reactions are the main chemical processes in examples 3 and 5 Each of these examples can be easily further modified to include additional chemical processes Only simple structural FE Meshes are used in all examples 29 4 1 Example 1 Transport and Cation Exchange Single Pulse 4 1 1 Problem Definition This example is adapted from Example 11 of the PHREEQC manual Parkhurst and Appelo 1999 and is also used in the HP1 manual Jacques and Simunek 2010 The chemical composition of the effluent from an 8 cm column containing a cation exchanger
13. equilibrium kinetic or mixed equilibrium kinetic reactions HP2 similarly as HPI uses the operator splitting approach with no iterations during one time step a non iterative sequential modeling approach The HP2 code is fully incorporated into the HYDRUS 2D 3D software package and hence is installed automatically together with selected examples when one obtains HYDRUS 2D 3D and HP2 licenses and downloads HYDRUS from the Hydrus website The purpose of this report is to documents the HP2 program for the HYDRUS 2D 3D software package im nek et al 2011 ejna et al 2011 simulating two dimensional variably saturated water flow heat transport solute transport and biogeochemistry The HP2 module as well as the description of the module in this report is largely based on the earlier one dimensional HPI module Jacques and Sim nek 2005 2010 One can find additional useful information especially related to biogeochemical reactions in the PHREEQC Parkhurst and Appelo 1999 and HPI Jacques and Sim nek 2005 2010 manuals The report serves as both a Technical Manual and a User Manual as well as a reference document of the Graphical User Interface of HP2 related parts of the HYDRUS software package DISCLAIMER The HP2 module was developed as a supplemental module of the HYDRUS 2D 3D software package to simulate the water flow heat transport solute transport and biogeochemical reactions in soils and groundwater The
14. gt Project Manager Button New New Project or File gt New Name 2D CEC Furrow Description HP2 Test Furrow Irrigation Transport and Cation Exchange Working Directory Temporary exists only when the project is open Button Next Domain Type and Units Edit gt Domain Geometry gt Domain Type and Units Type of Geometry 2D Simple 2D Domain Options 2D Vertical Plane XZ Units cm Initial Workspace X Min 0 X Max 100 Z Min 0 Z Max 100 cm Button Next Regular Domain Definition Edit gt Domain Geometry gt Simple Domain Dimensions Lx 100 cm Lz 100 cm Slope a 0 Button Next Main Processes Edit gt Flow and Transport Parameters gt Main Processes Check Water Flow Note this 1s transient water flow Check Solute Transport Check HP2 Button Next Time Information Edit gt Flow and Transport Parameters gt Time Information Time Units Days Final Time 5 d Initial Time Step 0 0005 d 50 Minimum Time Step le 05 d Maximum Time Step 5 d Button Next Output Information Edit gt Flow and Transport Parameters gt Output Information Print Options Check T Level Information Check Screen Output Check Press Enter at the End Print Times Count 8 Print Times 0 05 0 1 0 25 0 5 1 2 3 5 d Button Next HP2 3 Print and Punch Controls Number of Warnings 5 Button Next Water Flow Iteration Criteria Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Ite
15. is simulated in this example The column initially contains a Na K NO3 solution in equilibrium with the cation exchanger The column is flushed with three pore volumes of a CaCl solution Ca K and Na are at all times in equilibrium with the exchanger The simulation is run for one day the fluid flux density 1s equal to 24 cm d 0 00027777 cm s The column is discretized vertically into 40 finite elements and horizontally into two columns 1 e 82 nodes The example assumes that the same solution is initially associated with each node This is in general not necessary and different solutions can be defined for each node The solution however must be specified for each node The exchanger can be defined also for each node but it does not have to be this depends on the specific conceptual geochemical model for a project In this example we use the same exchanger composition at all nodes The initial Na K NO3 solution is made by using 1 x 10 M NaNO3 and 2 x 107M KNO M The inflowing CaCl solution has a concentration of 6 x 10 M Both solutions were prepared under oxidizing conditions 1n equilibrium with the partial pressure of oxygen in the atmosphere The amount of exchange sites X is 1 1 meqil dm soil The log K constants for the exchange reactions are defined in the PHREEQC dat database and do not have to be therefore specified at the input This project is available in the Project Group 2D Tests and is named 2D CEC 1 In this
16. mineral must be defined as mol 1 dm soil There is calcite 4 7e 4 mol dm soil 67 in the soil and gypsum 3 7e 3 mol dm3 soil in the waste zone Many other mineral phases see their names below are allowed to precipitate Additionally indicate to PHREEQC that this is a two dimensional project added by default equilibrium phases 1001 soil material 1 calcite 0 4 7E 4 gypsum 0 0 Autunite 0 0 Bassetite 0 0 Ca4H PO4 3 0 0 CaH PO4 QO Fe OH 2 0 0 Hydroxyapatite 0 0 Portlandste 0 0 Rutherfordine 0 0 Siderite 0 0 Vivianite 0 0 H UO2 PO4 0 0 beta Schoepite 0 0 equilibrium_phases 1002 waste zone material 2 Calcite 0 0 gypsum 0 3 7E 3 Autunite 0 0 Bassetite 0 0 Ca4H PO4 3 0 0 CaH PO4 QO Fe OH 2 0 0 Hydroxyapatite 0 0 Portlandite 0 0 Rutherfordine 0 0 Siderite 0 0 Vivianite 0 0 H UO2 PO4 0 0 beta Schoepite 0 0 Select Additional Output Define the additional output to be written to selected output files selected_output equilibrium phases calcite gypsum Rutherfordine Siderite Button Next Solute Transport Solute Transport Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Transport Parameters Bulk D 1 5 g cm Longitudinal Dispersivity Disp L 250 cm Transverse Dispersivity Disp T 25 cm Molecular Diffusion Coefficient for Liquid Phase Diffus W 0 68 Button Next Time Variable Boundary Conditions Edit gt Flow and
17. on the last row to 6 free drainage Set the initial pressure head h for all nodes equal to 200 Set the temperature Temp to 25 Set the solution concentration sc to 1501 Button Next 54 Properties of Horizontal Layers Layer z cm Code h em Mater Roots Anz Bsz Dez Temp C Cancel 100 00 25 l 93 00 25 Help 97 50 20 a S MS Excel 93 00 E Import Export 90 00 20 I 25 Copy Sel 84 Dn 2a Copy All 51 00 20 78 00 25 Lane 75 00 72 00 53 00 56 00 52 00 58 00 54 00 ili 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 eO TJI gae e d e 6 Edit in 25 Resizeable 35 Window 25 Open 2b eb 2h roo FF A AAAA oe co fF D of eo ef oe oe a 42 2 A AGAAGA AGAGA A 1 32 2 y Set Boundary Conditions for Solute Transport and Heat Transport for changed Codes Linear Interpolation of Pressure Heads between the first and last layer Water Flow Boundary Conditions Edit gt Boundary Conditions gt Water Flow Click on the Boundary Conditions Tab under the View Wi
18. ws a RII Ske 4Ca H 32047 gt lt CaH PO4 35 4 Ca Ht POY e 091102006 R42 Ca 2100 gt lt 2H Ca OH R43 3067 200407 e Fe3 PO4 25 4 Fe 2100 gt lt 2H 0016 R45 UO 2100 gt lt 2H 110200116 R46 UO 6037 gt lt UOJ CO3 5 R47 Fe 20027 22007 gt lt 6011020704 6 R48 H UO POs gt H UOj POj R49 wa ZTN The composition of the pore water in the tailings pore water outside of the tailing pile and the recharge water are given in Table 4 Cauchy boundary conditions are considered on all boundaries where boundary conditions are specified A total of 1000 days was simulated Table 4 Initial and boundary compositions of recharge water and pore water in the tailings and regions outside of the tailing for the uranium tailing problem ee xw xt ONTO Lo sor wo Ca CO UO PO SO H E 61 4 5 2 Input Project Manager File gt Project Manager Button New New Project or File gt New Name UTailing Description Mille Tailing Pile transient water flow and reactive transport Working Directory Temporary exists only when the project is open Button Next Domain Type and Units Edit gt Domain Geometry gt Domain Type and Units Type of Geometry 2D Simple 2D Domain Options 2D Vertical Plane XZ Units cm Initial Workspace X Min 0 X Max 10 500 Z Min 0 Z Max 2 400 cm Button Next Regular Domain D
19. 0 0014 0 0012 0 001 0 0008 0 0006 Cone mol dim 0 0004 0 2 0 10 20 30 40 50 60 Time hours Figure 17 Outflow concentrations for the multiple pulse cation exchange example 39 4 3 Example 3 Transport and Dissolution of Gypsum and Calcite This project is available in the Project Group 2D Tests and is named 2D HPI 1 4 3 1 Problem Definition Sulfate free water is infiltrated in a 50 cm long homogeneous soil column under steady state saturated flow conditions The reactive minerals present in the soil column are calcite CaCO3 and gypsum CaS04 2H20 both at a concentration of 2 176 x 10 mmol kg soil Physical properties of the soil column are as follows the porosity of 0 35 the saturated hydraulic conductivity of 10 cm day the bulk density of 1 8 g cm and the dispersivity of 1 cm The input solution contains 1 mM CaCl and is in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide The initial soil solution is in equilibrium with the reactive minerals and with the atmospheric partial pressure of oxygen As a result of these equilibria the initial soil solution contains only Ca and oxidized components of S and C Calculate the movement of dissolution fronts of calcite and gypsum over a period of 2 5 days 4 3 2 Input Project Manager File gt Project Manager Button New New Project or File gt New Name 2D HP1 1 Description Dissolution of calcite and gypsum in th
20. 0 3 7E 3 calcite 0 0 save solution 1002 end solution 1001 soil pH 2 charge Ca 1E 2 calcite Se Hest Add New Solution Previous Figure 6 The HP2 Definitions Definitions of Solution Compositions dialog window 2 1 4 3 Geochemical Model The definition of the geochemical model is done using the editor Geochemical Model Fig 7 in the HP2 3 Definitions dialog window and it typically involves the following PHREEQC data blocks 17 e EXCHANGE e EQUILIBRIUM PHASES e SURFACE e KINETICS e SOLID SOLUTIONS The numbering of geochemical keywords must either refer to the node numbers such as EXCHANGE 1 102 or to a particular material as defined using the HYDRUS GUI such as EXCHANGE 1001 material 1 While in the former case if the material distribution is changed the user must change the numbering of the geochemical model as well in the latter case there is no need for that Note that the exchanger number for the latter case should again be larger than the number of FE nodes Figure 7 shows an example of the Geochemical Model in which a pure phase assemblage with three minerals gypsum calcite and O2 are defined in nodes 1 through 202 using the data block EQUILIBRIUM_PHASES Cation exchange sites EXCHANGE with the cation exchange capacity X of 0 0011 mol kg and with exchange sites in equilibrium with the solution composition 1001 are defined are also defined B HP2 3 Definitions L
21. 1 c 3 and d 5 days for 0 HM T 57 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Table 1 Table 2 Table 3 Table 4 Sodium concentration profiles mol L at times a 0 5 b 1 c 3 and d 5 days for E D E E E E 0 E A ETE 57 Exchangeable concentrations of sodium mol kg profiles at times a 0 5 b 1 c and 1 5 days Citi RT 58 Description for the Uranium Tailing Problem Yeh and Tripathi 1991 J 59 The steady state pressure head cm top and flux cm d bottom profiles for the Taline Pre Leaching example esteso iver tacit ache a ER ERR De ador 74 Uranium concentration profiles at time 0 top 250 middle and 500 d bottom tor Taine Pile Leaching example ins 74 pH top calcite mol L middle and gypsum mol L bottom profiles after 1000 d for the Tailing Pile Leaching example esses 75 List of Tables Soil specific solute transport parameters 5 20 List of test examples Tor the HP2 module ooo cttusaiaaiennaeaennn 24 Reaction network for the uranium tailing problem cccccccccccessseeeseceeeeeeeeaeeeeees 60 Initial and boundary compositions of recharge water and pore water in the tailings and regions outside of the tailing for the uranium tailing problem 61 Abstract Sim nek J D Jacques M Sejna and M Th van Genuchten The HP2 Program for HYDRUS 2D 3
22. 10 M CaCl 8 18 hr 5 10 M CaCh 1 x 10 M NaNO and 2 x 10 M KNO 18 38 hr 6 x 10 M CaCl 38 60 hr 5 x 10 M CaCh 1 x 10 M NaNO and 8 x 10 M KNO 4 2 2 Input Project Manager File gt Project Manager Click on 2D CEC 1 Button Copy New Name 2D CEC 2 Description Transport and Cation Exchange multiple pulses Button OK Open Time Information Edit gt Flow and Transport Parameters gt Time Information Time Units hours Final Time 60 h Initial Time Step 0 1 h Minimum Time Step 0 1 h Maximum Time Step 0 1 h Check Time Variable Boundary Conditions Number of Time Variable Boundary Records 4 Button Next Output Information Edit gt Flow and Transport Parameters gt Output Information Number of Print Times 12 Default Button Next HP2 3 Print and Punch Controls Button Next Solute Transport General Info Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt General Information Button Next Solute Transport HP2 Components and Database Pathway o Button Next Solute Transport HP2 3 Definitions Definitions of Solution Composition Add additional solution compositions for boundary conditions with numbers 3002 and 3003 Solution 3002 Boundary solution units kgw ph 7 charge Na 1 K 0 2 NOS 1 2 Ca DB CL IE Z OO X 2 9g 90 69 Solution 3003 Boundary solution units kgw ph 7 charge Na 1 K 0 8 N 5 1 8
23. 11 The horizontal bottom of the region is impermeable The vertical left edge has the Dirichlet boundary condition Variable Head 1 with a groundwater table 12 m above the bottom of the transport domain exactly in the middle of the boundary The top boundary except for the mill tailing pile and the river has a flux boundary condition Variable Flux 2 with a net rainfall rate of 0 139 cm day The horizontal region on the top of the mill tailings pile is a Cauchy flow boundary Variable Flux 3 with an infiltration rate of 1 39 cm day The nodes on the vertical line on the right side and the nodes on the river bottom have the Dirichlet boundary condition Variable Head 1 reflecting the position of water in the river 4 5 m above the bottom of the transport domain A hypothetical pumping well with a withdrawal rate of 271 58 cm day is located at x z 400 100 The region is discretized using a structural FE mesh with 1564 elements and 852 nodes Table 3 lists chemical reactions and their thermodynamic equilibrium constants considered in this example For reactive hydrogeochemical transport the problem consists of eight components Total H Total O Ca C uranium sulfate phosphate and Fe A total of 35 species and 14 minerals is defined for the problem redox reactions were not considered Table 3 lists chemical reactions involved in this example 59 Table 3 Reaction network for the uranium tailing problem Aqueous Complexation R
24. 125 10250 10375 10500 dzicmi 1950 35 70 140 210 310 410 535 660 770 880 1005 1130 1190 1250 1295 1340 1370 1400 1430 1460 1490 1520 1550 1580 1610 1640 1670 1700 1730 1760 1785 1810 1830 1850 1865 1880 z cm 2400 2350 2300 2200 2100 2000 1900 1800 1650 1500 1250 1000 750 500 250 0 Button OK 69 Rectangular Domain Discretization lll zs Horizontal Discretizatian imn gt Vertical Discretization in 0 Count 55 Count 16 Cancel 0 00 250 00 500 00 73b 1000 00 1250 00 1500 00 1750 00 2000 00 22500 00 2500 00 2750 00 2000 00 3250 00 3500 00 Generate Coordinates Set relative size of finite elements Fat 1 52 i Mest Generate Previous Apply Click on the FE Mesh Tab under the View Window Zoom on the right side of the transport domain From the Tool Bar select the command Select by Rhomboid it Select by Rhomboid or Edit gt Select gt Select by Rhomboid Select the 6 elements vertically from the top and 4 element horizontally from the right On the Navigator Bar click on Remove Selected Elements uj Remove Selected Elements to get the domain as shown below V V V Vv llt Vv VV VV vv tll Vv lf V V V V Y li V v Y Mj V Y M AVV V Material Distribution Click on the Dom
25. 15 which has been the criteria defining the designation sodic soil The selected cation exchange capacity of 10 mmol kg is relatively low Selection of a higher exchange capacity and associated hydraulic properties of a finer textured soil would enhance both the time required for infiltration as well as quantity of water required for reclamation 3 400915 04 5 28848e 04 T 07780e 04 8 85712e 04 1 06564e 03 1244592035 1 323818 03 1602448 03 1 78137e 03 1 900308 03 2 13824e 03 2 318176e 0 2 HP2 mol HaX HP2 mol NaX mol kqw Min 0 000 Max 0 002 Figure 24 Exchangeable concentrations of sodium mol kgw profiles at times a 0 5 b 1 c 3 and d 5 days for example 4 58 4 5 Example 5 Leaching of the Uranium Tailings 4 5 1 Problem Definition This problem vvas inspired by and is a modification of to make it more realistic a problem reported by Yeh and Tripathi 1991 The problem considers the release and migration of uranium from a simplified uranium mill tailings pile towards a river The schematic of the transport domain is shown in Figure 25 The mill tailings pile is located adjacent to a surface that slopes down to a river The medium has the hydraulic properties of a loam with the saturated hydraulic conductivity of Ks 3 78 m day Cauchy Flow 0 139 dm day Infiltration Rate 0 0139 dm day 1 050 dm Figure 25 Problem Description for the Uranium Tailing Problem Yeh and Tripathi 199
26. 9 Time series of pH top left total aqueous C concentration top right total aqueous Ca concentration middle left total aqueous S concentration middle right the amount of gypsum bottom left and the amount of calcite bottom right at selected depths observation nodes during dissolution of calcite and gypsum 48 4 4 Example 4 Furrow Irrigation with Cation Exchange 4 4 1 Problem Definition A furrow irrigation problem similar to the one used in the UNSATCHEM manual was used to simulate two dimensional infiltration of gypsum saturated water into a sodic soil The example thus simulates sodic soil reclamation problem and demonstrates the cation exchange feature of HP2 The schematic representation of the flow domain for the considered furrow irrigation together with the finite element mesh is presented in Figure 20 It is assumed that every other furrow is flooded with water and that the water level in the irrigated furrow is kept constant at a level of 6 cm Due to symmetry it is necessary to carry out the simulation only for the domain between the axis of two neighboring furrows Free drainage is used as the bottom boundary condition and zero flux is considered on the rest of the boundary The initial pressure head condition is 200 cm and the soil hydraulic properties for silt are used 15 15 40 15 15 I Seo A Pian RARER 15 SSS SSS NININA ANAN NNNNA NNNSN SO S SONANIN SISTISISDESERDREEBIS SIN S SS
27. D A Coupled Code for Simulating Two Dimensional Variably Saturated Water Flow Heat Transport and Biogeochemistry in Porous Media Version 1 0 PC Progress Prague Czech Republic 78 pp 2012 This user manual documents the HP2 program that resulted from coupling Hydrus its two dimensional part with the PHREEQC geochemical code Parkhurst and Appelo 1999 to create this new comprehensive simulation tool HP2 acronym for HYDRUS PHREEQC 2D corresponding to a similar one dimensional module HP1 Jacques and Sim nek 2005 Jacques et al 2006 Sim nek et al 2006 2008 HP2 has apart from the dimensionality 2D the same capabilities as 1171 HP2 contains modules simulating 1 transient water flow 2 the transport of multiple components 3 mixed equilibrium kinetic biogeochemical reactions and 4 heat transport in two dimensional variably saturated porous media soils HP2 is thus a significant expansion of the individual HYDRUS 2D and PHREEQC programs by preserving most of their original features The code still uses the Richards equation for simulating two dimensional variably saturated water flow and advection dispersion type equations for heat and solute transport However the loosely coupled program can simulate also a broad range of low temperature biogeochemical reactions in water the vadose zone and in ground water systems including interactions with minerals gases exchangers and sorption surfaces based on thermodynamic
28. List of Pages The first four pages are four text editors using which one can edit 1 Additions to the Thermodynamic Database section 2 1 4 1 14 2 Definitions of Solution Compositions section 2 1 4 2 3 Geochemical Model section 2 1 4 3 and 4 Additional Output section 2 1 4 4 The fifth page 5 Database Viewer displays the selected database e g PHREEQC DAT Fig 4 List of Pages Page 5 of 5 Database Viewer lo d OF Additions to Thermodynamic Database SOLUTION MASTER SPECIES R Definitions of Solution Compositions 4 Cancel Geochemical Model E d SAT 5 element species gfw formula element gfw Help 5 Database Viewer Keywords double click to insert ns 0 ce pu achemical Model I Equilibrium phases I Exchange has phase l Kinetics Surface I Solid solution tput J Print Selected output 3 0 0 I User print Al 0 0 A 26 9815 E Userpunch at 0 0 137 34 H Chemical physical relaction Sr Srt 0 0 ST 87 62 Database 1 145104 0 Sijl 28 0843 E Advanced l di 35 153 E Miscellaneous 12 0111 a J a I baa el Figure 4 The HP2 3 Definitions dialog window with a displayed Database Viewer The section Keywords double click to insert bottom left part offers the most commonly used PHREEQC Keywords that are used in the fou
29. O a component related to O 2 that sums up all O 2 in the aqueous species except in H20 It is recommended to include this component in each project Total H a component related to H 1 that sums up all H 1 in the aqueous species except in H20 It is recommended to include this component in each project Charge a component related to the charge of the aqueous phase This component should be used when a non electrical surface complexation model involving charged species is used In the non electrical surface complexation model positive or negative charges on the surface are not compensated Therefore the aqueous phase also has a negative or positive charge Note that the complete system surface aqueous phase is charge balanced Each redox state of redox sensitive components has to be defined as a component Without a valence state a redox sensitive component will not be recognized Thus while Fe is not a valid component Fe 2 and Fe 3 are HP2 will issue a warning when a component is present in the aqueous phase during the geochemical calculations with PHREEQC but is not transported 1 e when it is not defined as a component in the HP2 3 Components and Database Pathway dialog windows Fig 3 2 1 4 HP2 3 Definitions The phreeqc in file can be modified by users using the text editors in the HP2 3 Definitions dialog window Fig 4 The HP2 3 Definitions dialog window has five pages that can be selected in the top left corner
30. Parameters gt Hydraulic Properties Model Leave default values as follows Radio button van Genuchten Mualem No Hysteresis Button Next Water Flow Soil Hydraulic Parameters Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Soil Hydraulic Parameters Number of Materials 2 Catalog of Soil Hydraulic Properties Loam both lines Name Loam Name 2 Mill Tailing Pile Ks 378 cm d for both materials Button Next Solute Transport General Info Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt General Information Number of Solutes 8 Button Next Solute Transport HP1 Components and Database Pathway Database Pathway Create an empty database which only defines a few obliged master components such as Alkalinity C E H H 0 H 1 O O 2 O 0 H e H20 and CO3 2 see below Database Empty Six Components Total O Total H Ca C U P S Fe Check Create PHREEQC IN file using HYDRUS GUI Button Next 63 Database for the UTailing example SOLUTION_MASTER_SPECIES Alkalinity 03 2 bat 50 05 0 CS 20 61 0173 E e 0 0 00 H H l 1 008 H 0 H2 Dt 1 008 H 1 ES l 1 008 O H20 UD es O 2 H20 0 0 18 016 O 0 O2 DD 16 00 SOLUTION_SPECIES H H gt Ded gamma 0 0 0 e e OK OJ H20 H20 _k 0 0 COS 2 Qe LL _k Oa gamma 5 4 O20 2 H 2 e H2 k delta_h 1 759 kcal 2H20 O2 41 4e k 86 08 delta_h 134 79 kca Solute Tran
31. Parkhurst and Apello 1998 and HP1 Jacques and Sim nek 2005 2010 manuals The HP2 module may be used to analyze water flow solute movement and biogeochemical reactions in unsaturated partially saturated or fully saturated porous media HP2 can handle flow domains 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 vertical plane the horizontal plane or in a three dimensional region exhibiting radial symmetry about a vertical axis The water flow part of the model considers prescribed head and flux boundaries as well as boundaries controlled by atmospheric conditions The governing flow and transport equations are solved numerically using standard Galerkin type linear finite element schemes The HP2 module is fully supported by the HYDRUS 2D 3D graphical user interface Sejna et al 2011 Applications of the HP2 module are demonstrated later 1n this report on several examples 10 2 Running HP2 from the HYDRUS 2D 3D Graphical User Interface The HP2 code is fully incorporated into the HYDRUS 2D 3D software package and hence is installed automatically together with selected examples when one obtains HYDRUS 2D 3D and HP2 licenses and downloads HYDRUS from the Hydrus website The documentation in this report focuses mostly on implementation of the HP2 module into HYDRUS 2D 3D All processes related t
32. The HP2 Program for HYDRUS 2D 3D A Coupled Code for Simulating Two Dimensional Variably Saturated Water Flow Head Transport Solute Transport and Biogeochemistry in Porous Media HYDRUS PHREEQC 2D Version 1 0 Jirka Simtinek Diederik J acques Miroslav Sejna and Martinus Th van Genuchten September 2012 Department of Environmental Sciences University of California Riverside Riverside CA 92521 USA Performance Assessments Belgian Nuclear Research Institute SCK CEN BE 2400 Mol Belgium PC Progress Ltd Prague Czech Republic Department of Mechanical Engineering Federal University of Rio de Janeiro Rio de Janeiro Brazil 2012 J Sim nekand M ejna All rights reserved Table of Contents TENG DE OCIS gn E 3 BS EL OS eee ee ee ee 5 DISC OF 1 EEEE REEERE ETES EEEE EEEE 6 NS 7 9 2 Running HP2 from the HYDRUS 2D 3D Graphical User Interface 11 2 1 Preprocessing and Input Data eeessssssseseeeenennnneeeneennnnnneeennnnnn 11 Da OCC SC e di pi eis aks ocean he Ded ta wats ak dou ia aah aera 11 2 1 2 Solute Transport General Information ssec 12 2 1 3 HP2 3 Components and Database Pathway essere 12 2 1 3 1 Thermodynamic Databases cesses 7 13 215 2 COMPONENTS esiti ou Maltese Mattei ee M oa bai Mats odis 14 PHA et a 14 2 1 4 1
33. Transport Parameters gt Solute Transport Parameters gt Variable Boundary Conditions Time Precip yap Transp Var Fl V ar H 1 days om dar em day em dar crn crm dar crm s00 I 0 10000 0 1200 1000 0 10000 0 var Fle V ar H Z Yar Fia V ar H 3 War Fle V ar H 4 ovale om dar crm om dar crm om dar em kad 0 139 1 39 0 139 1 33 V ar H 3 V ar FlA Var H 4 aluel EM aluez ovale crn om dar em kod kod kad 0 450 1001 1002 3001 0 450 1001 1002 3001 Button Next Why are we using Time Variable Boundary Conditions when the fluxes and concentrations are constant in time HYDRUS reports actual and cumulative water and solute fluxes for different boundary parts with different types of boundary conditions If we select everywhere Constant BC then we would get only one total flux integrated over all boundary parts By using different boundary types HYDRUS will report various fluxes for different boundary parts Rectangular Domain Spatial Discretization Edit gt FE Mesh gt FE Mesh Parameters Horizontal Discretization in X Count 55 Horizontal Discretization in Z Count 16 xlemi 0 250 500 750 1000 1250 1500 1750 2000 2250 2500 2750 3000 3250 3500 3750 4000 4250 4500 4750 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7550 7700 7850 8000 8150 8300 8450 8600 8750 8900 9050 9200 9350 9500 9625 9750 9875 10000 10
34. ain Properties Tab under the View Window On the Navigator Bar click on Domain Properties Material Distribution or Insert gt Domain Properties gt Material Distribution On the Edit Bar select Material 2 Mill Tailing and assign it as shown below ee ee ee or j SS a a 30 a lo c EE HONNNEENEMNEENENEENEENENEEMEENBBB ESS dh E E DDD SSS AEA HE Nodal Recharge On the Navigator Bar click on Domain Properties Nodal Recharge or Insert gt Domain Properties gt Nodal Recharge Double Click on the node with coordinates x 4 000 cm and z 1 000 cm In the Edit Nodal Recharge window set Value to 271 58 cm d Subregions On the Navigator Bar click on Domain Properties Subregions or Insert gt Domain Properties gt Subregions Click on Set Subregions Materials Edit bar On the Edit Bar select Subregion 2 Mill Tailing and assign it in the same part of the domain as Material 2 Observation Nodes On the Navigator Bar click on Domain Properties Observation Nodes or Insert gt Domain Properties gt Observation Nodes Click on the Insert Observation Node e Insert Observation Node command on the Edit Bar and insert observation nodes at similar locations as shown below E E sh Bac ee c i vh Fans
35. amount of the minerals gypsum or calcite with GNUPLOT To view these various plots the GNUPLOT code needs to be installed on your computer GNUPLOT is freeware software that can be downloaded from http www gnuplot info Note that GNUPLOT the wgnuplot exe program for the Windows OS is usually after being downloaded in the gnuplot bin folder and does not require any additional special installation 45 After opening the Windows version of GNUPLOT by clicking on wgnuplot exe a plot can be directly generated by carrying out these commands File gt Open Browse to the project folder Open the template file of interest plt The figure can be adapted using line commands see tutorials on the internet After adaptations the command lines can be saved to be used later on If you have trouble with the display of fonts it is possible that the terminal on your computer is set incorrectly In such case type at the GNUPlot prompt Gnuplot gt set terminal Windows The default terminal for the plots should be Window We illustrate here only how a plot can be transferred to another terminal Set terminal emf Set output name emi Replot Set terminal window Replot A name emi file is created in the project directory Figure 18 shows vertical profiles of pH total aqueous C concentration total aqueous Ca concentration total aqueous S concentration the amount of gypsum and the amount of calcite at selected print times during d
36. ate of uranium from inorganic phosphorus fertilizer applications in agriculture In L J De Kok and E Schnug eds Loads and Fate of Fertilizer Derived Uranium p 57 64 Backhuys Publ Leiden Netherlands 2008 Jacques D and J Sim nek Notes on HP1 a software package for simulating variably saturated water flow heat transport solute transport and biogeochemistry in porous media HP Version 2 2 SCK CEN BLG 1068 Waste and Disposal SCK CEN Mol Belgium 113 pp 2010 Millington R J and J M Quirk Permeability of porous solids Trans Faraday Soc 57 1200 1207 1961 Moldrup P T Olesen D E Rolston and T Yamaguchi Modeling diffusion and reaction in soils VII Predicting gas and ion diffusivity in undisturbed and sieved soils Soil Sci 162 9 632 640 1997 Moldrup P T Olesen J Gamst P Schjenning T Yamaguchi and D E Rolston Predicting the gas diffusion coefficient in repacked soil water induced linear reduction model Soil Sci Soc Am J 64 1588 1594 2000 Parkhurst D L and C A J Appelo User s guide to PHREEQC Version 2 A computer program for speciation batch reaction one dimensional transport and inverse geochemical calculations Water Resources Investigations Report 99 4259 Denver Co USA 1999 Sejna M J Sim nek and M Th van Genuchten The HYDRUS Software Package for Simulating Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Varia
37. ave been tested earlier Therefore verification and test examples presented in this section concentrate on the demonstration of the new features of the model Table 2 shows selected two dimensional examples that can be downloaded from the HYDRUS HP2 website Some of these examples are discussed in detail in the HP1 manuals Jacques and Simunek 2005 2010 Others are described in detail in Section 4 together with detailed step by step instructions how to develop them using the HYDRUS GUI We will be continuously expanding this list of examples and tutorials depending on users needs and interests Table 2 List of test examples for the HP2 module Verification examples that can be downloaded from the HYDRUS website 2D EQCL Physical equilibrium transport of chloride verification problem 1 2D NEQCL Physical nonequilibrium transport of chloride verification problem 1 2D TransCl Transient physical nonequilibrium transport verification problem 2 2D TransCla Transient equilibrium transport verification problem 2 verification problem 3 POSS Jonian eni plans o oE contaminant verification problem 4 2D SeasonChain First order decay chain of nonlinearly adsorbing contaminants during unsteady flow verification problem 5 2D CatExch Transport with multiple cation exchange verification problem 6 2D MinDis Transport with mineral dissolution 2D MCatExch Heavy metal transport in a medium with a pH dependent cation exchange
38. bly Saturated Media User Manual Version 2 0 PC Progress Prague Czech Republic pp 280 2011 Sim nek J D J acques M Th van Genuchten and D Mallants Multicomponent geochemical transport modeling using the HYDRUS computer software packages J Am Water Resour Assoc 42 6 1537 1547 2006 Sim nek J M Th van Genuchten and M Sejna Modeling Subsurface Water Flow and Solute Transport with HYDRUS and Related Numerical Software Packages In Garcia Navarro amp Play n eds Numerical Modelling of Hydrodynamics for Water Resources An International Workshop Centro Politecnico Superior University of Zaragoza Spain June 18 21 2007 Taylor amp Francis Group London ISBN 978 0 415 44056 1 95 114 2007 TI Sim nek J M Th van Genuchten and M Sejna Development and applications of the HYDRUS and STANMOD software packages and related codes Vadose Zone J 7 2 587 600 2008 Sim nek J D J acques N K C Twarakavi and M Th van Genuchten Modeling subsurface flow and contaminant transport as influenced by biological processes at various scales using selected HYDRUS modules Biologia 64 3 465 469 2009 Simunek J M Th van Genuchten and M Sejna The HYDRUS Software Package for Simulating Two and Three Dimensional Movement of Water Heat and Multiple Solutes in Variably Saturated Media Technical Manual Version 2 0 PC Progress Prague Czech Republic pp 258 2011 van Genuchten M Th A
39. days 2 50 days 0 50 Figure 18 Vertical profiles of pH top left total aqueous C concentration top right total aqueous Ca concentration middle left total aqueous S concentration middle right the amount of gypsum bottom left and the amount of calcite bottom right at selected print times during dissolution of calcite and gypsum 47 D p o e a 5e 005 4 4e 005 4 3e 005 4 2e 005 Total concentration of C mol kg water 1e 005 0 0 5 1 1 5 2 2 5 Time days Time days 10 0 cm 40 0 cm 20 0 cm 50 0 cm 30 0 cm 10 0 cm 40 0 cm 20 0 cm 50 0 cm 30 0 cm o Oo 0 016 er 9 o no 0 012 0 008 1 0 004 e o e ER Total concentration of S mol kg wa Total concentration of Ca mol kg water O eo eo co 0 4 4 0 i i d 0 0 5 1 1 5 2 2 5 0 1 5 2 5 Time days Time days 10 0 cm 40 0 cm 10 0 cm 40 0 cm 20 0 cm 50 0 cm 20 0 cm 50 0 cm 30 0 cm 30 0 cm 4e 005 3e 005 2e 005 1e 005 gypsum mol 1000 cm of soil calcite mol 1000 cm of soil 0 0 0 5 1 1 5 2 2 5 Time days 10 0 cm 40 0 cm 10 0 cm 40 0 cm 20 0 cm 50 0 cm 20 0 cm 50 0 cm 30 0 cm 30 0 cm Figure 1
40. e Uranium 1 gt aaa aaa e nanen nene eee eee eee eee nes 59 5l Problem DINO nn ma 59 Ads ANPUT e RE 61 Ee he OP een E EN VE 73 oy Wel et heen ene ee nea TUT PPM MM EA EE TI 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 List of Figures The Main Processes dialog utente du us 11 Th solut Transport didlos S3VITIIO WS nai eta nd r t dd 12 The HP2 3 Components and Database Pathway dialog window 13 The HP2 3 Definitions dialog window with a displayed Database Viewer 15 The HP2 Definitions Additions to Thermodynamic Database dialog window 16 The HP2 Definitions Definitions of Solution Compositions dialog window 17 The HP2 Definitions Geochemical Model dialog window 18 The HP2 Definitions Additional Output dialog window 19 The Solute Transport Parameters dialog window essere 20 The Reaction Parameters for Solute 1 dialog window sss 21 The Initial Conditions part of Data Tab of the Navigator Bar for the HP2 module xU neue Meetic I LM cec Mnt Aue MOM tatem 22 The HP2 related part of the Time Variable Bo
41. e dual porosity solute transport model is used Set equal to zero when this model is not used Om Immobile water content when the dual porosity solute transport model is used Set equal to zero when this model is not used 20 2 1 6 Solute Reaction Parameters All reaction parameters are specified in the PHREEQC in input file using PHREEQC specific text editors and thus the Reaction Parameters dialog window Fig 10 is not used to specify the reaction parameters that part of the window is disabled but only to assign Solution Compositions to boundaries with constant water flow boundary conditions Solution Compositions assigned to boundaries with time variable water flow boundary conditions are given in the Variable Boundary Conditions window Solution composition 3001 is used as the boundary condition in the example shown in Figure 10 Boundary Conditions c ndi c nd cBnd3 cBnd4 cRoot cWel cBnd 3001 0 0 0 0 0 Reaction Parameters Figure 10 The Reaction Parameters for Solute 1 dialog window 21 2 1 7 Initial and Boundary Conditions Solution composition numbers e g 1001 defined in Definitions of Solution Compositions window Fig 6 are used to assign different solution compositions to different parts of the transport domain as initial conditions Fig 11 similarly as other initial conditions Solution composition numbers used to assign solute transport initial conditions must correspond to the soluti
42. e soil profile Working Directory Temporary exists only when the project is open Button Next Domain Type and Units Edit gt Domain Geometry gt Domain Type and Units Type of Geometry 2D Simple 2D Domain Options 2D Vertical Plane XZ Units cm Initial Workspace X Min 0 X Max 1 Z Min 0 Z Max 5 cm Button Next Regular Domain Definition Edit gt Domain Geometry gt Simple Domain Dimensions Lx 1 cm Lz 50 cm Slope a 0 Button Next Main Processes Edit gt Flow and Transport Parameters gt Main Processes Uncheck Water Flow Note this is a steady state water flow Check Solute Transport Button Next 40 Time Information Edit gt Flow and Transport Parameters gt Time Information Time Units Days Final Time 2 5 d Initial Time Step 001 d Maximum Time Step 0 05 Button Next Output Information Edit gt Flow and Transport Parameters gt Output Information Print Options Uncheck T Level Information Check Interval Output Time Interval 0 025 Check Screen Output Check Press Enter at the End Print Times Count 5 Update Default Button Next HP2 3 Print and Punch Controls Check Make GNUplot Templates This allows easy visualization of time series and profile data for variables which are defined in the SELECTED OUTPUT section below in this dialog window and also defined later in the Additional Output part of the Solute Transport HP2 Definitions dialog Button Next Water Flow
43. e temperature Temp to 25 Set the solution concentration sc to 1001 Button Next 34 Default Domain Propertie Properties of Horizontal Layers Layer z em Code hlemi Mater Roots Aue Buz Dez Temo C 8 00 25 7 80 25 7 60 25 T 40 25 7 20 25 7 00 25 6 80 25 Copy sel 6 60 6 40 6 20 6 00 5 80 5 60 5 40 5 20 5 00 4 80 MS Excel Import E port 25 Oo J Oo mo ee dip 25 2H Paste 25 25 Resizeable 25 Window 25 pen 2h 25 25 Ooo Oo fo fo oo GA 3 AAG oc amp 2 l D Oo oo GAA Ad 1 2 l ee Next Set Boundary Conditions for Solute Transport E and Heal Transport fonchanged E ades Linear Interpolation of Pressure Heads between the first and last layer a Observation Nodes Click on the Domain Properties Tab under the View Window On the Navigator Bar click on Domain Properties Observation Nodes or Insert gt Domain Properties gt Observation Nodes Click on the Insert Observation Node Insert Observat
44. eactions HO lt H OH R1 14 00 Ca 00437 gt CaCO3 aq R2 Ca Ht CO lt CaHCO R3 11 43 Ca SO lt CaSO aq 2 31 Ca 2H PO gt lt CaH PO Ca PO lt CaPOs Ca H PO e CaHPO4 aq 15 08 Fe SO e FeSO4 aq R9 Fe HO lt H 4 FeOH R10 9 50 Fe 2100 gt lt 2H Fe OH aq R11 20 57 UO HO gt H UO OH 200 200 gt 2H UO2 OH 3U0 5100 e 5H UO2 OH s 400 70 gt 7H UO2 OH 3UO THJO gt TH UO 3 OH 7 28 34 UO CO lt UOs CO3 aq UO 2CO 7 gt UO CO3 UO 30047 lt UO CO3 3 21 70 20027 COS 3150 gt 3H UO CO OH UO 5047 gt UO SOs ag UO 280 e UO3 SO4 4 00 2H UO PO gt H3 UO POj 3H UO PO gt H UO PO Ca 4H UO 20007 gt lt CaHy UO gt POx 2 45 24 Ca 57 0027 22007 gt lt CaHs UO2 PO 2 H CO lt HCO R30 10 32 2H CO e H COsag R31 7 H SO 0 R32 60 H PO HPO R33 12 35 2H POL e 0 3 19 55 3 I 3H POg gt 4 R35 4 Precipitation Dissolution Reactions Ca SO gt lt CaSO 3 Ca 0037 gt lt CaCOx 3 5Ca 32047 150 gt lt H Cas OH PO4 36 R38 7 Fe 0037 gt lt FeCO R39 0 Ca 20027 22007 gt lt 0011020046 40 1 ZE N
45. ect the thermodynamic database to be used with HP2 calculations Path to Folder with Thermodynamic Databases Fig 2 Thermodynamic databases contain definitions of various chemical species and thermodynamic constants for various chemical reactions and related information e g temperature dependence ion activity model etc Using the Browse button it is possible to 13 locate and select a thermodynamic database Note that the format of the thermodynamic data in the database must follow the conventions of PHREEQC see PHREEQC 2 manual Parkhurst and Appelo 1999 A number of thermodynamic databases e g phreeqc dat wateq4f dat minteq dat IInl dat ex15 dat and others typically included in the PHREEQC 2 program are installed with HYDRUS into the ThermodynamicDB folder Users can create and use their own database files 2 1 3 2 Components The element names of components have to be listed in the Components column in the HP2 3 Components and Database Pathway dialog window The number of components is specified in the Solute Transport General Information dialog window Fig 2 Components must start with a capital letter and must be present as element_name in the SOLUTION_MASTER_SPECIES keyword block of the thermodynamic database or in the phreeqc in input file which can be defined in the GUI in the editor Addition to the Thermodynamic Database of the HP2 3 Definitions dialog window Fig 4 Three special components are Total
46. efinition Edit gt Domain Geometry gt Simple Domain Dimensions Lx 10 500 cm Lz 2 400 cm Slope a 0 Button Next Main Processes Edit gt Flow and Transport Parameters gt Main Processes Check Water Flow Check Solute Transport Check HP2 Button Next Time Information Edit gt Flow and Transport Parameters gt Time Information Time Units Days Final Time 1 000 d Initial Time Step 0 0001 d Minimum Time Step 0 00001 d Maximum Time Step 500 d Check Time Variable Boundary Conditions Number of Time Variable Boundary Records 2 Button Next Output Information Edit gt Flow and Transport Parameters gt Output Information Print Options Uncheck T Level Information Check Interval Output Time Interval 1 d Check Screen Output Check Press Enter at the End Print Times Count 20 62 Update Default Button Next HP2 3 Print and Punch Controls Check Make GNUplot Templates This allows easy visualization of time series and profile data for variables which are defined in the SELECTED_OUTPUT section below in this dialog window and also defined later in the Additional Output part of the Solute Transport HP2 Definitions dialog Button Next Water Flow Iteration Criteria Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Iteration Criteria Leave default values Button Next Water Flow Soil Hydraulic Model Edit gt Flow and Transport Parameters gt Water Flow
47. erties Tab under the View Window On the Navigator Bar click on Domain Properties Observation Nodes or Insert gt Domain Properties gt Observation Nodes Click on the Insert Observation Node Insert Observation Node command on the Edit Bar and insert observation nodes at a depth increment of 10 cm Run Calculations Click the Calculate Current Project command Es on the Toolbar or Calculation gt Calculate Current Project Execution time on 3 GHz PC 5 s 4 3 3 Output The standard HYDRUS output can be viewed using commands in the Results part of the Navigator Bar Only the total concentrations of the components which were defined in Solute Transport HP2 Components at the observation nodes can be viewed using the HYDRUS GUI HP2 creates a number of additional output files in the project folder The path to the project folder is displayed in the Project Manager File gt Project Information Path Gives the path to the project group folder The path can be copied into the Windows Explorer to locate all project files 44 Following HP2 output files are created for the HP2 1 project Createdfiles out Phreeqc out H3D2 2D HP2 l hse obs nod chem4l out obs nod chem l out obs nod chemi21 out obs nod cheml6l out An ASCII text file containing a list of all files created by HP2 in addition to the output files created by the HYDRUS module of HP2 An ASCII text file which 1s the standard output fi
48. file 0 0014 0 0012 0 001 0 0008 0 0006 0 0004 Concentration mol kg 0 0002 3 0 14400 28800 43200 57600 72000 86400 Time s Figure 15 Outflow concentrations of Cl Ca Na and K for the single pulse cation exchange example The results for this example are shown in Figure 15 The concentrations of node 41 the last node are plotted against time Chloride is a conservative solute and arrives in the effluent at about one pore volume The sodium initially present in the column exchanges with the incoming calcium and is eluted as long as the exchanger contains sodium The midpoint of the breakthrough curve for sodium occurs at about 1 5 pore volumes Because potassium exchanges more strongly than sodium larger log K in the exchange reaction note that log K for individual pairs of cations are defined in the database and therefore did not have to be specified potassium is released after sodium Finally when all of the potassium has been released the concentration of calcium increases to a steady state value equal to the concentration of the applied solution 36 4 2 Example 2 Transport and Cation Exchange Multiple Pulses This project is available in the Project Group 2D Tests and is named 2D CEC 2 4 2 1 Problem Definition This example is the same as Example 1 except that time variable concentrations are applied at the soil surface The following sequence of pulses is applied at the top boundary 0 8 hr 6 x
49. g_k 2 3H 002 2 PO4 3 3 002 04 2 log_k PAPE Cat 4H 002 2 2PO4 3 CaH4 UO2 POA 2 2 log_k 45 24 Cat 5H 002 2 2PO4 3 CaH5 UO2 PO4 2 3 log_k 46 H CO3 2 HCO3 log_k 10 32 2H 003 2 H2CO3 log_k 10 07 H SO4 2 HSO4 log_k 1 99 H POA 3 HPO4 2 log_k ld PHASES gypsum CaSO4 Cat SO4 2 log_k 4 62 calcite CaCO3 Ca 2 CO3 2 log_k 8 48 Hydroxyapatite 65 Ca5 OH PO4 3 Ht 90872 SPOASH H20 log k 77 Siderite FeCO3 Fet2 CO3 2 log k eL Autunite Ca UO2 2 PO4 2 Cat2 2U02 2 2PO4 3 log_k 45 06l1 Ca4H PO4 3 Ca4H PO4 3 4Cat 2 H 3P04 3 log_k 7 CaH PO4 CaH PO4 Ca 2 H PO4 3 log_k Portlandite Ca OH 2 2H Cat2 0 log_k 29 Vivianite Fe3 P04 2 3Fe 2 2PO4 3 log_k 3 Fe OH 2 e OH 2 2H Fe 2 2H20 log_k 12 1 beta Schoepite UO2 OH 2 2H UO2 42 2H20 log_k 5 4 Rutherfordine 002003 002 2 CO3 2 log k 14 11 Bassetite Fe U02 2 P04 2 Fe 2 2U02 2 2PO4 3 log_k 46 H UO2 PO4 H UO2 POA H UO242 POA 3 log k 25 O2 g 02 02 log_k 2 960 delta_h 1 844 kcal H2 g H2 H2 log_k 0 delta h 1 759 kcal Select Definitions of Solution Composition Define the initial condition 1 e the solution composition of water in the soil with the identifier 1001 e Bring it in equilibrium with gypsum calcite and O 0 to be in equilibrium with the partial pressure of oxygen in the at
50. he End Print Times Count 12 Update Default Button Next HP2 3 Print and Punch Controls Button Next Water Flow Iteration Criteria Edit gt Flow and Transport Parameters 2 Water Flow Parameters gt Iteration Criteria Leave default values except Lower Time Step Multiplication Factor 1 Note the constant time step Button Next Water Flow Soil Hydraulic Model Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Hydraulic Properties Model Leave default values as follows Radio button van Genuchten Mualem Radio button No hysteresis Button Next 3 Water Flow Soil Hydraulic Parameters Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Soil Hydraulic Parameters Catalog of Soil Hydraulic Properties Loam Qs 1 Note to have the same conditions as in the original comparable PHREEQC calculations Ks 0 00027777 cm s Button Next Solute Transport General Info Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt General Information Number 01 Solutes 7 Select HP2 HYDRUS PHREEQC Button Next Solute Transport HP2 3 Components and Database Pathway Database Pathway Leave the default PHREEQC database and default path Add seven components Total_O Total H Na K Ca Cl 5 Leave the checkbox on Create the PHREEQC IN file Using HYDRUS GUI Leave the radio button on In Solution Composition Button Next Solute Trans
51. he standard structure of HYDRUS input parameters is preserved also for the HP2 transport module The input parameters for individual components are described below Figure 9 shows the Solute Transport Parameters dialog window in which both soil specific and solute specific identified by their component names transport parameters are specified Note that the molecular diffusion coefficient in the liquid Diffus W and gas Diffus G phases LT are the only solute specific parameters Fig 13 A standard definition of a HP2 transport problem requires equal molecular diffusion coefficients for all components see Jacques and Simiinek 2005 However when a project is defined with no equilibrium aqueous complexation reactions and charged species different molecular diffusion coefficients can be used Solute Transport Parameters Soil Specific Parameters Solute Specific Parameters Bulk D Disp L Disp T Mass Ti Thimob Diffuz Wi Diffus G Cancel M cm 3 cr cr day om 2 dau om 2 dau IEEE 1 4 U2 U otal H otal Li Ca CI Mg Ma E 3 b Mat Help PoP PS Po Bo Po Po Po D AAAA GA G Previous Figure 9 The Solute Transport Parameters dialog window Table 1 Soil specific solute transport parameters BukD p Bukdmsy ML SSS Mass Tr Mass transfer coefficient describing the rate of exchange between the mobile and immobile water contents TJ This parameters is used only when th
52. ical Model l Additional Output RAUM HASTEN asc Hep Databaze Wiewer Fe Feta 55 647 55 847 Ca 2 0 40 08 40 08 UO242 0 0 238 0290 238 0290 Undo 304 2 0 0 96 0616 32 064 Beas 2 Balin Desh PO4 3 0 30 9738 30 9738 SOLUTION SPECIES Car2 Cat Keywords double click to insert Geochemical Model Qutput gt Chemical physical ejachon Database Advanced Miscellaneous log k Fet Fet log k PO4 3 PO4 3 log k 504 2 2 log k UO2 2 2 log k CO3 2 0212 3 log k 3 22 CO3 2 Cat H CaHCO3 log k 11 43 Fet H20 FeOH H log k 9 5 Nest Cat 504 2 4 E Hun Previous RP PP e pm Figure 5 The HP2 Definitions Additions to Thermodynamic Database dialog window 2 1 4 2 Definitions of Solution Compositions Compositions of the initial and boundary solutions are defined using the editor Definitions of Solution Compositions Fig 6 in the HP2 3 Definitions dialog window Typical PHREEQC data blocks are SOLUTION and SOLUTION SPREAD The solution number refers to the solution composition numbers of the initial and boundary solutions defined in the Hydrus GUI A following solution composition numbering is used throughout this manual 16 e Numbers 1001 2000 to define initial solutions for the mobile water phase e Numbers 2001 3000 to define initial solutions for the immobile water
53. initial and boundary conditions In Concentrations is disabled and only Solution Compositions can be used for this purpose In Solution Composition Also the check box Create PHREEQC IN file using HYDRUS GUI is selected by default Although the PHREEQC In file can be created outside of the HYDRUS GUI e g using specialized PHREEQC GUIs we do not recommend to do it that way Both these options as well as the format of the structured phreeqc in file are discussed in detail by Jacques and Sim nek 2010 When the option In Solution Composition is selected together with the option Create PHREEQC IN file using HYDRUS GUI then e the phreeqc in file the file with the definition of the geochemical model is a structured file which is created and can be modified using the HP2 Definitions dialog window Fig 4 e the composition of the initial and boundary solutions has to be defined in phreegc in using specific solution composition numbers e the temporal variation of the boundary solutions is defined in the HYDRUS GUI by specifying the solution composition number corresponding to the solution composition number defined in phreegc in e the spatial distribution of the initial solutions is defined in the HYDRUS GUI by specifying the solution composition number in the soil domain corresponding to the solution composition number defined in phreegc in 2 1 3 1 Thermodynamic Databases In the HP2 3 Components and Database Pathway window users have to sel
54. ion Node command on the Edit Bar and insert one observation nodes in the very bottom left node Run Calculations Click the Calculate Current Project command an on the Toolbar or Calculation gt Calculate Current Project Execution time on 3 GHz PC 7 s Note This exercise will produce following warnings Master species N 3 1s present in solution n but 1s not transported The same warning occurs for N 0 N 3 and N 0 are two secondary master species from the primary master species N Only the secondary master species N 5 was defined as a component to be transported Solute Transport HP2 Components HP2 however checks if all components which are present during the geochemical calculations are defined in the transport model If not a warning message is generated In our example the concentrations of the components N 0 and N 3 are very low under the prevailing oxidizing conditions Therefore they can be neglected in the transport problem If you want to avoid these warnings you have to either include N 0 and N 3 as components to be transported or define an alternative primary master species representing nitrate such as Nit using SOLUTION MASTER SPECIES and SOLUTION SPECIES 35 4 1 3 Output When the program finishes explore the output files Display results for Observation Points Figure below can be created using the Observation Points All Concentration information information from the obs nod out output
55. issolution of calcite and gypsum Figure 19 shows the time series of pH total aqueous C concentration total aqueous Ca concentration total aqueous S concentration the amount of gypsum and the amount of calcite at selected observation nodes during dissolution of calcite and gypsum 46 Distance cm 6 5 7 5 5 6 7 5 8 9 9 5 pH 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 3 Qu 0 o c S Q A 0 0 004 0 008 0 012 0 016 Total concentration of Ca mol kg water 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 5 DE o o c 5 5 A 50 0 1e 005 2e 005 3e 005 4e 00 gypsum mol 1000 cm of soil 0 days 0 50 days 1 00 days 1 50 days 2 00 days 2 50 days 4 I 3 LL Pa l e 005 5 5e 005 6e 00 ta tion of kg water i 1 lays day 1 50 0 10 5 20 0 o c 30 1 A 4 40 i i 1 50 0 016 0 012 0 008 0 004 0 Total concentration of S mol kg water days 1 00 days 2 00 days 0 days 1 50 days 2 50 days 0 50 5 S 20 FI h M M A o o c 5 0 A r r j 1 1 1e 005 2e 005 3e 005 4e 005 5e 00 calcite mol 1000 cm of soil days 1 00 days 2 00 days 0 days 1 50
56. ist of Pages Page 3 of 5 Geochemical Model 1 Additions to Thermodynamic Database Define geochemical model C we i E Definitions of Solution Compositions This block will not be overwritten by HP1 Help 5 Database Viewer Equilibrium phases 1 202 calcite 0 3 9E 5 el 02 g 0 68 Redo Keywords double click to insert l Solution Definition Geochemical Model Output Chemical physical rejaction Database Advanced reactive transport dimension 2 EXCHANGE 1 202 X 0 0011 equilibrate with solution 1001 B B B Miscellaneous L3 El Mest Add Exchange 5urface Equilibrium Phases Kinetics aay 0 0 Previous Figure 7 The HP2 Definitions Geochemical Model dialog window 18 Additionally the following two lines reactive_transport dimension 2 indicating to the PHREEQC part of the computational module that the application is two dimensional should be written into this window These two lines could be written to any part of the PHREEQC 1in file but we recommend to place them here Using the commands at the bottom of the window Add Exchange Surface Equilibrium Phases and Kinetics one can enter the Keyword for a particular process and a template guiding users how to define a particular process 2 1 4 4 Additional Output The user can define additional output using the editor Additional Output Fig 8 in the HP2 3 Definitions dialog wind
57. ity Criterion Temperature Dependence of Parameters Water Content Dependence of Parameters M Use Tortuosity i Millmgton amp Quirk CO Moldrup Attachment Detachment Concept virus bacteria transport Filtration Theory Fumigant Module Additional Fumigant Application at a GrvenT ime Iteration Criteria for Nonlinear Adsorption only Initial Conditions n Liquid Phase Concentrations Mass zolutes volume water on In Total Concentrations Mass salute alume oil Hest Nonequilibrium phase is initially at equilibrium with equilibrium phase Figure 2 The Solute Transport dialog window 2 1 3 HP2 3 Components and Database Pathway The next window that appears is the HP2 3 Components and Database Pathway window Fig 3 12 Path to Folder with Thermodynamic Databases D Suss HYDRUS3D 2 05ThermodynamicOBSPHREEQC DAT Browse Cancel Help Component Presets File PHREEGC IM Heb Total HI The PHREEGC IM file specifying the chemical composition and chemical reactions can be created using either the HYDRUS GUI see the Editar in the next dialog window or the PHREEGC GUI N Create PHREEGC IN file using HYDRUS GUI The PHREEUC In file will be created when the check bas above is checked Boundary Conditions In Concentrations Next In Solution Compositions Previous Figure 3 The HP2 3 Components and Database Pathway dialog window Note that the option to specify
58. l not check if a correct master species 1s entered Because the redox potential is high in this example a high partial pressure of oxygen the secondary master species C 4 and S 2 are not considered Check Create PHREEQC IN file using HY DRUS GUI Button Next Solute Transport HP2 3 Definitions Definitions of Solution Composition Define the initial condition 1 6 the solution composition of water in the soil column with the identifier 1001 e Pure water e Bring it in equilibrium with gypsum calcite and O 0 to be in equilibrium with the partial pressure of oxygen in the atmosphere Define the boundary condition 1 e the solution composition of water entering the soil column with the identifier 3001 e Ca Cl solution e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 and C 4 to be in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide respectively solution 1001 equilibrium_phases 1001 gypsum calcite O2 g 20 68 save solution 1001 end solution 3001 42 units mmol kgw pH 7 charge CIA Ca 1 O10 1 024g 0 69 Cid I COZ g 924 5 Button OK Geochemical Model Define for each node the geochemical model Note that the initial amount of a mineral must be defined as mol 1 dm soil i e 2 176 x 10 mol kg soil 1 8 kg 1 dm Additionally indicate to PHREEQC that this is a two dimensional project Equilibrium phases 1 101 Gypsum D
59. le created by the PHREEQC module in HP2 and can be viewed via the GUI Results gt HP2 Text Output or via the Project Navigator bar An ASCII text file tab delimited that includes a selected output of all geochemical calculations in HP2 carried out before actual transport calculations Inspection of this file can be done with any spreadsheet such as MS Excel obs nod chem201 out A series of ASCII files tab delimited with the selected output for ts pH plt ts pe plt ts tot Ca plt ts tot Cl plt ts tot S plt ts tot C plt ts eq gypsum plt ts eq calcite plt ts d eq gypsum plt ts d eq calcite plt the defined observation nodes 41 81 121 161 and 201 at specific times every 0 025 days Numerical values can be seen by opening this file in a spreadsheet such as Excel A single plot of time series at five observation nodes can be generated for each geochemical variable with the ts plt files using the GNUPLOT graphical program see below An ASCII file containing command line instructions to generate a plot of pH or pe or other variables using GNUPLOT An ASCII file containing command line instructions to generate a plot with total concentrations of Ca or Cl S and C using GNUPLOT An ASCII file containing command line instructions to generate a plot with the amount of the minerals gypsum or calcite with GNUPLOT An ASCII file containing command line instructions to generate a plot with the change in
60. mation is provided in the help file and in the user manual of the HP1 program Jacques and Simunek 2010 Selected Output Create Selected Output File water Temperature F Alkalinity lanic Strength Cancel Hep File M ame UT ailing hse w pH 1 Charge Balance pe Percent Error Punch Times and Locations Controlled by HYDRUS bserv Nodes Printed to Different Files Mobile and Immobile Cells in Different Files Make GNUplot Templates Print Options Main Switch No Printing in PHREEGC OUT J Printing in PHREEGC OUT FHREEUL Dump No Dump Files C Frequency by Print Times C Frequency by TLevel Print Times 0 Frequency Even n Time Steps Controlled by PHREEGC 1 1 Location D HYDRUS Observation Nodes Other Nodes le g 1 5 10 Print times 3 Controlled by HYDRUS Every n Time Step Next Number of warnings Figure 13 The HP2 Print and Punch Controls dialog window 23 Previous 24 2 2 Post Processing 2 2 1 Results Graphical Display The output for the HP2 module is similar as the output for the standard HYDRUS module and for standard variables such as pressure head water contents and so on Multiple variables can be displayed in the View window Figure 14 Main components defined in the HP2 3 Components and Database Pathway window Fig 3 variables selected in the HP2 Print and Pu
61. mosphere Define the initial condition 1 e the solution composition of water in the mine tailing with the identifier 1002 e pH2 3 e Bring it in equilibrium with O 0 to be in equilibrium with the partial pressure of oxygen in the atmosphere e Bring it in equilibrium with gypsum and calcite 66 e High level of U 56 4 mol kgw Define the boundary condition 1 e the solution composition of water entering the soil column with the identifier 3001 e Ca Cl solution e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 and C 4 to be in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide respectively solution 1001 soil temp 25 units kgw pH 2 charge Ca 1E 2 calcite C l9E 3 U 7 P 1E 6 S 201 gypsum Fe 1E 7 O 0 1 O2 g 0 68 O 0 initially in equilibrium with a partial pressure of oxygen of 10 0 68 atm end solution 1002 mine tailing temp 25 units kgw pH 2 3 Ca 1E 2 charge C l1E 2 U 5E 4 P 1E 6 S 2E 1 Fe 3 5E 2 O 0 1 02 g 0 68 4 O 0 initially in equilibrium with a partial pressure of oxygen of 10 0 68 atm equilibrium phases 1002 gypsum 0 3 7E 3 calcite 0 0 save solution 1002 end solution 3001 boundary condition temp 25 units kgw pH 7 charge Ca 1E 3 C l 5E 3 U P 1E 6 S 1E 4 Fe 1E 7 Select Geochemical Model Define for each node the geochemical model Note that the initial amount of a
62. n a soil profile f cadmium leaching in acid sandy soils g radionuclide transport and h long term uranium migration in agricultural field soils following mineral P fertilization Most of these examples have been rerun using HP2 which verified correct implementation of various components of the coupled program The HP2 code is fully incorporated into the HYDRUS 2D 3D software package and hence is installed automatically together with selected examples when one obtains HYDRUS 2D 3D and HP2 licenses and downloads HYDRUS from the Hydrus website The main purpose of this report is to document a two dimensional numerical module HP2 that incorporates flow and transport processes as well as biogeochemical reactions in variably saturated porous media HP2 was developed specifically for the HYDRUS 2D 3D software package Sim nek et al 2011 Sejna et al 2011 The general conceptual basis of the module is discussed in detail in reports of Jacques and Sim nek 2005 2010 and restated here for multi dimensional systems The documentation in this report focuses mostly on implementation of the HP2 module into HYDRUS 2D 3D All processes related to variably saturated water flow heat transport and solute transport are described in detail in the HYDRUS 2D 3D documentation Sim nek et al 2011 and will not be repeated here Similarly processes and reactions related to biogeochemical reactions are described in detail in the PHREEQC
63. nch Controls dialog window Fig 12 and variables specified in the Additional Output Fig 8 of the HP2 3 Definitions dialog window Fig 4 can be displayed this way Figure 14 below shows the Results Graphical Display part of Data Tab of the Navigator Bar for the Leaching of the Uranium Tailings example given below Section 4 5 From the HP2 variables first seven are the main components Total_H Total_O Ca C U P S and Fe defined in the HP2 3 Components and Database Pathway window Fig 3 the next two pH and pe are variables selected in the HP2 Print and Punch Controls dialog window Fig 12 and finally the last four calcite gypsum ratherfordine and siderite are mineral phases specified in the Additional Output Fig 8 of the HP2 3 Definitions dialog window jg Results Graphical Display MI Pressure Head Mi Water Content a eq calcite n eq gypsum Mi eq Rutherfordine eq Siderite Figure 14 The Results Graphical Display part of Data Tab of the Navigator Bar for the HP2 module 2 2 2 Results Other Information The content of the PHREEQC out output file is described in detail in the PHREEQC user manual Parkhurst and Appelo 1999 25 26 3 Example Problems The HP2 module supplements the standard HYDRUS program which includes variably saturated water flow and solute transport model and thus the water flow solute transport and colloids transport parts of the model h
64. ndow a Click on Zoom by Rectangle E at the Toolbar or View gt Zoom by Rectangle and zoom on the left furrow Select Constant Head Constant Head from the Edit Bar select bottom of the left furrow and 4 nodes on the side specify 6 cm with Equilibrium from the lowest located nodal point b Click on View All H at the Toolbar or View gt View All Select Free Drainage Wl Free Drainage from the Edit Bar and select the entire bottom of the transport domain c On the Navigator Bar double click on Solute Transport Click on Display codes on the Edit Bar E Display Codes and check that 1 or 1 is displayed in the furrow This means that solution composition will be applied with the irrigation water Uncheck Display Codes again Observation Nodes Click on the Domain Properties Tab under the View Window On the Navigator Bar click on Domain Properties Observation Nodes or Insert gt Domain Properties gt Observation Nodes Click on the Insert command on the Edit Bar and specify 5 points arbitrarily in the transport domain between the furrow and the bottom of the transport domain Save 55 Save the project using the Save command 5 on the Toolbar or File gt Save Run Calculations Click the Calculate Current Project command RR on the Toolbar or Calculation gt Calculate Current Project 4 4 3 Output Figure 21 shows the pressure head profiles for four different times The distribution
65. o geometry design finite element discretization variably saturated water flow heat transport solute transport initial and boundary conditions are described in detail in the HYDRUS 2D 3D documentation im nek et al 2011 Sejan et al 2011 and will not be repeated here Similarly processes and reactions related to biogeochemical reactions are described in detail in the PHREEQC Parkhurst and Apello 1998 and HP1 Jacques and Simunek 2005 2010 manuals 2 1 Preprocessing and Input Data HP2 projects are managed in the same way as other HYDRUS 2D 3D projects using the Project Manager The Project Manager is used to manage data of existing projects and to locate open delete copy or rename projects A new HP2 project is created in the same as any other HYDRUS 2D 3D project 1 e using the button New in the Project Manager Since all other inputs 1 e domain design FE discretization water flow and heat transport are the same as in standard HYDRUS 2D 3D projects only parts related specifically to HP2 are discussed below 2 1 1 Main Processes The HP2 module is activated in the Main Processes window Fig 1 by selecting the Solute Transport check box and the HP2 Hydrus Phreeqc radio button Simulate Dual Permeability Model Solute Transport Standard Solute Transport J Wetland CM 2 Major lon Chemistry Unsatchemn C allaid Facilitated Solute Transport HPZ Hydrus Phreeqc
66. of chloride concentrations a tracer is shown on Figure 22 209 913 190 264 170 656 151 027 131 399 111 770 92 142 72 514 52 665 33 257 13 628 6 000 Pressure Head h cm Min 209 913 Max 6 000 Figure 21 Pressure head cm profiles at times a 0 1 b 0 5 c 1 and d 2 days for example 4 0 00000e 00 5 00000e 04 1 00000e 08 1 50000e03 20000e03 2500002035 300000802 3500002023 400000802 450000 0 X 5 00000e 03 CI Cl moles dm 3 Min 0 000 Max 0 005 Figure 22 Chloride concentration profiles mol L at times a 0 1 b 1 c 3 and d 5 days for example 4 d 39989e 03 4 60865e 03 481742 03 5 02618e 03 5 224B5e 03 544372e 03 5 65249e 03 5 86125e 03 amp 07002e 03 6 27879e 03 amp 6 48755e 03 6 69632e 02 HENEN J h Dol O Figure 23 Sodium concentration profiles mol L at times a 0 5 b 1 c 3 and d 5 days for example 4 57 Figures 23 and 24 present the liquid phase and exchangeable concentrations of sodium respectively The exchange phase concentrations reflect the changes in aqueous Na and Ca concentration Note the significant lagging of the exchanger front to both the water and tracer front Also due to the high nonlinearity of Na Ca exchange the concentration and exchange fronts are very sharp in contrast to the more diffuse tracer fronts After 5 days less than 25 of the profile has been reclaimed to exchangeable sodium percentage less than
67. on composition numbers defined in phreeqc in aS Initial Conditions Pressure Head Solution Composition Figure 11 The Initial Conditions part of Data Tab of the Navigator Bar for the HP2 module Solution composition numbers e g 1001 defined in Definitions of Solution Compositions window Fig 6 are similarly used to assign different solution compositions to different boundaries as boundary conditions For boundaries with constant water flow conditions solution composition numbers are specified in the Reaction Parameters dialog window Fig 10 For boundaries with time variable water flow conditions solution composition numbers are specified in the Time Variable Boundary Conditions dialog window Fig 12 Time Variable Boundary Conditions Lad iis Di Parameters var H a 4 H 4 cv aljel cV aluez cV alue3 Cancel cm lem dar cm kad kod kod Cancel D 45 1001 1002 3001 Hep Add Line 0 45 1001 1002 3002 Figure 12 The HP2 related part of the Time Variable Boundary Conditions dialog window 22 2 1 8 HP2 Print and Punch Controls The HP2 Print and Punch Controls dialog window Fig 13 allows users to specify variables 1 e water temperature pH pe ionic strength alkalinity charge balance and percent error times Print Times and locations Observation Nodes for which output should be provided The information in this dialog should be self explanatory More infor
68. ow by using the PHREEQC data blocks SELECTED_OUTPUT and USER PUNCH Standard output in HP2 is limited to the concentration of the components In addition depending on the options selected in the HP2 3 Print and Punch Control dialog window Fig 13 a number of output files is created HP2 specific output files with the file name variable hpo have the same binary structure as other HYDRUS output files such as h out or concx out and can be displayed using the GUI Example shown in Figure 8 requests output for two mineral phases calcite and gypsum and Na and Ca concentrations at the cation exchange site X a HP2 3 Definitions List of Pages Page 4 of 5 Additional Output 1 Additions to Thermodynamic Database Define output eo This block will not be overwritten by 1 3 Geochemical Model 4 Additional Output 5 Database Viewer selected_output totals Ca Mg 61 5 6 equilibrium phases gypsum calcite molalities Nax CaX2 Keywords double click to insert Selected output be activities alkalinity ke calculate values charge balance distance equilibrium_phases file gases high precision Jonic strength isotopes kinetic_reactants te molalities pe percent_error pa kal gt gt teaction bu Next saturation indices Previous Figure 8 The HP2 Definitions Additional Output dialog window 19 2 1 5 Solute Transport Parameters T
69. phase e Numbers 3001 4000 to define boundary solutions Note that these numbers should all be larger than the maximum number of FE nodes Thus if the number of FE nodes is 10 000 numbers higher than 10 000 should be used to define the solution compositions otherwise these elements will be linked to a specific FE node The initial conditions spatial distribution of solution composition are then defined directly using the solution composition numbers Similarly boundary conditions are defined using the solution composition numbers An example of a solution composition defined using concentrations of various components i1 e Ca C U P S and Fe and in equilibrium with two phases 1 6 gypsum and calcite is shown in Figure 6 a HP2 3 Definitions List of Pages Page 2 of 5 Definitions of Solution Compositions Additions ta Thermodynamic Database Definition of the solution compositions initial and boundary 2 Definitions of Solution Compositions ance Geochemical Model V XH ES Additional Output solution 1002 mine tailing Help Database Viewer temp 25 units mol kgw pH 2 3 Ca l1E 2 charge Reda Undo Keywords double click to insert J Solution Definition J Geochemical Model Qutput gt Ehemical phusical rejaction Database Advanced O 0 1 O02 qg 0 68 O 0 initially in equilibrium with a partial pressu 1 F Miscellaneous equilibrium phases 1002 gypsum
70. port HP2 3 Definitions Definitions of Solution Composition Define the initial condition 1001 e K Na N 5 solution e use pH to charge balance the solution e Adapt the concentration of O 0 to be in equilibrium with the partial pressure of oxygen in the atmosphere Define the boundary condition 3001 e Ca Cl solution e Use pH to charge balance the solution e Adapt the concentration of O 0 to be in equilibrium with the partial pressure of oxygen in the atmosphere Solution 1001 Initial condition units kgw pH 7 charge Na 1 K 0 2 NiO 1 2 O0 L 02106 8 Solution 3001 Boundary solution units kgw 32 pH 7 charge Ca 0 Ch Lee OO 1 02 g 0 68 Geochemical Model Define for each node 82 nodes the geochemical model 1 e the cation exchange assemblage X 0 0011 moles 1000 cm and equilibrate it with the initial solution solution 1001 Note that since no equilibrium constants for cation exchange are specified they are taken from the PHREEQC dat database Additionally indicate to PHREEQC that this is a two dimensional project EXCHANGE 1 82 Glayer 6 1 equilibrate with solution 1001 reactive_transport dimension 2 Button OK Additional Output Since output is required only for the total concentrations and such output is available in the automatically generated file obs_node out there is no need to define additional output If we want to have spatial profiles of cation exchange concentrations then
71. r PHREEQC editors The Keywords are hierarchically organized in a tree like structure in seven main groups Solution Definition Geochemical Model Output Chemical Physical Reaction Database Advanced and Miscellaneous A single click opens a particular tree subsection a double click copies the selected keyword to the Editor Window 2 1 4 1 Additions to Thermodynamic Database Additional thermodynamic definitions can be added to the phreegc in file not to the thermodynamic database file itsel using the editor Additions to Thermodynamic Database in the HP2 3 Definitions dialog window Fig 4 Typical PHREEQC data blocks used here are found under the Database group of the Keywords e SOLUTION MASTER SPECIES e SOLUTION SPECIES 15 e PHASES e EXCHANGE MASTER SPECIES e EXCHANGE SPECIES e SURFACE MASTER SPECIES e SURFACE SPECIES e RATES Users are referred to the PHREEQC 2 manual Parkhurst and Appelo 1999 for the conventions used for the input of thermodynamic data An example of Additions to Thermodynamic Database is shown in Figure 5 in which three SOLUTION MASTER SPECIES U S and P 7 SOLUTION SPECIES PO4 SO4 UO CaPO CaHPO UO2 OH and UO OH and 2 PHASES gypsum and calcite are defined B HP2 3 Definitions List of Pages Additions to Thermodynamic Database add new thermodynamic data This block will not be overwritten by 1 Cae Definitions of Solution Compositions ance Geochem
72. ration Criteria Leave default values Button Next Water Flow Soil Hydraulic Model Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Hydraulic Properties Model Leave default values as follows Radio button van Genuchten Mualem Radio button No hysteresis Button Next Water Flow Soil Hydraulic Parameters Edit gt Flow and Transport Parameters gt Water Flow Parameters gt Soil Hydraulic Parameters Catalog of Soil Hydraulic Properties Silt Button Next Solute Transport General Info Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt General Information Number of Solutes 8 Button Next Solute Transport HP2 3 Components and Database Pathway Database Pathway Leave the default PHREEQC database and default path Add seven components Total_O Total_H Ca Mg Na K Cl S 6 Leave the checkbox on Create the PHREEQC IN file Using HYDRUS GUI Leave the radio button on In Solution Composition Button Next 51 Solute Transport HP2 3 Definitions Select Definitions of Solution Composition Define the initial condition 1501 e Ca Na SO solution e use pH to charge balance the solution e Adapt the concentration of O 0 to be in equilibrium with the partial pressure of oxygen in the atmosphere Define the boundary condition 3001 e Ca Na Cl SO solution e Use pH to charge balance the solution e Adapt the concentration of O 0 to be in equilibrium with the pa
73. rtial pressure of oxygen in the atmosphere Solution 1501 Initial condition units kgw pH 7 charge Na 5 Ca Ls CL Du S 6 O 0 KJO c C 5 02 4 8 Solution 3001 Boundary solution units kgw pH 7 charge Car LO Na 4 4 Od enu S46 16 0 O O X O02 90 8 Select Geochemical Model Define for each node 1170 nodes the geochemical model 1 e the cation exchange assemblage X 0 01 moles dm and equilibrate it with the initial solution solution 1501 Note that since no equilibrium constants for cation exchange are specified they are taken from the PHREEQC dat database EXCHANGE 1 1170 X 0 01 equilibrate with solution 1501 Additionally you may indicate to PHREEQC that this is a two dimensional project However this information will be added by default in GUI if not specified manually 52 reactive_transport dimension 2 Select Additional Output Define the additional output to be written to selected output files selected_output equilibrium phases gypsum calcite molalities CaX2 Button Next Solute Transport Solute Transport Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Transport Parameters Leave default values Bulk Density 1 4 cm g Longitudinal Dispersivity Disp L 2 cm Transverse Dispersivity Disp T 0 2 cm Molecular Diffusion Coefficient for Liquid Phase Diffus W 2 cm d for all components Button Nex
74. software has been verified against selected test cases However no warranty is given that the program is completely error free If you do encounter problems with the code find errors or have suggestions for improvement please contact the senior author at Jirka Sim nek Tel Fax 1 951 827 7854 Email jiri simunek ucr edu 1 Introduction This user manual documents the HP2 program that resulted from coupling Hydrus its two dimensional part with the PHREEQC geochemical code Parkhurst and Appelo 1999 to create this new comprehensive simulation tool HP2 acronym for HY DRUS PHREEQC 2D corresponding to a similar one dimensional module HP1 Jacques and Sim nek 2005 Jacques et al 2006 Sim nek et al 2006 2008 HP2 has apart from the dimensionality 2D the same capabilities as 1171 HP2 contains modules simulating 1 transient water flow 2 the transport of multiple components 3 mixed equilibrium kinetic biogeochemical reactions and 4 heat transport in two dimensional variably saturated porous media soils HP2 is thus a significant expansion of the individual HYDRUS 2D and PHREEQC programs by preserving most of their original features The code still uses the Richards equation for simulating two dimensional variably saturated water flow and advection dispersion type equations for heat and solute transport However the loosely coupled program can simulate also a broad range of low temperature biogeochemical reactions in
75. sport HP2 3 Definitions 90 4 05 I Fet 14 008 6 DU Select Additions to Thermodynamic Database SOLUTION MASTER SPECIES Fe Fet2 Ca Cat2 U UOZT2Z 0 S 504 2 0 P PO4 3 VAR SOLUTION SPECIES Cat2 2 log_k 0 0 Fet2 Fet2 log_k 0 0 PO4 3 PO4 3 log_k 0 0 504 2 504 2 log_k 0 0 00292 2 log k 0 0 CO3 2 Cat2 3 log_k 3 002 2 0872 Ht CaHCOST log k Ll Es Fe 2 H20 FeOH Ht log_k 9 5 Cat2 SO4 2 4 log_k Asal Ca 2 2H PO4 3 CaH2P04 55 9041 40 08 238 0290 96 0616 390 9738 OOO C 64 55 847 40 08 238 0290 32 064 30 9138 log_k 20 96 Cat2 PO4 3 CaPO4 log_k 6 46 Ca 2 H PO4 3 4 log_k 15 08 Fe 2 SO4 2 4 log_k 2 2 Fe 2 2H20 Fe OH 2 2H log_k S Us Fe 2 3220 Fe OH 3 32 log_k 31 Fe 2 4H20 Fe OH 4 2 4H log_k ed 20 UOZ2T2 UO2 OH H log_k 220 2002 2 UO02 2 0H 2Z 2H log k 5 68 4H20 3002 2 UO2 3 0H 4 2 4H log_k 11 88 SH20 3UO242 U0O2 3 0H 5 5H log_k 15 82 7H20 4002 2 U02 4 OH 7 7H log_k A 7H20O 200252 U0O2 3 0H 7 7H log_k 26 64 5 CO3 2 002 2 002 003 log k PM ONG 2CO3 2 002 2 UO2 CO3 2 2 log k 17 08 3CO3 2 002 2 UC2 003 4 log_k 21 7 ZUOZ 2 gt CO3 2 3820 UO2 2 COS OH 3 3H log_k 0 002 2 SOA 2 UO2 504 log k 2 5 UO2 2 2004 2 U0Z S04 2 2 log_k 4 2H UO2 2 POA 3 H2 UO2 PO4 lo
76. t Solute Transport Reaction Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Reaction Parameters Boundary Condition cBnd1 3001 the solution composition number for the upper boundary condition Button Next Rectangular Domain Spatial Discretization Edit gt FE Mesh gt FE Mesh Parameters Horizontal Discretization in X Count 45 Entries in the x column 0 3 6 9 12 15 16 5 18 19 5 21 22 5 24 25 5 27 28 5 30 32 34 36 5 39 42 46 50 54 58 61 63 5 66 68 70 71 5 73 74 5 76 77 5 79 80 5 82 83 5 85 88 91 94 97 100 Entries in the dz column 15 15 15 15 15 15 13 5 12 10 5 9 7 5 6 4 5 3 1 5 0 0 0 O 0 0 0 O 0 O 0 O 0 O 0 1 5 3 4 5 6 7 5 9 10 5 12 13 5 15 15 15 15 15 15 Horizontal Discretization in Z Count 26 Entries in z column 100 99 97 5 95 5 93 90 87 84 81 78 75 72 69 66 62 58 54 50 45 40 34 28 21 14 7 0 Button Next 53 Rectangular Domain Discretization Horizontal Discretization Count 45 amp cm 0 00 3 00 6 00 9 00 12 00 15 00 16 50 18 00 19 50 21 00 22 50 24 00 25 50 27 00 20 50 m M ee 0063 n3 Generate Coordinates Set relative size of finite elements R51 1 Generate Default Domain Properties Edit gt Domain Properties gt Default Domain Properties Set Code
77. undary Conditions dialog window 22 The HP2 Print and Punch Controls dialog 23 The Results Graphical Display part of Data Tab of the Navigator Bar for the 25 Outflow concentrations of Cl Ca Na and K for the single pulse cation exchange EKAM PI T E E 36 Time series of K concentrations at four depths for the multiple pulse cation EX CHAINS CCK AIA DC gr ann Gatansatenantes 39 Outflow concentrations for the multiple pulse cation exchange example 39 Vertical profiles of pH top left total aqueous C concentration top right total aqueous Ca concentration middle left total aqueous S concentration middle right the amount of gypsum bottom left and the amount of calcite bottom right at selected print times during dissolution of calcite and gypsum 47 Time series of pH top left total aqueous C concentration top right total aqueous Ca concentration middle left total aqueous S concentration middle right the amount of gypsum bottom left and the amount of calcite bottom right at selected depths observation nodes during dissolution of calcite and gypsum 48 Schematic representation and finite element mesh of the flow domain for the furrow System Tor example Fy ajde se densitet dd e ea eu d 49 Pressure head cm profiles at times a 0 1 b 0 5 c 1 and d 2 days for example 4 Chloride concentration profiles mol L at times a 0 1 b
78. water the vadose zone and in ground water systems including interactions with minerals gases exchangers and sorption surfaces based on thermodynamic equilibrium kinetic or mixed equilibrium kinetic reactions HP2 similarly as HP1 uses the operator splitting approach with no iterations during one time step a non iterative sequential modeling approach Jacques et al 2006 evaluated the accuracy of the operator splitting approach for a kinetic reaction network 1 e sequential and parallel kinetic degradation reactions by comparing HP1 with an analytical solution for TCE degradation as well as for mixed equilibrium and kinetic reactions involving different flow conditions steady State and transient Jacques and Sim nek 2005 Sim nek et al 2006 Jacques et al 2008ab demonstrated the versatility of HP1 on several examples which included a the transport of heavy metals Zn Pb and Cd subject to multiple cation exchange reactions b transport vvith mineral dissolution of amorphous S1O and gibbsite AI OH 3 c heavy metal transport in a medium vvith a pH dependent cation exchange complex d infiltration of a hyperalkaline solution in a clay sample this example considers kinetic precipitation dissolution of kaolinite illite quartz calcite dolomite gypsum hydrotalcite and sepiolite e long term transient flow and transport of major cations Na K Ca and Mg and heavy metals Cd Zn and Pb i
79. we can use the following command selected_output molalities Nax KX CaX2 Button Next Solute Transport Solute Transport Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Transport Parameters Leave default values Bulk Density 1 5 cm g Longitudinal Dispersivity Disp L 0 2 cm Transverse Dispersivity Disp T 0 02 cm Molecular Diffusion Coefficient for Liquid Phase Diffus W 0 Button Next Solute Transport Reaction Parameters Edit gt Flow and Transport Parameters gt Solute Transport Parameters gt Solute Reaction Parameters Boundary Condition cBnd1 3001 the solution composition number for the upper boundary condition Button Next 33 Rectangular Domain Spatial Discretization Edit gt FE Mesh gt FE Mesh Parameters Horizontal Discretization in X Count 1 Entries in the x column 0 1 Horizontal Discretization in Z Count 41 Default Entries in the z column Button Next Rectangular Domain Discretization Horizontal Discretizatian In o Vertical Discretization in Count 2 Count 4 Cancel cm dz cm 5 0 00 0 00 1 00 1 2 3 4 5 5 T B Generate 2 Coordinates Set relative size of finite elements Fist 1 1 Generate Default Domain Properties Edit gt Domain Properties gt Default Domain Properties Set Code on the first and last row to 1 Set the initial pressure head h for all nodes equal to zero Set th

The HP2 Program for HYDRUS (2D/3D) - PC

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