Home

Notes on HP1 – a software package for simulating - PC

1. 0 05 0 1 0 15 0 2 0 25 0 3 0 35 Mass of water kg 1000 cm of soil 0 min 12 00 min 144 00 min 2 29 min 27 47 min 54min 62 90 min 0 Pao eres A A 8 10 1 s m a 15 1 20 r i r i T 0 0045 0 006 0 0075 0 009 Total concentration of Na mol kg water 0 min 12 00 min 144 00 min 2 29 min 27 47 min 524min 62 90 min 0 5J S 8 104 E 2 a 154 720 _ 0 008 0 01 0 012 0 014 0 016 0 018 0 02 0 022 Total concentration of Ca mol kg water 0 min 12 00 min 144 00 min 2 29 min 27 47 min 524min 62 90 min Distance cm 20 i i i i i i pt FLETI TEETE PO EA EE 0 0 005 0 01 0 015 0 02 0 025 0 03 0 035 Total concentration of Cl mol kg water 0 min 12 00 min 144 00 min 2 29 min 27 47 min 524min 62 90 min 0 5 Ex 8 10 s 2 a 15 4 720 _ gt _ gt 0 001 0 002 0 003 0 004 0 005 0 006 0 007 0 008 Total concentration of K mol kg water 0 min 12 00 min 144 00 min 2 29 min 27 47 min 5 24 min 62 90 min 0 5 2 8 104 E S E a 15 4 20 ra 2d 7 4j 0 24 0 003 0 004 0 005 0 006 0 007 0 008 Total concentration of Mg mol kg water 0 min 12 00 min 144 00 min 2 29 min 27 47 min 5 24 min 62 90 min Figure 24 Profiles of water content top left and
2. 300 00 days 8 S 1 p S Eh D E a a 100 a 100 a 5e 005 0 0001 0 00015 0 5e 005 0 0001 0 00015 Total concentration of CI mol kg water Total concentration of Cl mol kg water Figure 4 Profile plots of Cl concentrations in the mobile phase left and immobile phase right at selected times for the example TRANSCL 3 4 STADS Transport of nonlinearly adsorbed contaminant for steady state flow conditions In this problem saturated steady state water flow and single component transport of a nonlinearly adsorbing contaminant Pola through a soil column of 1 m length for a period of 1000 d are considered Transport and reactive parameters are as followed the saturated hydraulic conductivity K 1 cm d the saturated water content 0 5 cm cm the dispersivity 1 cm the bulk density 1 5 g cm the Freundlich distribution coefficient 5 cm g and the Freundlich exponent is 0 8 Initially no contaminant is present in the soil The contaminant concentration in the percolating water is 1 mol kgw Profiles of Pola concentrations are shown in Figure 5 Verification problem 3 in Jacques and Sim nek 2005 21 0 days 250 00 days 500 00 days 750 00 days 1000 00 days Distance cm i I i 0 0 2 0 4 0 6 0 8 1 Total concentration of Pola mol kg water Figure 5 Profiles of Pola concentrations for the example STADS 3 5 STDECAY Transport of Nonlinearly Adsorbing Conta
3. OPEN REPORT SCK CEN BLG 1068 09 DJa P 129 Notes on HP1 a software package for simulating variably saturated water flow heat transport solute transport and biogeochemistry in porous media HP1 Version 2 2 Diederik Jacques and Jiri Sim nek Department of Environmental Sciences University of Riverside Riverside CA USA Jiri Simunek ucr edu January 2010 SCK CEN IPA PAS Boeretang 200 BE 2400 Mol Belgium OPEN REPORT OF THE BELGIAN NUCLEAR RESEARCH CENTRE SCK CEN BLG 1068 09 DJa P 129 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 Diederik Jacques and Jiri im nek Department of Environmental Sciences University of Riverside Riverside CA USA Jiri Simunek ucr edu January 2010 Status Unclassified ISSN 1379 2407 SCK CEN IPA PAS Boeretang 200 BE 2400 Mol Belgium SCK CEN Studiecentrum voor Kernenergie Centre d tude de l nergie Nucl aire Boeretang 200 BE 2400 Mol Belgium Phone 32 14 33 21 11 Fax 32 14315021 http www sckcen be Contact Knowledge Centre library sckcen be RESTRICTED All property rights and copyright are reserved Any communication or reproduction of this document and any communication or use of its content without explicit authorization is prohibited Any infringement to this rule is illegal and entitles to cla
4. The U concentration in the initial solution composition is considered to be very low U 10 M and much larger 107 M in the boundary solution This problem is carried out using the PHREEQCU DAT database This is the PHREEQC DAT database with the definition of additional U species from Langmuir 1997 a database from www geo tu freiberg de merkel Wat4f U dat Sorption is described using solid complexation reactions on the surface site called Hfo w line 3448 in the database Solution complexation species are defined further in the database Note that only one U species adsorbs uranyl Hfo wOH UO2 2 Hfo wOUO2 H log k 2 8 4 6 2 Calculation of the Size of the Surface Sorption Site The capacity of the surface should be expressed in mol 1000 cm of soil The capacity is calculated as 0 0002 g Fe2O3 g soil 1 31 g soil cm3 1 160 mol Fe203 g Fe203 2 mol Fe mol Fe203 0 875 moles sites mol Fe 1000 cm 1000cn 0 00286 mol 1000 cm 73 4 8 3 Input Project Manager Button New Name UTransport Description U transport and complexation Button OK Main Processes Heading U transport and complexation Uncheck Water Flow steady state saturated water flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Depth of the Soil Profile 50 cm Button Next Time Information Final Time 200 days Button Next Print Informatio
5. Button Copy New Name HP1 3 Description Mineral dissolution precipitation Cd transport and effect of Cl Button OK Main Processes Heading Mineral dissolution precipitation Cd transport and effect of Cl Button OK Time Information Check Time Variable Boundary Conditions Number of Time Variable Boundary Conditions 2 Button OK Solute Transport HP1 Definitions Definitions of Solution Compositions Add solution 3002 The boundary solution with the higher CaCl concentration Add solution 4001 The bottom boundary solution pure water solution 3002 pH 7 charge Cl 20 Ca 10 O 0 1 O2 g 0 68 C 4 1 CO2 g 3 5 Cd 1E 3 solution 4001 Button OK Button OK Time Variable Boundary Conditions 44 Time 1 2 5 in column cTop 3001 3002 cBot 4001 4001 Button OK Run Application 4 3 3 Output Figure 18 compares the time series of Cd concentrations and the profile of the amount of otavite between the project described in paragraph 4 2 and the current project At the first observation depth breakthrough curves of Cd are quite similar The calcite and otavite dissolution fronts already reached this depths after 1 day see Figure 17 and the high Cl concentration entering the system after 1 day has only a small effect on these dissolution fronts However deeper in the soil an increase in Cd concentration occurs already after 1 5 days at 20 cm depth in the case when
6. Initial Conditions gt Pressure Head Button Edit Condition 76 Select All Top Value 0 Menu Conditions gt Observation Points Button Insert Insert 5 observation nodes add observation nodes at 0 5 2 5 15 25 and 50 cm Menu File gt Save Data Menu File Exit Soil Profile Summary Button Next Run Application 4 6 4 Output U profiles at selected print times are shown in Figure 26 0 days 40 00 days 80 00 days 120 00 days 160 00 days 200 00 days Distance cm 50 T T 7 0 1e 009 2e 009 3e 009 Total concentration of U mol kg water Figure 26 Profiles of aqueous concentration of U for the example described in section 4 8 77 4 9 First Order Kinetic PCE Degradation Network 4 9 1 Background Perchloroethylene PCE also called tetrachloroethylene degrades slowly under reducing conditions mainly due to microbiological transformations One of the most important pathways for anaerobic biodegradation of PCE is by reductive dechlorination in a sequential way Figure 27 after Schaerlaekens et al 1999 shows this pathway for six components PCE trichloroethylene TCE cis 1 2 dichloroethylene cis DCE trans 1 2 dichloroethylene trans DCE 1 1 dichloroethylene 1 1 DCE and vinyl chloride VC VC then eventually degrades to ethylene ETH which is environmentally acceptable and does not cause direct health effects Although the rea
7. Make GNUplot Templates Button Next Water Flow Iteration Criteria Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters Qs 0 4 Ks 0 2 m hr Button Next 94 Water Flow Boundary Conditions Upper Boundary Condition Constant Pressure Head Lower Boundary Condition Constant Pressure Head Solute Transport General Information Stability Criteria 0 25 Number of Solutes 7 Button Next Solute Transport HP1 Components and Database Pathway Database Pathway Browse ex15 dat Six Components Total O Total H C Nta Na Cl N Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Additions to Thermodynamic Database Define rate equations RATES degradNTA start 10 qm parm 1 20 Ks parm 2 30 Ka parm 3 40 Xm kin Biomass 50 D mol HNta 2 Ks mol HNta 2 60 A mol 02 Ka mol 02 70 rate qm Xm D A 80 moles rate time 90 put rate 1 100 SAVE moles end Biomass start 10 Y parm 1 20 b parm 2 30 degradNta get 1 40 rate Y degradNta b M 50 moles rate Tim 60 if Mtmoles lt 0 then moles M 70 SAVE moles end Definitions of Solution Compositions Define the initial condition 1001 Define the boundary condition 3001 solution 1001 pH 7 charge units mol kgw O 0 6 25E 005 C 4 9E 7 Na 0 001 Cl 0 00
8. 0 0 The thermodynamic constants for the other half reactions are then calculated from the defined Gapon selectivity coefficients relative to Kana Calculate log Kox log Koca and log Keng Solution Exchange reactions are written in terms of half reactions The reaction Na G 0 5 Ca Na Caos G Kacana is written as the sum of the half reactions 1 G Na Na G Kana 2 G 0 5 Ca Cao s G Kaca Consequently log Kcana log Koca z log KGna We express the exchange coefficients relative to Na Thus taking log Kgna equal to 0 log KGca log KGcana Similarly for the reaction K G 0 5 Ca2 K Caos G Kecak the following two half reactions can be written as 1 G K K G Kek 2 G 0 5 Ca Cag s G Kaca Then log Kacak log Keca log Kak And similarly log Kgx log Koci log Kacak The same reasoning is applied also to derive Kay 66 Answer log Kok 1 16 log Kaca 0 462 log Kawg 0 383 4 7 3 Input Project Manager Button New Name CEC 4 Description Horizontal infiltration with Cation Exchange Button OK Main Processes Heading Horizontal infiltration with Cation Exchange Check Water Flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Depth of the soil profile 20 cm Decline from vertical axes 0 horizontal flow Button Next Time Information Time Units Minutes Final Time 144 min Init
9. 0 003 0 006 0 009 0 012 0 015 0 0 003 0 006 0 009 0 012 SiO2 a mol 1000 cm of soil gibbsite mol 1000 cm of soil 0 days 8 00 days 50 00 days 0 days 8 00 days 50 00 days 2 00 days 15 00 days 100 00 days 2 00 days 15 00 days 100 00 days 4 00 days 25 00 days 150 00 days 4 00 days 25 00 days 150 00 days Figure 12 Profiles of pH top total Si middle left and Al middle right concentrations and amounts of amorf SiO bottom left and gibbsite bottom right at selected times for the example MINDIS 3 9 MCATEXCH Transport of Heavy Metals in a Porous Medium with a pH Dependent Cation Exchange Complex This example considers the transport of several major cations Na K Ca and Mg and three heavy metals Cd Zn and Pb through a 50 cm deep multi layered soil profile during unsaturated steady state flow Each soil layer has different soil hydraulic properties and cation exchange capacities CEC Table 4 The top 28 cm of the soil is assumed to be contaminated with three heavy metals initial pH 8 5 while an acid metal free solution pH 3 infiltrates into the soil Table 3 Assuming that the cation exchange complex is associated solely with the organic matter CEC increases significantly with increasing pH due to the acid base properties of 29 its functional groups The higher the pH the more functional groups of the organic matter are deprotonated an
10. 4 2 1 Problem Definition Transport of a heavy metal through the soil column is investigated Under high pH conditions Cd precipitates as otavite CdCO3 However due to changing geochemical conditions in the soil column solubility of Cd is changing This example studies Cd mobility through the soil column The physical and geochemical set up as in paragraph 4 1 1 is used as the basis The infiltrating water is contaminated with a small amount of Cd 1 x 10 M Cd Otavite is added to the geochemical model with a small initial amount 1 x 10 mol 1000 cm of soil Calculate the percentage of Cd in the aqueous phase The basic statement SYS Cd gives the total moles of Cd in the system whereas the statement TOT Cd gives the total concentration of Cd in the aqueous phase The total amount of water in kg is obtained using the BASIC statement TOT water 4 2 2 Input Project Manager Select project HP1 1 Button Copy New Name HP1 2 Description Mineral dissolution precipitation Cd transport Button OK Main Processes Heading Mineral dissolution precipitation Cd transport Button OK Solute Transport General Information Number of Solutes 7 Button Next Solute Transport HP1 Components and Database Pathway Add Cd Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Add the concentration of Cd into the boundary solution solution 3001 solution 3001
11. 5 days 4 1 2 Input Project Manager Button New Name HP1 1 Description Dissolution of calcite and gypsum in the soil profile Button OK Main Processes Heading Dissolution of calcite and gypsum in soil profile Uncheck Water Flow Note this is a steady state water flow problem Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Depth of the Soil Profile 50 cm Button Next Time Information Final Time 2 5 days Maximum Time Step 0 05 days Button Next 33 Print Information Unselect T Level information Select Print at Regular Time Interval Time Interval 0 025 days Print Times Number of Print times 5 Button Next Print Times Button Default Button OK HP1 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 in later in the editor Additional output of the Solute Transport HP1 Definitions dialog window Button Next Water Flow Iteration Criteria Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters Qs 0 35 Ks 10 cm d Button Next Water Flow Boundary Conditions Upper Boundary Condition Constant Pressure Head Lower Boundary Condition Constant Pressure
12. 6 40E 02 4 00E 03 3 90E 02 8 00E 03 4 30E 04 2 30E 02 2 30E 02 1 00E 03 1 00E 03 1 00E 03 3 8 0 0690 6 40E 02 4 00E 03 3 30E 02 8 00E 03 4 10E 04 2 10E 02 2 10E 02 1 00E 03 1 00E 03 1 00E 03 4 4 0 0690 6 40E 02 4 00E 03 5 50E 02 8 00E 03 6 30E 04 3 30E 02 3 30E 02 1 00E 03 1 00E 03 1 00E 03 4 4 0 0690 6 40E 02 4 00E 03 7 60E 02 8 00E 03 3 30E 04 2 10E 02 2 10E 02 1 00E 03 1 00E 03 1 00E 03 4 5 0 0690 6 40E 02 4 00E 03 2 70E 02 8 00E 03 2 00E 04 1 40E 02 1 40E 02 1 00E 03 1 00E 03 1 00E 03 Define the boundary condition 3001 e Ca Cl solution low concentration e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 to be in equilibrium with the atmospheric partial pressure of oxygen Define the boundary condition 3002 e Ca Cl solution high concentration e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 to be in equilibrium with the atmospheric partial pressure of oxygen Define the boundary condition 4001 e Pure water 59 3I dT dT dT dT dT Saat E 9 9 5 Zoo 3I dT dT dT dT dT WHE 89 0 0 0 5 zo 3T UT aT aT aT UT aT obaeuo ad 20 3v 0 3T 20 s3E 20 31 20 s3E 20 s3v 0 dsS qa NNN N MNA 20 3v 20 3T 20 s3E 20 3T 20 3E 20 3v 0 30 uz ONN N 00 QN r8 v0 30 v0 sE v0 s3E v0 S3TI v0 3E v0 38 v0 30 po antrtTOM
13. Add the bulk density for the seven layers 1 31 1 59 1 3 1 38 1 41 1 52 1 56 g cm Disp 1 cm Button Next Solute Transport Boundary conditions Upper Boundary Condition Concentration Flux BC Lower Boundary Condition Zero Concentration Gradient 61 Time Variable Boundary Conditions Time days cTop cBot 27 9 3001 4001 28 9 3002 4001 80 3001 4001 Soil Profile Graphical Editor Button Edit Condition Select with the mouse nodes 8 to 19 specify Material 2 nodes 20 to 24 specify Material 3 nodes 25 to 28 specify Material 4 nodes 29 to 50 specify Material 5 nodes 51 to 75 specify Material 6 nodes 76 to 100 specify Material 7 Menu Conditions gt Initial Conditions gt Pressure Head Button Edit Condition Select AII Top Value 128 3 Bottom Value 28 3 Deselect Use top value for both Menu Conditions gt Observation Points Button Insert Insert 4 observation nodes one every 25 cm Menu File gt Save Data Menu File Exit Soil Profile Summary Button OK Solute Transport HP1 definitions Geochemical Model Button Exchange Add for each layer the cation exchange complex X with its size in mol 1000cm of soil Equilibrate each cation exchange complex with the corresponding initial solution for a particular soil layer i e 1001 to 1007 EXCHANGE 1 7 Layer 1G X 0 216 equilibrate with solution 1001 EXCHANGE 8 19 GLayer 28 X 0 072 equilibrate with solution
14. Gypsum and Calcite and Transport of Cd ssssssss 40 4 2 1 Problemi Definitionen nan rb Ra HG uU ot A 40 4 2 2 EDU isi bees e p ER Re asd sed DATUR Uds qa easi iu iil tita NO rase dedu iue P i UR Mead 40 4 2 3 usi aE 42 4 3 Dissolution of gypsum and calcite and transport of Cd the effect of higher Cl concentrations on the Cd mobility sos acne etr estas datu dede Ete ue tbt a uiss aspe dun Ee ice 43 4 3 1 Problem Deftones ie eite peor t ods ota Ret dts URB ed odds 43 4 3 2 ojos Dm 43 4 3 3 OO aes ot ca Eu i Nube ENS ME ED LA DLE MIA LE 44 4 4 Transport and Cation Exchange Single Pulse essen 46 4 4 1 Problem Deftione s ausos eei rose set ra bp acd nisu p nds mitad phe aid 46 4 4 2 Input ence E bee dite plated te gn vp e A ta dee Cana akc VERA CU Een 46 4 4 3 ODIUUE S s oda du nda Etats n ue Le S pu ease SH 49 4 5 Transport and Cation Exchange Multiple Pulses esee 51 4 5 1 Problem Definition iiie estie ive ro justo eti dn eder elec etg 5 4 5 2 Mputa e NT ST e E On EOS PEDE EDD TUE BC POETE 51 4 5 3 CUI UE seo casi esu E Ed uM M LL MM EE 53 4 6 X Transport of Cations and Heavy Metals in a Multi Layered Soil 54 4 6 1 Backeroutiqd au ioi dotata eati ades basi ave eM nee abe Ls ia uo Regu 54 4 6 2 Problem Definition seii tete eei oa deals itin pras ed e ra eI A Re tR e 54 4 6 3 Cation Exchange Capac ieee
15. HYDRUS ID projects Depending on the choice of selected processes models and options a number of pre processing menus will be displayed Options which are not available in HP1 are disabled in the HID GUI The main difference between HYDRUS 1D and HP1 projects is that the Solute Transport Solution Reaction Parameters dialog window which is not needed in HP1 is replaced by the HP1 Definitions dialog window 2 5 Define the Thermodynamic Database The definition of the thermodynamic database is in the HP1 Components and Database Pathway dialog window Using the Browse button it is possible to 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 is installed with HYDRUS 1D 2 6 Define Components The element names of components are defined in the HP1 Components and Database Pathway dialog window The number of components is specified in the Solute Transport General Information dialog window 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 HID GUI in the editor Addition to the thermodynamic database of the HP1 Definitions dialog window see paragraph 2 7 4 Three special components are Total O a co
16. Head Solute Transport General Information Stability Criteria 0 25 to limit the time step Number of Solutes 6 Button Next Solute Transport HP1 Components and Database Pathway Six Components Total O Total H Ca C 4 Cl S 6 Note Redox sensitive components should be entered with the secondary master species ie with their valence state between brackets The primary master species of a redox sensitive component i e the element name without a valence state is not recognized as a component to be transported Therefore the primary master species C can not 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 will not check if a correct master species is entered Since 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 34 Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Define the initial condition i e the solution composition of water in the soil column with the solution number 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 i e the solution composition of water entering the soil column with the solution
17. Initial and Boundary Solutions Compositions of the initial and boundary solutions are defined using the editor Definitions of Solution Compositions in the HP1 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 HID GUI The following solution composition numbering is used throughout this manual 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 phase e Numbers 3001 4000 to define upper boundary solutions e Numbers 4001 5000 to define lower boundary solutions The link between the initial solution composition numbers and the spatial distribution is defined in the Soil Profile Summary dialog window The link between the boundary solution composition numbers and the boundary conditions is defined in the Solute Transport Boundary condition dialog window or the Variable Boundary Conditions dialog window 2 7 6 Define the Geochemical Model The definition of the geochemical model is done using the editor Geochemical Model in the HP1 Definitions dialog window and it typically involves the following PHREEQC data blocks e EXCHANGE e EQUILIBRIUM PHASES e SURFACE e KINETICS e SOLID_SOLUTIONS There is currently no automatic li
18. Mg 2 Mg0 5G log_k 0 383 Button OK Definitions of Solution Compositions e Define the initial solution as solution 1001 e Define the boundary solution as solution 3001 e Assume that the solutions are in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide solution 1001 initial solution pH 5 2 68 Cl 1 Ca 20 K 2 Na 5 Mg 7 5 C 4 1 CO2 g 3 5 O 0 1 O2 g 0 68 S 6 1 charge solution 3001 boundary solution pH 3 2 Ca 2 345 Na 10 K 20 CI 35 C 4 1 CO2 g 3 5 O 0 1 02 g 0 68 S 6 1 charge Button OK Geochemical Model Define an exchange assemblage for 101 nodes Equilibrate the exchange sites with the initial solution Exchange 1 101 G 0 09625 equilibrate with solution 1001 Button OK Additional Output Add SELECTED OUTPUT to ask for output of total concentrations of the components Add USER PUNCH to save the absorbed concentrations as meq kg soil The default output in HP1 for an exchange species is mol kg water This can be asked by molalities NaG in SELECTED OUTPUT or as a BASIC statement 10 punch mol NaG in USER PUNCH BASIC statements to convert mol kg water to meq kg soil can be added to USER PUNCH The following two variables are needed o The bulk density use the HPl specific BASIC statement bulkdensity number where number is the cell number of a given node to obtain the bulk density for a given node The number of the cell i
19. Uncheck Water Flow steady state saturated water flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Depth of the Soil Profile 200 cm Button Next Time Information Final Time 150 days Initial Time Step 1 E 5 days Minimum Time Step 1E 5 days Maximum Time Step 0 25 days Button Next Print Information Unselect T Level information Select Print at Regular Time Interval Time Interval 1 day Print Times Number of Print times 5 Button Next Print Times Button Default Button OK HP1 Print and Punch Controls Check Make GNUplot Templates Button Next Water Flow Iteration Criteria Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters Qs 0 5 Ks 1 em days Button Next Water Flow Boundary Conditions 80 Upper Boundary Condition Constant Pressure Head Lower Boundary Condition Free drainage Solute Transport General Information Stability Criteria 0 25 Number of Solutes 9 Button Next Solute Transport HP1 Components and Database Pathway Six Components Total O Total H Pce Tce Dcecis Dcetrans Dceee Vc and Eth Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Additions to Thermodynamic Database Define new solution master species Define new solution species Define Rate equations SOLU
20. 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 one of the authors at Diederik Jacques Tel 32 14 333209 Fax 32 14 323553 Email djacques skcen be Jirka Sim nek Tel 1 951 827 7854 Fax 1 951 827 3993 Email jiri simunek ucr edu xi LIST OF TABLES Table 1 Hydrological transport and reaction parameters for the example SEASONCHAIN eee eeeeeee 22 Table 2 Initial and inflow concentrations for the example CA TEX CH eere e eee etes eene teen etna tn sen tn senatu 24 Table 3 pH and solution concentrations used in the simulation umol LO eRe RCO RO ae ein dum csi 29 Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers Seuntjens 2000 29 Table 5 Overview of aqueous equilibrium reactions and corresponding equilibrium constants data from phreeqc dat database Parkhurst and Appelo 1999 s ssssseressessssssssscssssscescssssssesssessesesscescssssssssenesssseesees 29 Table 6 Log K parameters for multi site exchange complex eere eee e eese seen eese enean tasas enses enses tn 30 Table 7 Soil hydraulic and other properties of six soil horizons from Seuntjens 2000 eee 55 Table 8 Initial pH and concentration for 9 components eere e
21. cm of soil 4 6 4 Input Project Manager Button New Name CatExch Description Cation exchange in a multilayered soil Button OK Main Processes Heading Cation exchange in a multilayered soil Check Water Flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Lenghts Units cm Number of Soil Materials 7 Depth of the Soil Profile 100 cm Button Next Time Information Final Time 80 days Initial Time Step 0 001 days Minimum Time Step 1E 5 days Maximum Time Step 0 5 days Check Time Variable Boundary Conditions Number of Time Variable Boundary Records 3 Button Next Print Information Unselect T Level information Select Print at Regular Time Interval Time Interval 0 5 days Print Times Number of Print times 4 Button Next Print Times Button Default 57 Button OK HP1 Print and Punch Controls Check Make GNUplot Templates Button Next Water Flow Iteration Criteria Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters Insert the hydraulic properties from Table 7 Water Flow Parameters x Button Next Water Flow Boundary Conditions Upper Boundary Condition Constant Flux Lower Boundary Condition Constant Pressure Head Water Flow Constant Boundary Fluxes Upper Boundary Flux 1 cm day downward flux Solute Tr
22. et al 1997 A S A C In To 1 12 pe Kl S Fs n 04 12 1 o cm A H ACT 13 3 zl Ip o ug 1 A A C n 14 4 7 308R Gp n 10 14 Calculate coefficients 41 45 and 44 Answer Aj 127 10 45 5612 A4 7 42 64 4 10 2 Input Project Manager Select project TCE 1 86 Button Copy New Name TCE 2 Description TCE first order degradation network initial value problem Button OK Main Processes Heading TCE first order degradation network initial value problem Button OK Solute Transport HP1 Definitions Addition to Thermodynamic Database Add the definition of the solid phase TCE PHASES PCE lq Pce Pce analytical expression 127 10 0 5612 42 64 0 Definitions of Solution Compositions Define an initial solution 1002 in equilibrium with the PCE_lq phase Define a pure water boundary solution solution 1002 initial solution top layer Pce 1 Pce_lg 0 solution 3001 boundary solution Button OK Geochemical Model Add initial pollution in the top 50 cm Equilibrium phases 1 26 PCE_lq 0 0 01 Button OK Additional Output Add PCE Iq to equilibrium_phases selected_output totals Pce Tce Dcecis Dcetrans Dceee Vc Eth equilibrium phases PCE lq Button OK Button OK Soil Profile Graphical Editor Menu Conditions gt Initial Conditions gt Concentrations Concentration number 1 Button Edit Condition Select nodes
23. high Cl concentrations enter the system after 1 day Note that in the case of a constant low Cl concentration the Cd peak does not pass the depth of 20 cm until after 2 5 days In the case when a high Cl concentration enters the system after 1 day the otavite dissolution front does not follow the calcite dissolution front as was observed in the case when a constant low Cl concentration enters the system Otavite dissolution follows the Cl concentration 4 5e 006 3 5e 006 3e 006 ss m 2 5e 006 i 26 008 esos metae e tee 1 5e 006 1 16 006 5e 007 4 0 0 5 1 1 5 2 2 5 Time days Total concentration of Cd mol kg water Total concentration of Cd mol kg water 0 Distance cm Distance cm 50 50 i T i T i T i T i T i T i T i T i T 0 1e 006 2e 006 3e 006 4e 006 5e 006 6e 00 0 5e 007 1e 006 1 5e 006 2e 006 2 5e 00 otavite mol 1000 cm of soil otavite mol 1000 cm of soil 0 days 1 00 days 2 00 days 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 0 50 days 1 50 days 2 50 days Figure 18 Comparison between a simulation when a solution with a low Cl concentration enters the system described in paragraph 4 2 left figures and a simulation when a solution with a high Cl concentration enters the system after 1 day described in paragraph 4 3 right figures for time serie
24. in the blocks GENERAL to GEOCHEMICAL in the Phreegc in Input File but not during the TRANSPORT calculations This option is recommended because otherwise an enormous amount of output will be generated during the transport calculations The running time will also increase when all the geochemical information is written into p reeqc out Selected output file xxx hse The name of the selected output file is defined in the Fi e Name text box of the HP1 Print and Punch Controls dialog window Information which is printed into this file is status solution number time depth options selected in the Selected Output section of the HP1 Print and Punch Controls dialog window and options the user defines using the PHREEQC data block SELECTED OUTPUT in the text editor Additional Output of the Solute Transport HP1 Definitions dialog window When the user selects only the option that punch times and locations are controlled by HYDRUS see the HP1 Print and Punch Controls dialog window the selected output file contains only information for the initial PHREEQC calculations i e the PHREEQC calculations before the TRANSPORT keyword Geochemical information during the transport calculations is saved in output files described below When the user selects the option that punch times and locations are controlled by PHREEQC see the HP1 Print and Punch Controls dialog window geochemical information during the transport calculations is a
25. information from the H1D GUI and print punch and dump related identifiers as defined in the HP1 Print and Punch Controls dialog window All relevant identifiers for the TRANSPORT keyword are defined using the HID GUI This block is automatically updated by the HID GUI when the project is saved 2 7 3 Modify the Structured phreeqc in File The user can modify the pAreeqc in file using the four editors in the HP1 definitions dialog window HP1 Definitions x m PHREEQC Definitions Additions to Thermodynamic Database OK Definitions of Solution Compositions Cancel Recommendation Geochemical model should be Previous defined only after the soil profile is spatially discretized Geochemical Model Nest Additional Output Help didis 2 7 4 Define Additions to the Thermodynamic Database Additional thermodynamic definitions are added to the pAreeqc in file not to the thermodynamic database file using the editor Additions to Thermodynamic Database in the HP1 Definitions dialog window Typical PHREEQC data blocks used here are e SOLUTION MASTER SPECIES e SOLUTION SPECI e PHASES ES e EXCHANGE MASTER SPECIES e EXCHANGE SPECI ES 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 2 7 5 Define the Composition of
26. mol end Define the initial c e Pure water solution 1001 LOS Definitions of Solution Compositions ondition 1001 Define the boundary condition 3001 Pce concentration initial solution solution 3001 Pce 10 boundary solution 82 Button OK Geochemical Model Define for each node the geochemical model i e KINETIC keywords KINETICS 1 101 Layer 16 PCEdegrad formula Pce 1 0 Tce 0 79 parms 0 075 TCEdegrad formula Tce 1 0 Dcecis 0 5328 Dcetrans 0 111 Dceee 0 0962 parms 0 070 DCEcisdegrad formula Dcecis 1 0 Vc 0 64 parms 0 020 DCEtransdegrad formula Dcetrans 1 0 Vc 0 64 parms 0 035 DCEeedegrad formula Dceee 1 0 Vc 0 64 parms 0 055 VCdegrad formula Vc 1 00 Eth 0 45 parms 0 030 ETHdegrad formula Eth 1 00 parms 0 000001 Button OK Additional Output Define the additional output to be written to selected output files selected output totals Pce Tce Dcecis Dcetrans Dceee Vc Eth Button OK Button Next Solute Transport Solute Transport Parameters Bulk density 1 5 g cm Disp 10 cm Button Next Solute Transport Boundary conditions Upper Boundary Condition Bound Cond 3001 83 Soil Profile Graphical Editor Menu Conditions gt Initial Conditions gt Pressure Head Button Edit Condition Select All Top Value 0 Menu Conditions gt Observation Points Button Insert Ins
27. number 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 0 68 save solution 1001 end solution 3001 units mmol kgw pH 7 charge Cl 2 Ca 1 O 0 1 O02 g 0 68 C 4 1 CO2 g 3 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 1000 cm soil i e 2 176 x 10 mol kg soil 1 8 kg 1000 cm soil Equilibrium phases 1 101 gypsum 0 3 9E 5 calcite 0 3 9E 5 O2 g 0 68 Button OK 35 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 Bulk D 1 8 g cm Disp 1 cm Button Next Solute Transport Boundary conditions Upper Boundary Condition Bound Cond 3001 Soil Profile Graphical Editor Menu Conditions gt Initial Conditions gt Pressure Head Button Edit Condition Select AII Top Value 0 Menu Conditions gt Observation Points Button Insert Insert 5 observation nodes one for every 10 cm Menu File gt Save Data Menu File Exit Soil Profile Summary Button Nex
28. pH 7 charge Cl 2 Ca 1 O 0 1 O2 g 0 68 41 C 4 1 CO2 g 3 5 Cd 1E 3 Button OK Geochemical Model Add the mineral otavite to the EQUILIBRIUM_PHASES assemblage and define its initial amount equilibrium phases 1 101 gypsum 0 3 9E 5 calcite 0 3 9E 5 Otavite 0 1E 10 O2 g 0 68 Button OK Additional Output Add Cd to the list of totals Add otavite to the list of equilibrium phases Add a USER PUNCH to calculate the percentage of Cd in solution selected output totals Ca Cl S C Cd equilibrium phases gypsum calcite otavite user punch headings Percentage Cd in solution start 10 if Sys Cd gt 0 then perCd 100 tot Cd tot water sys Cd else perCd 0 20 punch perCd end Note on headings A specific format of the headings can be used to have an appropriate labeling of the axes in the GNUPLOT templates The underscore _ is interpreted as a white space the symbol separates the name of a variable from its unit Thus for the headings defined above the corresponding axis text in the GNUPLOT template is Percentage Cd in solution Button OK Button OK Run Application 42 4 2 3 Output Profiles of Cd otavite and percentage of Cd in the solution are shown in Figure 17 The plot of the percentage of Cd in the solution is generated by opening the file pd_user Percentage Cd in solution plt using GNUPLOT USER PUNCH variables are indicated by use
29. reactions The exchange coefficients for major cations and heavy metals were assumed to be the same for all exchange sites Table 6 gives parameters for this multi site exchange complex Selected results are shown in Figure 13 and Figure 14 Table 6 Log K parameters for multi site exchange complex Y NaY KY MgY CaY CdY PbY ZnY exchanger 1 0 0 3 0 4 0 2 0 2 0 05 0 2 HY HYa HYb HYc HYd HYe HYf 1 65 33 4 95 6 85 9 6 12 35 The value for NaY is taken from Appelo et al 1998 Values for the other complexes are taken from the phreeqc dat database Parkhurst and Appelo 1999 and adapted relative to the K for NaY Values taken from Appelo et al 1998 9 f 1 2 ncs 14 cs E E 5 0 8 4 d E i oO I i Ed i d 9 0 6 ics E i eee 2044 N i o 3 0 a ae ee 0 0 25 0 5 0 75 1 0 0 25 0 5 0 75 1 Time years Time years 0 5 m 0 5m Figure 13 Outflow curves of pH left and Cd right for the example MCATEXCH 31 0 E o2 E o o o 4 o S S 03 a a a E Mee Reo dS RM 0 5 3 9 0 0 2 0 4 0 6 0 8 1 1 2 Cd umol kg water 1 mE 0 years 0 70 years 0 yearss 0 70 yearss 0 30 years 1 00 years 0 30 yearss 1 00 yearss 0 50 years 0 50 yearss 0 0 0 1 E 0 2 z 8 ri c q o 3 03 i 5 H e a l 0 4 4 de 05 i i 2 0 0 1 0 2 0 3 0 4 0 5 0 6 1 Hsite over to
30. sequential transformation reactions Journal of Environmental Quality 30 1354 1360 Jacques D and J Sim nek 2005 User manual of the multicomponent variably saturated flow and transport model HP1 Description Verification and Examples Version 1 0 BLG 998 SCK CEN Belgium Jacques D J Sim nek D Mallants and M Th van Genuchten 2008a Coupling hydrological and chemical proceses in the vadose zone A case study on long term uranium migration following mineral P fertilization Vadose Zone Journal 7 698 711 Jacques D J im nek D Mallants and M Th van Genuchten 2008b Detailled modeling of coupled water flow solute transport and geochemical reactions Migration of heavy metals in a podzol soil profile Geoderma 145 449 461 Jacques D J Sim nek M Th van Genuchten and D Mallants 2006 Operator splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles Journal of Contaminant Hydrology 88 197 218 Knauss K G M J Dibley R N Leif D A Mew and R D Aines 2000 The aqueous solubility of trichloroethene TCE an dtetrachloroethene PCE as a function of temperature Applied Geochemistry 15 501 512 Langmuir D 1997 Aqueous environmental geochemistry Prentice Hall New Jersey Parkhurst D L and C A J Appelo 1999 User s guide to PHREEQC Version 2 A computer program for speciation batch reacti
31. the HP1 manual Jacques and im nek 2005 Starting with version 4 0 of HYDRUS 1D the HID GUI provided more support to HP1 One additional pre processing menu allowed one to define the thermodynamic database and the components i e the species in file was automatically created by the HID GUI In addition HP1 projects were managed by the Project Manager and HP1 was executed from the HID GUI Later HYDRUS 1D versions starting with version 4 06 also included an option to create a template of the phreegqc in file but editing of this file was still done outside of the HID GUI In version 4 13 of HYDRUS 1D the user can create a HP1 project using the HID GUI without the need to use any external programs The GUI of version 4 13 of HYDRUS 1D allows one to create a structured pAreeqc in file which can be defined and or modified using the HID GUI see paragraph 2 7 Note that projects created with previous versions of HP1 or HYDRUS 1D can be opened and executed with the GUI of version 4 13 of HYDRUS 1D Furthermore the user can still create the pAreeqc in file in an ASCII text editor or graphical user interface of PHREEQC Another major difference between version 2 2 002 of HP1 and its older versions is the possibility to define the composition of the initial and boundary solutions in the phreegc in file However the spatial distribution of the initial solutions and the temporal variations of the boundary solutions are defined using the HID GUI
32. water Ca 20 mmol kg water K 2 mmol kg water Na 5 mmol kg water Mg 7 5 mmol kg water and C 4 1 mmol kg water The pH is 5 2 and the solution contains an unknown concentration of SOF as a major anion The inflowing solution has the following composition Ca 0 002345 mol kg water Na 0 01 mol kg water K 0 0201 mol kg water Mg 0 and CI 0 035 mol kgw The pH is 3 2 and the solution contains an unknown concentration of SO as major anion Look at profile data of the water content pH concentrations of the cations and anions and the amount of sorbed cations Express sorbed concentration in meq kg soil 4 7 2 Definition of the Geochemical Model and its Parameters 1 The CEC should be expressed in mol 1000 cm of soil in HP1 Recalculate the amount of CEC 65 Answer 0 09625 mol 1000 cm soil 2 Define the thermodynamic data for describing the exchange process with the Gapon convention and the Gapon selectivity coefficients A new master exchange species have to be defined say G The exchange reactions Eq 2 have to be written in terms of half reactions G K KG 4 G Na NaG 5 G 0 5 Ca 2 Ca0 5G 6 G 0 5 Mg 2 Mg0 5G 7 with appropriate values of the exchange coefficients Thus log Kox log Kana log Kaca and log Kgmg are needed for equations 4 5 6 and 7 respectively It is assumed that the Kg value for the half reaction with Na is 1 i e log Kena
33. 0 MgOH H 6 X H 0 XOH H 8 96 7 X 2H 0 X OH 2 H 16 90 8 X 3H 0 X OH 3 H 28 40 9 X 4H 0 X OH j 4H 41 20 10 X cr xcr 0 43 11 X 2Cr XCl 0 45 12 X 3 CT XCI 0 5 13 X 4Cr xcly 0 2 The soil profile is assumed to contain five distinct layers with different soil hydraulic properties and cation exchange capacities Table 4 gives thicknesses of the different horizons parameters for the van Genuchten s equations for the water retention and hydraulic conductivity functions van Genuchten 1980 and the total cation exchange capacities The higher exchange capacities of the Bh1 and Bh2 horizons reflect their enrichment with the immobilized organic matter Flow is assumed to be steady at a constant flux of 0 05 m day 18 25 m year which causes the soil profile to be unsaturated water contents vary between 0 37 and 0 15 as a function of depth The 30 bottom boundary condition for water flow is free drainage HY DRUS 1D was used to calculate the steady state water content profile corresponding to these boundary conditions The dispersivity and diffusion coefficient were taken to be 0 05 m and 9 2 10 m s respectively An overview of the considered aqueous equilibrium reactions is given in Table 5 The role of chloride as a complexing agent is described by reactions 10 through 13 Other geochemical reactions that are considered are the heterogeneous multi site ion exchange
34. 0 0 0001 0 0002 0 0003 Total concentration of Cd mol kg water Distance cm Distance cm ON Ln PEL PPE POE 0 0 001 0 002 0 003 0 004 0 005 Total concentration of Ca mol kg water L 4 O 0 00010 00020 00030 00040 00050 0006 Total concentration of Zn mol kg water 0 days 0 50 days 1 00 days 3 00 days 9 00 days 15 00 days 0 days 0 50 days 1 00 days 3 00 days 9 00 days 15 00 days Figure 10 Profiles of pH top left Ca top right Cd bottom left and Zn bottom right at selected times for the example CATEXCH 27 0 days 0 days 0 50 days 0 50 days 1 00 days 1 00 days 3 00 days 3 00 days 9 00 days 9 00 days 15 00 days 15 00 days E Ee 2 2 8 8 c s s i2 vD a B glo 0 dg T R eee e E S 0 0 0005 0 001 0 0015 0 002 0 0025 0 0 002 0 004 0 006 0 008 0 01 KX mol kg water CaX2 mol kg water 0 days 0 days 0 50 days 0 50 days 1 00 days 1 00 days 3 00 days 3 00 days 9 00 days 9 00 days 15 00 days 15 00 days E E7 S S 8 8 f G s s i2 D a d amp id coe ee ae gloire ee O 0 0001 0 0002 0 0003 0 0004 0 0005 O 0 00030 00060 00090 00120 00150 0018 CdX2 mol kg water ZnX2 mol kg water Figure 11 Profiles of molalities of sorbed K top left Ca top right Cd bottom left and Zn bottom right at selected
35. 0 40 60 80 100 120 140 160 Time day TCE trans DCE Eth PCE 1 1 DCE cis DCE a VG Figure 35 Outflow concentrations for the example described in section 4 11 91 92 4 12 Coupled Nta Degradation and Biomass Growth 4 12 1 Background The exercise is based on example 15 from the PHREEQC 2 manual Parkhurst and Appel 1999 and on the paper of Tebes Stevens et al 1998 The main topic is the biodegradation of nitrylotriacetate Nta The degradation of Nta in presence of oxygen and biomass is written as HNta amp 1 6205 1 272H 0 2 424H 15 0 576C5H7O2N 3 12H CO 4 0424NHj where HNta is CeHzO N A multiplicative Monod rate expression is used to describe the Nta degradation Runta2 4m Xn CHNTA i 702 16 Ks Cyntra 2 A Ka Coo where Rynraz is the rate of degradation mol l hr gm is the maximum specific rate 1 418E 3 mol g cells hr Xm is the biomass initially 1 36E 4 g cells per liter of water K is the half saturation constant for substrate 7 64E 7 mol l and Ka is the half saturation constant for acceptor 6 25e 6mol l The biomass production is described as Reens YRynta 2 5 bXm 17 where Reens is the rate of cell growth g cells L hr Y is the microbial yield coefficient 65 14 g cells mol Nta and b is the first order biomass decay coefficient 0 00208 hr The two equations 16 and 17 are coupled Eq 16 needs the current amount of biomass w
36. 03 E eL ss 01002 etel 0 001 LL ss T T T T 0 3 6 9 12 15 Time days 2 0 cm 6 0 cm 4 0 cm 8 0 cm 0 3 0 mr 6 9 12 15 Time days 2 0 cm 6 0 cm 4 0 cm 8 0 cm Figure 8 Time series of pH top left total concentrations of Ca top right Cd bottom left and Zn bottom right at four depths for the example CATEXCH 0 0025 0 002 4 X mol kg water 0 001 4 0 0005 Ne 0 0005 3 6 9 12 Time days 2 0 cm pu 6 0 cm 4 0 cm 8 0 cm 0 0004 mol kg water eo e e Q N CdX2 0 0003 0 0001 Heroiinin 3 6 9 12 Time days 2 0 cm mE 6 0 cm 4 0 cm 8 0 cm 0 01 mol kg water CaX2 Time days 2 0 cm 6 0 cm 4 0 cm 8 0 cm 0 0018 0 0015 1 NEN ZnX2 mol kg water 0 0009 edet 0 00122 Nered NA e 0 0009 res aN rs een 0 0006 ee ij 6 9 12 15 Q2 Time days 2 0 cm 6 0 cm 4 0 cm A 8 0 cm Figure 9 Time series of molalities of sorbed K top left Ca top right Cd bottom left and Zn bottom right at four depths for the example CATEXCH 25 26 0 days 0 50 days 1 00 days 3 00 days 9 00 days 15 00 days Distance cm 0 days 0 50 days 1 00 days 3 00 days 9 00 days 15 00 days Distance cm T i i T
37. 1 solution 3001 pH 7 charge units mol kgw O 0 6 25E 005 C 4 9E 7 Na 0 001 Cl 0 001 Nta 5 23E 6 Button OK Geochemical Model Define for each node the geochemical model i e KINETICS keywords kinetics 1 101 degradNTA formula Nta 1 C 3 12 H 1 968 O 4 848 N 0 424 parms 1 407E 3 7 64E 7 6 25e 6 biomass formula H 0 0 parms 65 14 0 00208 mO 50E 6 Button OK Additional Output Define the additional output to be written to selected output files SELECTED OUTPUT totals Nta kinetics biomass Button OK Button Next Solute Transport Solute Transport Parameters Disp 0 05 m Button Next Solute Transport Boundary conditions Upper Boundary Condition Bound Cond 3001 Soil Profile Graphical Editor 96 Menu Conditions gt Initial Conditions gt Pressure Head Button Edit Condition Select All Top Value 0 Menu Conditions gt Observation Points Button Insert Insert 5 observation nodes at a depth interval of 1 m Menu File gt Save Data Menu File Exit Soil Profile Summary Button Next Run Application 4 12 4 Output Time series and profiles of selected variables are shown in Figure 36 and Figure 37 5e 006 0 00025 4e 006 mm sh ME T S 3e 006 TOT ee TEM a 280084 d 4 Pa o ee ote DLOQO TI Lassus scenic le I MEN MENU AT MM Im biomass mol 1000 cm of soil Total concentr
38. 1 These examples are the verification examples that were described in the manual of HP1 version 1 0 Jacques and im nek 2005 Details on these examples and the corresponding HP1 input are given in Jacques and Sim nek 2005 and are not repeated here Graphs given below were generated using the GNUPLOT software based on the GNUPLOT templates generated with HP1 Note that some figures differ from those in the manual of HP1 version 1 0 Jacques and Sim nek 2005 because the temperature in the simulations reported here was 25 C whereas it was 20 C in the manual of version 1 0 of HP1 3 1 EqCI Physical Equilibrium Transport of Cl for Steady State Flow Conditions This problem simulates the transport of chloride a geochemically inert tracer during saturated steady state flow in a 20 cm long soil column The saturated hydraulic conductivity K is 1 cm d and the saturated water content is 0 5 cm cm The dispersivity is 8 cm Initially no Cl is present in the soil column The Cl concentration in the percolating water is 1 mmol kgw Simulated time series of Cl at two depths are shown in Figure 1 0 001 0 0009 0 0008 0 0007 0 0006 0 0005 _ 0 0004 0 0003 0 0002 0 0001 1 9 Total concentration of Cl mol kg water 0 Time days 10 0 cm 20 0 cm Figure 1 Time series of Cl at two depths for the example EQCL 3 2 NEQCL Physical Nonequilibrium Transport of Cl for Ste
39. 1 26 Solution composition 1002 Menu File gt Save Data Menu File Exit Run Application 4 10 3 Output Selected output is shown in Figure 32 and Figure 33 Distance cm Distance cm T T j T t 0 002 0 004 0 006 0 008 0 01 0 0 0003 0 0006 0 0009 0 0012 0 0015 0 001 PCE Iq mol 1000 cm of soil Total concentration of Pce mol kg water mE 0 days 60 00 days 120 00 days 0 days 60 00 days 120 00 days 30 00 days 90 00 days 150 00 days 30 00 days 90 00 days 150 00 days Figure 32 Profiles of the solid phase PCE_lq left and the aqueous concentrations of Pce right at selected print times for the example described in section 4 10 87 88 Concentration mol kg water Time day TCE trans DCE Eth PCE 1 1 DCE cis DCE VC Figure 33 Outflow concentrations for the example described in section 4 10 89 4 434 First Order Kinetic PCE Degradation Network Initial Source Trapped in Immobile Water Phase 4 11 1 Problem Definition It is assumed that the solid PCE phase is trapped in immobile zones in the soil profile instead of in the mobile aqueous phase as assumed in the example in section 4 10 Degradation reactions occur only in the mobile aqueous phase Assume the following properties in addition to those assigned in paragraph 4 10 the immobile water content 0 1 the first order exchange c
40. 1 ky 0 075 de First order degradation rate 2 ky 0 070 dq First order degradation rate 3 ks 0 020 d First order degradation rate 4 ka 0 035 d First order degradation rate 5 ks 0 055 d First order degradation rate 6 Ke 0 030 d First order degradation rate 7 ky 0 000001 d Distribution factor TCE to cis DCE on 0 72 Distribution factor TCE to trans DCE 0 15 Distribution factor TCE to 1 1 DCE 03 0 13 Yield coefficient PCE to TCE y 0 79 Yield coefficient TCE to DCE y2 0 74 Yield coefficient DCE to VC y3 0 64 Yield coefficient VC to ETH V4 0 45 4 9 2 Problem Definition In this example we will simulate the transport and degradation of PCE and its daughter products in a soil column Degradation not only occurs as sequential reactions but also partly as parallel degradation reactions see Figure 28 Degradation coefficients yield factors and distribution factors are given in Table 9 Saturated flow conditions in a 2 0 m long soil column are maintained for 150 days The inflowing solution contains only 10 mmol of PCE kg of water Physical properties of the soil are a porosity of 0 5 the saturated hydraulic conductivity of 1 cm day and a dispersivity of 10 cm Other soil hydraulic parameters are irrelevant for saturated conditions 4 9 3 Input Project Manager Button New Name TCE 1 Description TCE first order degradation network Button OK Main Processes Heading TCE first order degradation network
41. 1002 EXCHANGE 20 24 Layer 38 X 0 384 62 equilibrate with solution 1003 EXCHANGE 25 28 Layer 46 X 0 312 equilibrate with solution 1004 EXCHANGE 29 50 Layer 5Q X 0 075 equilibrate with solution 1005 EXCHANGE 51 76 Layer 6Q X 0 011 equilibrate with solution 1006 EXCHANGE 77 101 Layer 7Q X 0 007 equilibrate with solution 1007 Button OK Button OK Run Application 4 6 5 Output Time series of Cl Ca and Cd at selected depths are shown in Figure 23 Cd concentration increases when Cl concentration increases due to aqueous complexation between Cd and CI 63 0 035 Total concentration of Ca mol kg water Total concentration of Cl mol kg water d i l l f f 0 10 20 30 40 50 60 70 80 Time days Time days 25 0 cm 75 0 cm 25 0 cm 75 0 cm c 50 0 cm 100 0 cm 50 0 cm 100 0 cm 0 00025 0 0002 1 Ld ee 0 00015 0 0001 E WENN 5e 005 Total concentration of Cd mol kg water 0 10 20 30 40 50 60 70 80 Time days 25 0 cm 75 0 cm 50 0 cm 100 0 cm Figure 23 Time series of Cl top left Ca top right and Cd bottom concentrations at selected depths observation nodes for the example described in section 0 64 4 7 Horizontal Infiltration of Multiple Cations and Cation Exchange 4 7 1 Problem Definition This exercise simulates horizontal infiltrati
42. 2 released November 2009 is different with respect to following points amongst others e includes the computational module of version 4 0 of HYDRUS 1D e includes version 2 15 0 2697 of PHREEQC 2 e is based on the source code of the HYDRUS 1D computational module rewritten in double precision e considers new components Total O Total H and Charge to allow simulations of redox processes and surface complexation e allows initial concentrations of components to be zero e defines solution compositions using solution composition numbers e is fully integrated in the graphical user interface of version 4 13 of HYDRUS 1D This note provides an overview of how to set up and execute a HP1 project using version 2 2 002 of HP1 and version 4 13 of the graphical user interface GUI of HYDRUS 1D Chapter 2 describes how an HP1 project is created modified and executed using GUI of HYDRUS 1D Chapter 3 shows the implementation of the verification examples from the first manual Jacques and im nek 2005 using version 2 2 of HP1 Chapter 4 describes a number of simple HP1 projects and gives step by step instructions for their implementation using HP1 2 Running HP1 from the HYDRUS 1D Graphical User Interface HPI version 2 2 002 released 31 10 2009 is embedded in version 4 13 of HYDRUS 1D released 31 10 2009 The graphical user interface of HYDRUS 1D HID GUI provides support to the HP1 code in order to Manage HP projects using the Project M
43. 4 13 of the graphical user interface GUI of HYDRUS 1D Version 2 2 of HP1 is embedded in the graphical interface of version 4 13 of HYDRUS 1D The graphical user interface of HYDRUS 1D H1D GUI provides support to the HP1 code in order to Manage HP1 projects using the Project Manager Create new HP1 projects Define the physical part water flow solute transport heat transport Define the thermodynamic database Define the components for the transport problem Create the phreeqc in input file o Define additions to the thermodynamic database o Define the composition of the initial and boundary solutions o Define the geochemical model o Define the output e Define the spatial distribution of the initial solutions and the temporal variation of the boundary solutions Control output Create templates to produce graphs with GNUPLOT Run HP projects Display selected numerical results e Display the help file A large part of this note are step by step instructions for selected examples involving mineral dissolution and precipitation cation exchange surface complexation and kinetic degradation networks The implementation of variably saturated flow conditions changing boundary conditions a layered soil profile or immobile water is also illustrated Keywords HP1 reactive transport model variably saturated water flow multicomponent solute transport heat transport biogeochemical processes numerical model HYDRUS 1D Warranty The software has
44. 4 Define Additions to the Thermodynamic Database sess 8 2 7 5 Define the Composition of Initial and Boundary Solutions s 9 2 7 6 Define the Geochemical Model senate aet vitreo e re ERE E uae anne 9 2 7 7 Define the Outpt sirsiran iaaa hash ed aa papali teg o esha sates 10 2 8 Define the Spatial Distribution of the Initial Solutions and Temporal VariationS of the Boundary Solutions sesei or eb deed bae stas dnd dest me nana REA bia ae tue 10 2 9 Control Qutp t scc se Lt ob cen tede idens etes es ctu eN AC ra m es 11 2 9 1 Punch Times and Locations tete eee reinen odes cuapestasncgersanseviavedcraes 11 2 9 2 Selected OUtDUE coris Ip evite a ond eed ad itas boa ed sense eoa p oe 13 2 9 3 osx desi aisin o DEP 13 2 9 4 PHREEQG DUMP S soc to RI SER beu eei tema tatam usd a tte EDU 13 2 9 5 HP1 Output Files with Geochemical Information eee I3 2 10 Create Templates to Produce Graphs with GNUPLOT eee 15 Dall v R niing a HPI PIOIGCUS ere be vet POR Rel o ee e hob mtu cit e ardt 16 2 12 Looking at Selected Numerical Results ue e p oerte headed 16 233 Help Pies 5ioitesu ie eq er Erde ee e sata bx uit ds eect aA ia 16 Exaniples Installed with HP T use cpiccdis ote rad dt Ro Fm eae pe eed quie i AER Eai 18 3 1 EqCl Physical Equilibrium Transport of Cl for Steady State Flow Conditions 18 3 2 NEQCL Physical Nonequilibrium Transport of Cl for St
45. File gt Exit Soil Profile Summary Button Next Run Project 4 5 3 Output Figure 21 gives the K concentration at different depths in the profile Figure 22 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 0 0012 0 001 0 0008 0 0006 hL d 0 0004 0 0002 Total concentration of K mol kg water Time hours 2 0cm 6 0 cm 4 0 cm 8 0 cm Figure 21 Time series of K concentrations at four depths for the multiple pulse cation exchange example 54 0 0012 0 001 0 0008 0 0006 0 0004 Concentrations mol kg water 0 0002 30 Time hours cl Na K Ca Figure 22 Outflow concentrations for the multiple pulse cation exchange example 4 6 Transport of Cations and Heavy Metals in a Multi Layered Soil 4 6 1 Background Cation adsorption onto negatively charged solid surfaces can greatly affect the rate of the heavy metal transport in soils The degree of adsorption of a particular cation depends on its concentration the concentration of other cations in the soil solution and the adsorbed concentration of the major cations and heavy metals The competition between major cations and heavy metals for adsorption sites can be
46. In previous releases of HP1 initial solutions were defined only in the pAreeqc in file whereas boundary solutions were defined via the HID GUI Version 2 2 002 of HP1 defines solutions in terms of solution composition numbers instead of concentrations Solution composition numbers are used to define the spatial distribution of the initial solutions and the temporal variations of the boundary solutions in the HID GUI Concentrations of the components of a solution composition are defined in the phreeqc in file 2 2 Manage HP1 Projects HP1 projects are managed in the same way as HYDRUS 1D 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 2 3 Create a New Project A new HP1 project is created using the button New in the Project Manager After defining a name and a description of a project the Main Process dialog window allows users to select the HP1 model from available solute transport models x Heading Dissolution of calcite and gypsum Simulate qr M Water Flow Vapor Flo Snow Hydrolog IV Solute Transport C General Solute Transport Major lon Chemistr Lx Heat Transport Cancel Root Water Uptake Nm Root Growth Help 2 4 Define the Physical Part of a Project The physical part of a HP1 project water flow solute transport and heat transport is defined using the HID GUI in the same way as for
47. NnN 0 d0 0 d0 0 d0 0 d0 0 30 0 30 0 d0 DW OO CO OO CO CO CO 20 3L 20 39 20 38 20 s3E 20 36 20 38 c0 3L eD O oO m m i0 r e ap dp Uv Uv Uv Uv EaP d79 dp9 dv9 dv9 dv9 dv9 dp9 eN d69 d69 d69 d69 d69 d69 d69 TO zo uoztTzo0y IO uoztzo0y 2g uoziaou zya uozrxou Tug uozrxou a uozriaiou XV euoziaou lt Nn XO OO Pos 6 qc c c me mp os Hd uoradraoseg LOOT 900T SOOT vOOT 001 2001 TOOT aiequnuw aqvwauds NOILNTOS 60 solution 3001 pH 7 charge units mol kgw Ca 0 005 Cl 02 03 O 0 1 02 g 0 68 solution 3002 pH 7 charge units mol kgw Ca 0 05 CL 0s O 0 1 O2 g 0 68 solution 4001 pure water Button OK Geochemical Model The geochemical model will be defined after different layers of the soil profile have been defined using Soil Profile Graphical Editor Information about the distribution of different layers can then be used in the definition of the geochemical model see below Additional Output Define the additional output to be written to selected output files selected output totals Cd Ca Cl user punch headings Adsorbed Cd8mol kg soil start 10 bd bulkdensity cell no 40 PUNCH mol CdX2 tot water bd end Button OK Button Next Solute Transport Solute Transport Parameters
48. Series Time days 10 0 cm 40 0 cm 20 0 cm 50 0 cm 30 0 cm 0 016 0 012 4 0 008 0 004 1 Total concentration of Ca mol kg water olke 1T om 0 0 5 il 1 5 2 2 5 Time days 10 0 cm 40 0 cm 20 0 cm 50 0 cm 30 0 cm 4e 005 6 3e 005 4 t o S 2e 005 4 8 E 1e 005 4 Qa gt o 0 1 0 0 5 1 1 5 2 2 5 Time days aas 10 0 cm 40 0 cm e 20 0 cm 50 0 cm 30 0 cm Figure 16 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 Total concentration of C mol kg water Total concentration of S mol kg water calcite mol 1000 cm of soil o Ed o o a 5e 005 4e 005 3e 005 0 016 0 0 5 1 1 5 2 2 5 Time days i i 10 0 cm 40 0 cm 20 0 cm 50 0 cm 30 0 cm 0 012 4 0 008 4 1 0 004 4 0j 0 0 5 1 1 5 2 2 5 Time days m 10 0 cm 40 0 cm ies 20 0 cm 50 0 cm _ 30 0 cm 0 0 5 1 1 5 2 2 5 Time days n 10 0 cm 40 0 cm 20 0 cm 50 0 cm 39 40 4 0 Dissolution of Gypsum and Calcite and Transport of Cd
49. TION MASTER SPECIES Pce Pce 0 Pce Tce Tce 0 Tce Dcecis Dcecis 0 Dcecis Dcetrans Dcetrans 0 Dcetrans Dceee Dceee 0 Dceee Vc Vc 0 Vc Eth Eth 0 Eth SOLUTION SPECIES Pce Pce log k 0 0 Tce Tce log k 0 0 Dcecis Dcecis log k 0 0 Dcetrans Dcetrans log k 0 0 Dceee Dceee log k 0 0 Vc Vc log k 0 0 Eth Eth log k 0 0 RATES PCEdegrad start 10 REM parl k 20 rate parm 1 TOT water MOL Pce 30 moles rate TIME 40 SAVE moles end TCEdegrad start 10 REM parl k 20 rate parm 1 TOT water MOL Tce 30 moles rate TIME 81 40 SAVE moles end DC start 10 RI 20 rate 30 moles EM par1 parm 1 TOT water MOL Dcecis Ecisdegrad k ME rate TI 40 SAVE mol end DC start 10 RI 20 rate 30 moles EM parl parm 1 TOT water MOL Dcetrans Les Etransdegrad k rate TI ME 40 SAVE mol end DCEeedegrad start 10 REM parli parm 1 TOT water MOL Dceee 20 rate 30 moles Les k pate TI ME 40 SAVE mol end VCdegrad start 10 RI 20 rate 30 moles EM parl parm 1 TOT water MOL Vc LOGS k ME rate TI 40 SAVE mol end ETHdegrad start 10 RI 20 rate 30 moles EM par1 parm 1 TOT water MOL LES k Eth ME rate TI 40 SAVE
50. a node number x One file is created for each observation point o Obs node chemxim out for the time series of the immobile water phase for the observation point with a node number x One file is created for each observation point 13 o Node inf chem m out for the profile data of the mobile water phase o Node inf chem im out for the profile data of the immobile water phase If controlled by PHREEQC is checked the user can defined a series of punch cells e g 1 2 5 25 or 1 5 25 and a punch frequency The punch frequency indicates the number of time steps between printing of data All data are printed in a single output file The user specifies the name of the output file in the File name text box of the Selected Output section 2 9 2 Selected Output This submenu allows specifying a number of output variables to be written to the selected output files Additional variables can be specified using the PHREEQC data blocks SELECTED OUTPUT and USER PUNCH in the editor Additional Output of the HP1 Definitions dialog window It is not needed to specify a file name in the editor Additional Output 2 9 3 Print Options This submenu allows specifying the print times and locations to write geochemical information to the standard PHREEQC text output file phreeqc out Print locations can be linked to the HYDRUS observation points specified in the Soil Profile Graphical Editor module using the option HYDRUS Observation Nodes Alterna
51. acqeoeessesae masa eo boe MER RII qu ge Sb eb ED ES 56 4 6 4 Inpede tuns A M PL cM ce 56 4 6 5 nudo ea 62 4 7 Horizontal Infiltration of Multiple Cations and Cation Exchange 64 4 7 1 Problem PS TET OT oet be EO E d it aint naa acs b eS 64 4 7 2 Definition of the Geochemical Model and its Parameters ssssss 64 4 7 3 PUE AS cue Iu qr EU TE D TRE EU omnes nce conde een wee 66 4 7 4 uud aa a 69 4 8 U Transport and Surface CompleXatlOD uei veut v ety eno cute e toe b etn 72 4 8 1 Problem definitions s en aes ia E AE rM A a I ae 72 4 8 2 Calculation of the Size of the Surface Sorption Site sss 72 4 8 3 LEEY ejr i DAE TE T E 73 4 8 4 Outpt taa a eee a a V pM DM a LA UN E 76 4 9 First Order Kinetic PCE Degradation Network sese 77 4 9 1 Backeroufd c os aes e a bod ates ett A deponit ee oats e NN gales 77 4 9 2 Problem Definition cs seo deer eto vene TREE SESTO notus voa Re i 78 4 9 3 JEU oro sere Vier cit edite etx pesce is me ied at e tu EE MD UE 78 4 9 4 OUMU ren tee ntes bc n d cta e E Apa E a 83 4 10 First Order Kinetic PCE Degradation Network Leaching of Initial PCE Source 85 4 10 1 Background and Problem Definition esses 85 ZA UIBBUDS tede ote Mea LN Cu M COD NE 85 MANOS OUI eei s edi et me dA Me e Eam ess 87 4 11 First Order Kinetic PCE Degradation Networ
52. ady State Flow Conditions This problem simulates the transport of chloride a geochemically inert tracer during saturated steady state flow in a 20 cm long soil column The saturated hydraulic conductivity Ks is 1 cm d and the saturated water content is 0 5 cm cm The dispersivity is 8 cm the immobile water content m is 0 1 cm cm and the first order exchange coefficient is 0 01 d Initially no Cl is present in the soil column The Cl concentration in the percolating water is 1 mmol kgw Simulated time series of Cl at two depths are shown in Figure 2 Small changes in the GNUPLOT graphs presented here were made compared to the HP1 generated templates in order to improve the layout for this report Changes are related only to line colors thickness and text sizes These changes are easily done using the command line definition of GNUPLOT Verification problem 1 in Jacques and Sim nek 2005 Verification problem 1 in Jacques and Sim nek 2005 19 Total concentration of Cl mol kg water T T j T j T j T 0 10 20 30 40 50 Time days 10 0 cm 20 0 cm Figure 2 Time series of Cl at two depths for the example NEQCL 3 3 TRANSCL Physical Nonequilibrium Transport of Chloride for Transient Flow Conditions This problem simulates the transport of chloride through a 1 m deep soil profile subject to a transient upper boundary condition given by daily values of precipitation and evaporat
53. anager Create new HP1 projects Define the physical part water flow solute transport heat transport Define the thermodynamic database Define the components for the transport problem Create the phreeqc in input file o Define additions to the thermodynamic database o Define the composition of the initial and boundary solutions o Define the geochemical model o Define the output e Define the spatial distribution of the initial solutions and the temporal variation of the boundary solutions Control output Create templates to produce graphs with GNUPLOT Run HP projects Display selected numerical results Display the help file In chapter 4 a number of step by step examples are given to illustrate the implementation and execution of a HP1 project using the HID GUI A short description of the provided support is given in this chapter 2 1 Differences Between Version 2 2 002 of HP1 HYDRUS 1D Version 4 13 and Older Versions of HP1 and HYDRUS 1D Previous releases of HP1 were less embedded in the HID GUI No HID GUI support was available for the geochemical part of HP1 projects of versions 1 0 and 2 0 Users had to prepare the HP1 input files species in and phreeqc in in an ASCII text editor or graphical user interface for PHREEQC and saved them in the project directory In addition a path dat file was needed to identify the project directory HP1 itself was executed from the Windows Explorer or the Command Prompt Detailed instructions were given in
54. ance cm 750 9 4 gt 9 gt 750 4 9 9 a a SE S 5 5 6 6 5 7 7 5 8 8 5 9 9 5 5 5 6 6 5 7 7 5 8 8 5 9 9 5 pH pH 0 days 1 00 days 2 00 days 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 0 50 days 1 50 days 2 50 days 0 10 4 o o g 2 B30 J E a a 40 50 r i r i r i r 50 r i r i i r 0 0 004 0 008 0 012 0 016 0 004 0 008 0 012 0 016 Total concentration of Ca mol kg water Total concentration of S mol kg water 0 days 1 00 days 2 00 days 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 0 50 days 1 50 days 2 50 days 0 10 5 20 5 o o o o S S 5 30 E a a 40 80 50 1 1e 005 2e 005 3e 005 4e 00 6 1e 005 2e 005 3e 005 4e 005 5e 00 gypsum mol 1000 cm of soil calcite mol 1000 cm of soil 0 days 1 00 days 2 00 days 0 days 1 00 days 2 00 days 0 50 days 1 50 days 2 50 days 0 50 days 1 50 days 2 50 days Figure 15 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 4 1 5 Overview of Selected Results Time
55. ansport General Information Stability Criteria 0 25 Number of Solutes 12 Button Next Solute Transport HP1 Components and Database Pathway Twelve Components Total O Total H Na K Ca Mg Cd Zn Pb Cl Br C 4 Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Define the initial solutions for each of the seven layers Table 8 and use solution numbers 1001 1007 and the keyword SOLUTION_SPREAD 58 1001 A 1002 E 1003 Bhl 1004 Bh2 1005 BC 1006 Cl 1007 C2 seres e Use pH to obtain 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 Note columns of SOLUTION SPREAD as well as the headings and the subheadings must be tab delimited see PHREEQC 2 manual Parkhurst and Appelo 1999 A convenient way to prepare the input for the SOLUTION SPREAD keyword is to use MS Excel to make different input rows and columns and to copy it to the HID GUI A W c o E F c uH i s x L M N Number descri tion pH cl Na K Ca Mg Cd zn Pb Br O 0 C 4 charge 02 g 0 68 CO2 g 3 5 3 4 0 0690 6 40E 02 4 00E 03 9 70E 02 8 00E 03 8 00E 04 5 00E 02 2 50E 03 1 00E 03 1 00E 03 1 00E 03 3 5 0 0690 6 40E 02 4 00E 03 6 50E 02 8 00E 03 3 80E 04 2 40E 02 2 40E 02 1 00E 03 1 00E 03 1 00E 03 3 6 0 0690
56. ation of 6 x 10 M Both solutions were prepared under oxidizing conditions in equilibrium with the atmospheric partial pressure of oxygen The amount of exchange sites X is 1 1 meq 1000 cm 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 In this example only the outflow concentrations of Cl Ca Na and K are of interest 4 4 2 Input Project Manager Button New Name CEC 1 Description Transport and Cation Exchange single pulse Button OK Main Processes Heading Transport and Cation Exchange single pulse Uncheck Water Flow steady state water flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Depth of the soil profile 8 cm Button Next Time Information Time Units Seconds Note that you can also just put it in days this would also be OK Final Time 86400 s Initial Time Step 180 s Minimum Time Step 180 s Maximum Time Step 180 s Note constant time step to have the same conditions as in the original comparable PHREEQC calculations 47 Button Next Print Information Number of Print Times 12 Button Select Print Times Button Next Print Times Button Default Button OK HP1 Print and Punch Controls Button Next Water Flow Iteration Criteria Lower Time Step Multiplication Factor 1 Button Next Water Fl
57. ation of Nta mol kg water i i i H 0 i i 0 5 10 15 20 25 0 5 10 15 20 25 Time hours Time hours 1 0m 4 0m 1 0m 4 0m 2 0m 5 0m 2 0m 5 0m 3 0m 3 0m Figure 36 Time series of Nta concentrations and biomass at selected depths observation nodes for the example described in section 4 12 Distance m 5 bend 5e 006 Total concentration of Nta mol kg water ox een chere 0 1e 006 2e 006 3e 006 4e 006 0 hours 16 00 hours 4 00 hours 20 00 hours 8 00 hours 24 00 hours 12 00 hours Figure 37 Profiles of Nta concentrations and biomass at selected print times for the example described in section 4 12 6e 00 Distance m 5e 005 0 0001 0 00015 0 0002 biomass mol 1000 cm of soil 0 hours 16 00 hours 4 00 hours 20 00 hours 8 00 hours 24 00 hours 12 00 hours 0 0002 97 98 5 References Appelo C A J E Verweij and H Schafer 1998 A hydrogeochemical transport model for an oxidation experiment with pyrite calcite exchangers organic matter containing sand Applied geochemistry 13 257 268 Carsel R F and R S Parish 1988 Developing joint probability distributions of soil water retention characteristics Water Resources Research 24 755 769 Casey F M im nek J 2001 Inverse analyses of transport of chlorinated hydrocarbons subject to
58. base typically defined using the following PHREEQC data blocks SOLUTION MASTER SPECIES SOLUTION SPECIES OUTPUT SOLUTIONDEFINITION INITIAL GEOCHEMICAL TRANSPORT PHASES EXCHANGE MASTER_SPECIES EXCHANGE SPECIES SURFACE MASTER SPECIES SURFACE SPECIES and RATES The content is defined in the editor Additions to Thermodynamic Database of the Solute Transort HP1 Definition dialog window This block consists of two parts The first part starts with the PHREEQC keyword SELECTED OUTPUT followed by the information defined in the HP1 Print and Punch Controls dialog window This block is automatically updated by the HYDRUS GUI when the project is saved The second part contains additional specifications to be written to the output files and is typically defined using the following PHREEQC data blocks USER PUNCH USER PRINT and SELECTED OUTPUT The content is defined in the editor Additional Output of the Solute Transport HP1 Definitions dialog window This block contains the definitions of the initial solutions and boundary solutions The latter is only read from the phreeqc in input file when the radio button n Solution Compositions in the Solute Transport HP1 Components dialog window is selected The content is defined in the editor Definitions of Solution Composition of the Solute Transport HP1 Definitions dialog window This block contains definitions of the initial s
59. ction kinetics of the biodegradation depend on a variety of environmental conditions such as redox potential biomass and compounds affecting solubility the kinetics here is described independently of environmental conditions When the DCE dichloroethylene species are lumped the transport problem can be formulated as a transport of a single sequential degradation chain which can then be solved directly using HYDRUS ID e g Schaerlaekens et al 1999 Casey and Sim nek 2001 see also one of the HYDRUS 1D tutorials However the HP1 code can handle the full reaction network as defined in Figure 28 i e with three separate DCE species while considering different distribution factors a and yield coefficients 7 m cl H H H H jpn gt m CI Cl H Cl CI CI CI CI vc TCE c DCE PCE 1 2 DCE Figure 27 Perchloroethylene PCE degradation pathway Figure from Schaerlaekens et al 1999 78 1 cis DCE ks 5 Ya 7 VC ETH gt k YA k As PCE TCE trans DCE O3 1 1 DCE Figure 28 Degradation pathway of PCE using first order rate constants Table 9 Definition of parameters and their values for the PCE biodegradation problem from Case 1 and 2 in Sun et al 2004 Rate parameters are for a reference temperature of 20 C Parameter Symbol Values Unit Verification Velocity v 0 4 md Dispersion coefficient D 0 4 m d First order degradation rate
60. d thus the higher the cation exchange capacity This behavior is represented by a multi site cation exchange complex consisting of six sites each having a different selectivity coefficient for the exchange of protons see Appelo et al 1998 Finally chloride is present in the soil solutions resulting in the formation of aqueous complexes with the heavy metals Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers Seuntjens 2000 Horizon Layer 0 0 a n K l Cation exchange thickness em cm day capacity cm eq 1000 cm soil A 13 0 065 0 476 0 016 1 94 93 0 5 0 0183 E 10 0 035 0 416 0 015 321 311 0 5 0 0114 Bhl 5 0 042 0 472 0 016 1 52 39 0 5 0 0664 Bh2 5 0 044 0 455 0 028 2 0 860 0 5 0 0542 Bh C 17 0 039 0 464 0 023 2 99 1198 0 5 0 0116 Table 3 pH and solution concentrations used in the simulation umol I Solution pH Na K Ca Mg Br Cl Cd Pb Zn 0 28 cm depth 8 5 4019 120 98 5 780 0 O8 25 50 28 50 cm depth 85 4540 120 98 5 7800 0 00 0 0 Applied water 35 1275 120 98 5 7800 0 00 0 0 Concentration of Na is adjusted to obtain the desired pH Table 5 Overview of aqueous equilibrium reactions and corresponding equilibrium constants data from phreeqc dat database Parkhurst and Appelo 1999 Nr Aqueous speciation reaction Log K 1 H O OH H 14 2 Na H O NaOH H 14 18 3 K H 0 KOH H 14 46 4 Ca H O CaOH H 12 78 5 Mg H
61. described using a multicomponent equilibrium ion exchange approach e g Selim and Amacher 1997 and references therein In addition to major cations and heavy metals protons also adsorb to the solid surfaces Due to the acid base properties of the functional groups on the surfaces of minerals and organic matter the percentage of H adsorption decreases significantly with increasing pH This leads to an increased capacity of the surfaces to adsorb major cations and heavy metals at higher pH values This behavior can also be described by means of a multi site cation exchange complex consisting of several sites each having a different selectivity coefficient for the exchange of protons see also paragraph 3 9 Appelo et al 1998 for example used six sites to describe cation exchange in the presence of organic matter and Fe oxyhydroxides 4 6 2 Problem Definition This example simulates the migration of major cations and heavy metals in a multi layered 1 m deep soil profile using the multi site cation exchange model Soil hydraulic and physical parameters of the dry Spodosol located at the Kattenbos site near Lommel Belgium were taken from Seuntjens 2000 Tables 3 1 and 7 1 The cation exchange complex was assumed to be associated solely with organic matter The cation exchange capacity hence is directly related to the amount of exchangeable protons on the organic matter taken to be 6 meq g of the organic 55 matter proton d
62. e The sodium initially present in the column exchanges with the incoming caleium 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 51 4 5 Transport and Cation Exchange Multiple Pulses 4 5 1 Problem Definition This example is the same as the one described in paragraph 4 5 except that time variable concentrations are applied at the soil surface The following sequence of pulses is applied at the top boundary 0 8hr 6x 10 M CaCl 8 18 hr 5x 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 CaCL 1 x 10 M NaNO and 8 x 10 M KNO 4 5 2 Input Project Manager Click on CEC 1 Button Copy New Name CEC 2 Description Transport and Cation Exchange multiple pulses Button OK Open Main Processes Heading Transport and Cation Exchange multiple pulses Button Next Geometry Information Button Next Time Information Time Units hours Final Time 60 h
63. eady State Flow Conditions18 33 TRANSCL Physical Nonequilibrium Transport of Chloride for Transient Flow CONGIIONS EN 19 3 4 STADS Transport of nonlinearly adsorbed contaminant for steady state flow CODGOITIOIIS oio Decore tieni ubivis ebiobiediuus de uo cars Mousa aba nay une oM dea oiu erus 20 3 5 STDECAY Transport of Nonlinearly Adsorbing Contaminant with First Order Decay for Steady State Flow Conditions 4 4 2 ae d nant es pegar sed Ex e RERRE e RA You ed ERN Ie En edo RR EAE TIA 21 3 6 SEASONCHAIN First Order Decay Chain of Nonlinearly Adsorbing Contaminants D ring Unsteady FloW cones od D ieat a ae bie Sette o Ra a Sat eae eue lcu gu ee aaa qus 22 3 7 CATEXCH Transport of Heavy Metals Subject to Multiple Cation Exchange 29 3 8 MINDIS Transport with Mineral Dissolution essen 27 3 9 MCATEXCH Transport of Heavy Metals in a Porous Medium with a pH Dependent CauomExchause Complex sess att e NDS deci Sancta dessine aede d 28 Step By Step Instructions for Selected Examples sse 32 4 1 Dissolution of Gypsum and Calcite ire orte cred adead ba beue vito aea 32 4 1 1 Problem Definition ios o die eere dede etis EA dd Od CMM a TE 32 4 1 2 e td M CA E M uM E 32 4 1 3 orit E 35 vi 4 1 4 Overview of Selected Results Profile Data 38 4 1 5 Overview of Selected Results Time Series ssec onde e ee ranean nadvaaseasein 39 4 2 Dissolution of
64. ection 4 12 97 1 Introduction HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating reactive transport and biogeochemical processes in variably saturated porous media HP1 results from coupling the water and solute transport model HYDRUS 1D Sim nek et al 2009a and PHREEQC 2 Parkhurst and Appelo 1999 The combined code contains modules simulating 1 transient water flow in variably saturated media 2 transport of multiple components 3 mixed equilibrium kinetic biogeochemical reactions and 4 heat transport HP1 is a significant expansion of the individual HYDRUS 1D and PHREEQC programs by combining and preserving most of the features and capabilities of the two codes into a single numerical simulator The code uses the Richards equation for variably saturated flow and advection dispersion type equations for heat and solute transport The program can also simulate 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 equilibrium kinetics or mixed equilibrium kinetic reactions Various applications of HP1 were presented by Jacques and Sim nek 2005 Jacques et al 2006 2008a b and im nek et al 2006 2009b The first version of HP1 was released in November 2004 and is described in Jacques and Sim nek 2005 The HP1 version 2 2 00
65. ed in paragraph 4 9 0 0012 ee cet PN a cent 0 0008 0 0006 0 0004 0 0002 Concentration mol kg water Time day TCE trans DCE Eth PCE 1 1 DCE cis DCE VC Figure 31 Outflow curves for the example described in section 4 9 85 4 10 First Order Kinetic PCE Degradation Network Leaching of Initial PCE Source 4 10 1 Background and Problem Definition In this example the boundary condition problem described in paragraph 4 9 is changed to an initial condition problem It is assumed that the top 50 cm of the soil profile is contaminated with PCE We assume that the amount of non aqueous immobile PCE is 0 01 mol 1000 cm of soil Knauss et al 2000 reported the following partial molal thermodynamic quantities for the PCE liquid aqueous dissolution reaction AH 1790 J mol 8 A S 59 J mol K 9 ArC 354 6 J mol 10 where R is the gas constant 8 31441 J mol and A H AS and ArC are the change of entropy enthalpy and heat capacity of reaction at standard conditions To 298 K The following equation is used in PHREEQC to define the temperature dependence of solubility constants Parkhurst and Appelo 1999 log K A AT A A log T 2 11 Temperature dependence of the solubility coefficient can be described with a three term extrapolation expression with coefficients 4i 45 and 44 using the following relations Puigdomenech
66. ee eese eese n nennen enata th seta tuae en sone ta sens en sensns estu 55 Table 9 Definition of parameters and their values for the PCE biodegradation problem from Case 1 and 2 in Sun et al 2004 Rate parameters are for a reference temperature of 20 C ceca eerte eene enetnne 78 xli xiii LIST OF FIGURES Figure 1 Time series of Cl at two depths for the example EQCL 18 Figure 2 Time series of Cl at two depths for the example NEQCL 19 Figure 3 Time series of Cl concentrations in the mobile phase at four depths for the example TRANSCL 20 Figure 4 Profile plots of Cl concentrations in the mobile phase left and immobile phase right at selected times for the example TRANSCL 20 Figure 5 Profiles of Pola concentrations for the example STADS 21 Figure 6 Profiles of Pola concentrations for the example STDECAY 21 Figure 7 Profile plots of Conta Contb and Contc concentrations at selected times for the example SEASONCHAIN 23 Figure 8 Time series of pH top left total concentrations of Ca top right Cd bottom left and Zn bottom right at four depths for the example CATEXCH 24 Figure 9 Time series of molalities of sorbed K top left Ca top right Cd bottom left and Zn bottom right at four depths for the example CATEXCH 25 Figure 10 Profiles of pH top left Ca top right Cd bottom left and Zn bottom right at selected times for the example CATEXCH 26 Figure 11 Profi
67. elected print times during dissolution of calcite and gypsum and Cd transport 42 Figure 18 Comparison between a simulation when a solution with a low Cl concentration enters the system described in paragraph 4 2 left figures and a simulation when a solution with a high Cl concentration enters the system after 1 day described in paragraph 4 3 right figures for time series of Cd concentrations at different depths top figures and profiles of the amount of otavite bottom figures 44 Figure 19 Time series of Cl at selected depths observation nodes for the example described in section 4 3 45 Figure 20 Outflow concentrations of Cl Ca Na and K for the single pulse cation exchange example 50 Figure 21 Time series of K concentrations at four depths for the multiple pulse cation exchange example 53 Figure 22 Outflow concentrations for the multiple pulse cation exchange example 54 Figure 23 Time series of Cl top left Ca top right and Cd bottom concentrations at selected depths observation nodes for the example described in section 4 6 63 Figure 24 Profiles of water content top left and total aqueous concentrations of Cl Na K Ca and Mg at selected print times during horizontal infiltration of multiple cations the example is described in section 4 7 70 Figure 25 Profiles of sorbed concentrations of Na K Ca and Mg at selected print times during horizontal infiltration of multiple cations
68. enerate time series fs or profile pd plots with the amount of the minerals gypsum and calcite using GNUPLOT ts d eq gypsum plt pd d eq gypsum plt ts d eq calcite plt pd d eq calcite plt A series of ASCII files containing command line instructions to generate time series s or profile pd plots with the change in the amount of the minerals gypsum and calcite using 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 wgnuplotexe program for the Windows OS is usually after being downloaded in the gnuplot bin folder and does not need any additional special installation After opening the Window version of GNUPLOT by clicking on wgnuplot exe a plot can be directly generated by carrying out these commands File gt Open Browse to project folder Open the template file of interest plt The figure can be adapted using line commands see tutorials for GNUPLOT on the internet After adaptations the command lines can be saved to be used later on The default terminal for the plots is Windows We illustrate here only how a plot can be transferred to another terminal Set terminal emf Set output name emf Replot Set terminal window Replot A name emf file is created in the project folder 38 4 1 4 Overview of Selected Results Profile Data Distance cm Dist
69. entrations Concentration number 1 Button Edit Condition Select nodes 1 26 Solution composition 2001 Button Edit Condition Select nodes 27 101 Solution composition 1001 Menu File gt Save Data Menu File Exit Run Application 4 11 3 Output Selected output is shown in Figure 34 and Figure 35 Distance cm 200 0 008 0 002 0 004 0 006 PCE Iq mol 1000 cm of soil 0 days 30 00 days 60 00 days 90 00 days 120 00 days 150 00 days 0 Distance cm gt eo 150 200 oo 1 0 5e 005 0 0001 0 00015 0 0002 0 00025 0 0003 0 0003 Total concentration of Pce mol kg water 0 days 30 00 days 60 00 days 90 00 days 120 00 days 150 00 days Distance cm 200 T 0 0 0005 0 001 0 0015 Total concentration of Pce mol kg water 0 002 0 days 30 00 days 60 00 days 90 00 days 120 00 days 150 00 days Figure 34 Profiles of the solid phase PCE_lq top aqueous concentrations of Pce in the mobile right and immobile right water phases at selected print times for the example described in section 4 11 0 00014 0 00012 J NE M E se a MEE MEM NES DF eek ea EE p i p essei ae a poeem y pm o S 66 005 ee eee di uM QUNM ca MIR S j 5 4e 005 o 4 2e 005 O 0 0 2
70. ert 5 observation nodes one every 50 cm Menu File gt Save Data Menu File Exit Soil Profile Summary Button Next Run Application 4 9 4 Output Time series profiles and outflow curves are shown in Figure 29 Figure 30 and Figure 31 respectively E 0 002 F o 0 0018 J Ed D T 010016 1 ei g E 8 00014 eecemee 8 0 0012 9 amp 40 001 o H c c 0 0008 S S S 0 0006 J E t i o 0 0004 1 8 e o 5 00002 8 e i i s E 8 e eee ae a a e f e 2 0 20 40 60 80 100 120 140 160 0 20 40 60 80 100 120 140 160 Time days Time days 0 0 cm 150 0 cm 0 0 cm 150 0 cm 50 0 cm 200 0 cm 50 0 cm 200 0 cm 100 0 cm 100 0 cm Figure 29 Time series of Dcecis left and Vc righ at selected depths observation nodes for the example described in section 4 9 84 50 Distance cm Distance cm z eo 150 200 200 j j r r 0 0005 0 001 0 0015 0 002 0 002 0 0 0002 0 0004 0 0006 0 000 Total concentration of Tce mol kg water Total concentration of Eth mol kg water EN 0 days 60 00 days 120 00 days 0 days 60 00 days 120 00 days 30 00 days 90 00 days 150 00 days 30 00 days 90 00 days 150 00 days Figure 30 Profiles of Tce left and Eth righ at selected print times for the example describ
71. es Biologia 64 465 469 Sim nek J D J acques M Th van Genuchten and D Mallants 2006 Multicomponent geochemical transport modelling using HYDRUS 1D and HP1 Journal of the American Water Resources Association 46 1537 1547 Smiles D E and C J Smith 2004 Absorption of artificial piggery effluent by soil A laboratory study Australian Journal of Soil Research 42 961 975 Sun Y X Lu J N Petersen and T A Buscheck 2004 An analytical solution of tetrachloroethylene transport and biodegradation Transport Porous Media 55 301 308 Tebes Stevens C A J Valocchi J M VanBriesen and B E Rittman 1998 Multicomponent transport with coupled geochemical and microbiological reactions model description and example simulations Journal of Hydrology 209 8 26 Tipping E 2002 Cation binding by humic substances Cambridge University Press Cambridge UK van Genuchten M Th 1980 A closed form equation for predicting the hydraulic conductivity of unsaturated soils Soil Sci Soc Am J 44 892 898 Waite R D J A Davis T E Payne G A Waychunas and N Xu 1994 Uranium 6 adsorption to ferrihydrite Application of a surface complexation model Geochimica et Cosmochimica Acta 58 5465 5478 White N and L W Zelazny 1986 Charge properties in soil colloids In Soil Physical Chemistry edited by D L Sparks CRC Press BOCA Raten Florida
72. fined in the HID GUI by specifying the solution composition number in the soil profile corresponding to the solution composition number defined in phreegc in Note that the pAreeqc in file is automatically updated when changes are made in initial settings in the HID GUI e g different material distributions initial water contents or spatial distribution of initial solutions but only for initial distribution of the solutions and the initial water content Alternatively the phreeqc in file can be first created and saved using the HID GUI when the option Create PHREEQC IN file using HYDRUS GUI is selected The option Create PHREEQC IN file using HYDRUS GUI can then be deselected The phreeqc in file will not be automatically updated any longer by the HID GUI and can be modified outside the HID GUI 2 7 2 Structured phreeqc in File The structured phreegc in file consists of seven blocks Each block starts with the identifier H HPIBEGIN and ends with the identifier HP END The seven blocks are written in this sequence GENERAL This block contains general information such as the path to the database the project folder a number of soil layers and corresponding node numbers and the project title All this information except the last one is saved as comments 1 e with the sign in front This block is automatically updated by the HYDRUS GUI when the project is saved DATABASE This block contains additions to the thermodynamic data
73. g the HID GUI and modify it using an ASCII text editor or the PHREEQC graphical user interface e Create and modify the pAreeqc in file using an ASCII text editor or the PHREEQC graphical user interface The selection of this option is done in the HP1 Components and Database Pathway dialog window HP1 Components and Database Pathway ps Database Pathway Ic software Hydrus1 D 4 12 H1D_4_12 HP1 Databases phreeqc dat Browse Component Presets The PHREEGC IN file specifying the chemical Total H s composition and chemical reactions can be created Total 0 M using either the HYDRUS GUI see the Editor in the next dialog window or the PHREEGC GUI D Ca cu The PHREEQC In file will be C o created when the check box S 6 __ below is checked Cancel Previous m Boundary Conditions Nest C In Concentrations didis n Solution Compositions Help When the option Create PHREEQC IN file using HYDRUS GUI is not selected the phreeqc in file has to be created and modified outside the H1D GUI e When the option In Concentrations is selected the approach of specifying initial and boundary conditions as described in Jacques and Sim nek 2005 has to be followed This implies that e the phreeqc in file has to be created and modified outside the H1D GUI e the composition of the boundary solutions has to be defined within the H1D GUI e the initial conditions and their spatial distributi
74. hereas Eq 17 needs the biodegradation rate of Nta PHREEQC Basic statements to be used in the rate equation allows for this coupling 4 12 2 Problem Definition Consider a column of 5 m The porosity is 0 4 A constant water flux of 0 2 m hr is applied under saturated steady state flow conditions The dispersivity is 5 cm and the bulk density is 1 5 g cm The Nta concentration in the infiltrating water is 5 23 umol kgw Both the initial and infiltrating water contain 0 49 umol kgw C 31 25 umol kgw O 1000 umol kgw Na and 1000 umol kgw Cl Initially there is 50 ug biomass per 1000 cm of soil All other parameters are as defined above Investigate time series and profile data of Nta and Biomass for an infiltration experiment of 24 hr 93 4 12 3 Input Project Manager Button New Name Nta Description Nta degradation and biomass growth Button OK Main Processes Heading Nta degradation and biomass growth Check Water Flow Check Solute Transport Select HP1 PHREEQC Button Next Geometry Information Length Units m Depth of the Soil Profile 5 m Button Next Time Information Time Units Hours Final Time 24 hours Button Next Print Information Unselect T Level information Select Print at Regular Time Interval Time Interval 0 025 Print Times Number of Print times 6 Button Next Print Times Button Default Button OK HP1 Print and Punch Controls Check
75. ial Time Step 0 01 min Minimum Time Step 0 01 min Maximum Time Step 2 Button Next Print Information Number of Print Times 6 Button Select Print Times Button Default log Button Next HP1 Print and Punch Controls Select Make GNUPLOT templates Button Next Water Flow Iteration Criteria Lower Time Step Multiplication Factor 1 3 Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters 67 Catalog of Soil Hydraulic Properties Loam Qr 0 Qs 0 307 Alpha 0 259 cm n 1 486 Ks 0 170833 cm min Button Next Water Flow Boundary Conditions Initial Condition in Water Contents Upper Boundary Condition Constant Water Content Lower Boundary Condition Free Drainage Button Next Solute Transport General Information Number of Solutes 9 Button Next Solute Transport HP1 Components and Database Pathway Add the nine components Total O Total H Ca Na K Mg Cl C 4 S 6 Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Additions to Thermodynamic Database e Define the master exchange species G e Define the master species An identical reaction for the master exchange species has to be included EXCHANGE MASTER SPECIES G G EXCHANGE SPECIES G G log k 0 G K KG log_k 1 16 G Na NaG log_k 0 G 0 5 Cat2 Ca0 5G log_k 0 462 G 0 5
76. im damages from the infringer without prejudice to any other right in case of granting a patent or registration in the field of intellectual property SCK CEN Studiecentrum voor Kernenergie Centre d Etude de l Energie Nucl aire Stichting van Openbaar Nut Fondation d Utilit Publique Foundation of Public Utility Registered Office Avenue Herrmann Debroux 40 BE 1160 BRUSSEL Operational Office Boeretang 200 BE 2400 MOL Table of contents 1 2 FTO AUCTION WE esee Pe E eae E san feiu 1 Running HP1 from the HYDRUS 1D Graphical User Interface sese 2 2 1 Differences Between Version 2 2 002 of HP1 HYDRUS 1D Version 4 13 and Older Versions ob HP land EEXDRUS 1D orsus hata E I eec dS ahha tet Sa 2 22 Manage HPE Projects o eod e Re ane Ma tte ooh m n aol 3 2 3 Create a New Projects nsus ibd ba Ae bao ASIN SATA EOKA AERE a AATAS 3 24 Define the Physical Part of a Project edi qe rie certe iae ncaa 3 25 Define the Thermodynamic Database uter ates ges Pe b Roe e edades 4 26 Define Compotes i eei odd tend Oa dba latte bte ers oneal qas usd 4 2 7 Greate the phreeqe dm Pile ean a Cone dette t br etre eddie e ui ADR aes 5 2 7 1 Options to create and modify the phreeqc in file 0 0 eee ee eesceeeteceteeeeeeeeeeeseees 5 2 7 2 Str ct red phreeqec in PAG 52st ee t e ot oe ES E ARE 6 2 1 2 Modify the Structured phreeqc in File c cee ceeceesceessecsseceeeeeeeeeeseeceaeceeeeeeeeenseees 8 2 7
77. imes are shown in Figure 7 Table 1 Hydrological transport and reaction parameters for the example SEASONCHAIN Parameter Value Conta Contb ContC Hydraulic parameters 0 cm em 0 078 O cm em 0 43 o cm 0 036 n 1 56 K cm d 24 96 Transport parameters Dz em DOO p g cm 1 5 Reaction parameters Ki cmg 05 25 8 ny 1 0 9 0 8 Lu d 0 005 0 06 pa 002 Ka is the Freundlich distribution coefficient np is the Freundlich exponent wy and u wx are the first order decay coefficients see Eq 1 Verification problem 5 in Jacques and Sim nek 2005 23 9 0 days Odays H 250 00 days 250 00 days 500 00 days 500 00 days 20 id 1000 00 days 1000 00 days 1095 00 days 1095 00 days B eee 5 o o 5 l p H D n 2 60 Cees eee ce a 80 iL SNNT ars Pca rRpEE ME ue xum FEE PERS C 0 0 2 0 4 0 6 0 8 1 0 02 0 04 0 06 0 08 0 1 Total concentration of Conta mol kg water Total concentration of Contb mol kg water d 0 days 250 00 days 500 00 days 20 1000 00 days 1095 00 days 40 S 8 Ln H S i 60 L a 804 100 Mp 0 0 02 0 04 0 06 0 08 0 1 Total concentration of Contc mol kg water Figure 7 Profile plots of Conta Contb and Contc concentrations at selected times for the example SEASONCHAIN 3 7 CATEXCH Transport
78. in amount of a kinetic reactant mol 1000 cm time kinetics in SELECTED OUTPUT ss amount of a component in a solid solution mol 1000 cnr solid solutioins in SELECTED OUTPUT iso isotopes isotopes in SELECTED OUTPUT cale value of a calculated variable calculate value in SELECTED_OUTPUT 16 user values of the punch variables in the PHREEQC USER PUNCH data block e Name of a variable e g Ca in case totals or Ca 2 in case of molalities e m im m indicates values in the mobile water phase im indicates values in the immobile water phase A specific format of the headings in the PHREEQC data block USER PUNCH can be used for appropriate definitions of texts at axes in the GNUPLOT templates An underscore _ is translated to a space and the symbol separates the name of a variable from its unit Thus for the heading Total Cd umol per kgw the corresponding text in the GNUPLOT template is Total Cd umol per kgw To view a plot the GNUPLOT code should be installed on the computer GNUPLOT is freeware software and can be downloaded from http www gnuplot info After opening the window version of GNUPLOT wgnuplot exe a plot can be directly generated by File gt Open Browse to project directory Open the template file of interest plt The figure can be adapted using line commands see tutorials of GNUPLOT on the internet Afte
79. in the HP1 Definitions dialog window The name of the template file can consists of up to four parts separated by an underscore e pd or ts These two template files are made for each variable o The file which begins with pa contains information to produce depth profiles of a particular variable at selected times The times are specified as the Print Times in the Print Information dialog window o The file which begins with ts contains information to produces time series of a particular variable at selected observation points The observation points are defined in the Soil Profile Graphical Editor module The times are defined in the Print Options of the Print Information dialog window e Type of a variable o Name of the variable pH pe Temperature Total alkalinity Ionic strength mass of water Electrical balance Percent error on electrical balance o Type of the variable tot total aqueous concentration totals in SELECTED_OUTPUT mol molality molalities in SELECTED_OUTPUT act activity activities in SELECTED_OUTPUT eq amount of an equilibrium phase mol 1000 cm equilibrium phases in SELECTED OUTPUT d eq change in amount of an equilibrium phase mol 1000 cm time unit equilibruim phases in SELECTED OUTPUT si saturation index of an equilibrium phase saturation indices in SELECTED OUTPUT kin amount of a kinetic reactant mol 1000 cm kinetics in SELECTED OUTPUT d kin change
80. inf chem out ts pH plt pd pH plt ts pe plt pd pe plt ts tot Ca plt pd tot Ca plt ts tot Cl plt pd tot Cl pit ts tot S plt pd tot S plt ts tot C plt pd tot C plt ts eq gypsum plt pd eq gypsum plt ts eq calcite plt the defined observation nodes 21 41 61 81 and 101 at specific times every 0 025 days Numerical values can be seen by opening this file in any ASCII editor or a spreadsheet such as MS 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 tab delimited with the selected output for a complete soil profile at the defined observation times Numerical values can be seen by opening this file in any ASCII editor or a spreadsheet such as MS Excel A single plot of the profile data at different observation times can be generated for each geochemical variable with the pd plt files using GNUPLOT see below A series of ASCII files containing command line instructions to generate time series ts or profile pd plots of pH or pe using GNUPLOT A series of ASCII files containing command line instructions to generate time series s or profile pd plots with total concentrations of Ca Cl S and C using GNUPLOT note that this information can also be viewed through the H1D GUI 37 pd eq calcite plt A series of ASCII files containing command line instructions to g
81. ion i e 28 3 at the bottom and 128 3 cm at the top and linearly increasing with depth between Table 8 nitial pH and concentration for 9 components Concentration pH Cl Na K Ca Mg Cd Zn Pb umol l A 3 4 69 64 4 97 8 0 80 50 2 5 E 3 5 69 64 4 65 8 0 38 24 1 2 Bhl 3 6 69 64 4 39 8 0 43 23 1 1 Bh2 3 8 69 64 4 33 8 0 41 21 1 0 BC 4 4 69 64 4 55 8 0 63 33 1 6 Cl 4 4 69 64 4 76 8 0 33 21 1 0 C2 4 5 69 64 4 27 8 0 20 14 0 7 The transport of 10 components is considered Na K Ca Mg Cd Zn Pb Cl Br and C 4 In addition Total_O and Total_H are included Initial concentrations for the first nine components are given in Table 8 Br is used as a charge balance ion to have the desired initial pH also defined in Table 8 O 0 and C 4 are considered in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide Initial concentrations of Ca Cd and Zn were 56 obtained from Seuntjens 2000 Table 7 1 Pb concentrations were arbitrarily set to be 20 times smaller than the Zn concentrations no data available 4 6 3 Cation Exchange Capacities Assuming an average exchange capacity of 6 meq g of organic matter the exchange capacity is obtained as p gram soil cm x OC or gram organic matter 100 g soil x 6 meq gram of organic matter For example for the A horizon this results in 0 216 meq cm of soil This value must then be transformed to units of moles 1000 of cm soil i e 0 216 moles 1000
82. ion over a 300 d period Physical nonequilibrium i e the presence of immobile water in the soil profile was considered in this problem The soil hydraulic properties are typical for a loamy soil 0 0 078 cm cm 6 0 43 cm cm a 0 036 cm n 1 56 and K 24 96 cm d from Carsel and Parish 1988 Solute transport parameters were as follows a dispersivity Dz of 8 cm an immobile water content Q of 0 05 cm cm and a first order exchange coefficient w of 0 0125 d Precipitation and evaporation rates were typical for the Campine region in Belgium The soil profile was discretized into 100 elements of 1 cm each Chloride was applied during the first 53 days of the simulation with a concentration of 0 1 mmol I Time series of Cl outflow concentrations and concentration profiles are shown in Figure 3 and Figure 4 respectively Similar to Verification problem 2 in Jacques and Sim nek 2005 20 o o eo a Total concentration of Cl mol kg water ee M 0 50 100 150 200 250 300 Time days 25 0 cm 75 0 cm 50 0 cm 100 0 cm Figure 3 Time series of Cl concentrations in the mobile phase at four depths for the example TRANSCL 0 o 0 days 0 days 10 00 days 10 00 days 30 00 days 30 00 days 50 00 days 50 00 days 100 00 days 100 00 days 200 00 days 200 00 days Eg 800 00 days B
83. issociating groups on fulvic acids are 6 10 meq g and 4 6 meq g on humic acids Tipping 2002 Table 7 Soil hydraulic and other properties of six soil horizons from Seuntjens 2000 Horizon Depth p Organic 9 0 a n K cm g cm Carbon cm cm day A 0 7 1 31 2 75 0 065 0 48 0 016 1 94 95 04 E 7 19 1 59 0 75 0 035 0 42 0 015 321 311 04 Bhl 19 24 1 3 4 92 0 042 0 47 0 016 1 52 38 88 Bh2 24 28 1 38 3 77 0 044 0 46 0 028 2 01 864 BC 28 50 1 41 0 89 0 039 0 46 0 023 2 99 1209 6 Cl 50 75 1 52 0 12 0 030 0 42 0 021 2 99 1209 6 C2 75 100 1 56 0 08 0 021 0 39 0 021 2 99 1209 6 Steady state water flow of 1 cm day is assumed in this example The composition of the inflowing water changes as a function of time e 0 27 9 days Ca 0 005 mol I Cl 0 01 mol I e 27 9 289 days Ca 0 05 mol I CI 0 1 mol I e 28 9 80 days Ca 0 005 mol I Cl 0 01 mol I These upper boundary conditions correspond with experimental conditions in a lysimeter experiment described in Seuntjens 2000 At the bottom of the lysimeter capillary wicks with a length of 38 cm were installed Taking into account the hydraulic properties of the wick and the steady state water flow of 1 cm d the lower boundary pressure head is 28 3 cm For the initial distribution of the pressure heads it is assumed that the pressure head throughout the soil profile is initially in gravitational equilibrium with the lower boundary condit
84. k Initial Source Trapped in Immobile Water dip PT 89 a MCI BRO DISH MPS ETM DIT quos eate Ore EOS ER Liens acne tai oat dente Stara lapt afe hus 89 q1527 pU eaa a a OR CU oR C d LO E 89 LEM UM aeas 90 4 12 Coupled Nta Degradation and Biomass Growth seen 92 4 12 T Z2BackerOutid iie echo e om ae RE casas e uo avis es cI eu e ure td 92 vii 442 2 Problem Definition iiia ice tietectiekdeesta ees esta ed Desa Pha ed i 92 2 12 3 Input osd esee tela iliac embed on ples etant catia ted tel eat ua EA 93 AAD A OUtDUEI cioe e eoa eie dads tudo dae lecditedect vesci bocas qois eig ecd 96 References acc o tuu o EC coi pe oe ANS d A LE hah Rh 98 viii ix ABSTRACT Jacques D and J im nek 2010 Notes HP1 a software for simulating variably saturated water flow heat transport solute transport and biogeochemistry in porous media Version 2 2 SCK CEN Mol Belgium BLG 1068 HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating reactive transport and biogeochemical processes in variably saturated porous media HP1 results from coupling the water and solute transport model HYDRUS 1D im nek et al 2009a and PHREEQC 2 Parkhurst and Appelo 1999 This note provides an overview of how to set up and execute a HP1 project using version 2 2 002 of HP1 and version
85. lations with PHREEQC and thus some modifications for the use with HP1 may be needed Phreeqc log This file contains information about each calculation The information includes the number of iterations in revising the initial estimates of the master unknowns 15 the number of Newton Raphson iterations and the iteration at which any infeasible solution was encountered while solving the system of nonlinear equations An infeasible solution occurs if no solution to the equality and inequality constraints can be found At each iteration the identity of any species that exceeds 30 mol an unreasonably large number is written to the log file and noted as an overflow Any basis switches are noted in the log file The pAreeqc log file is created when the identifier logfile is true under the PHREEQC data block KNOBS 2 10 Create Templates to Produce Graphs with GNUPLOT If the options Observ Nodes Printed to Different Files and Mobile and Immobile Cells in Different Files are checked in the HP1 Print and Punch Controls dialog window the user can also check the option Make GNUplot Tempates in the same dialog window HP1 creates a series of templates p t two for each variable printed in the selected output files These variables are specified in the Selected Output section of the HP1 Print and Punch Controls dialog window and using the PHREEQC data block SELECTED OUTPUT and USER PUNCH in phreeqc in or the editor Additional output
86. les of molalities of sorbed K top left Ca top right Cd bottom left and Zn bottom right at selected times for the example CATEXCH 27 Figure 12 Profiles of pH top total Si middle left and Al middle right concentrations and amounts of amorf SiO bottom left and gibbsite bottom right at selected times for the example MINDIS 28 Figure 13 Outflow curves of pH left and Cd right for the example MCATEXCH 30 Figure 14 Profiles of pH top left Cd top right the fraction of deprotonated cation exchange sites bottom left and the fraction of cation exchange sites with Cd bottom right at selected times for the example MCATEXCH 31 Figure 15 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 38 Figure 16 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 39 Figure 17 Profiles of total aqueous Cd top left the amount of otavite top right and the percentage of Cd in solution bottom at s
87. lso printed in the selected output file for the locations and times defined in the text editors Punch Cells and Punch Frequency in the HP1 Print Information dialog window Obs node chem out obs node chemx out obs nod chem m out obs nod chem im out obs node chem mx out and obs node chem imx out These are files containing time series of the geochemical variables at the observation nodes defined in the Soil Profile Graphical Editor module The content is identical to the selected output file but information is only written during the transport calculations The exact names of the files created depend on the options the user selected in the HP1 Print and Punch Controls dialog window see paragraph 2 9 1 Nod inf chem out nod inf chem m out and nod inf chem im out These are files containing profile information of the geochemical variables for the Print Times defined in the Print Information dialog window The content is identical to the selected output file but information is only written during the transport calculations The exact names of the files created depend on the options the user selected in the HP1 Print and Punch Controls dialog window see paragraph 2 9 1 Phreeqc dmp This is a file which contains complete geochemical conditions at a specific time as defined in the HP1 Print and Punch Controls dialog window This file can be used to start a new simulation Note that the dump file was created for transport simu
88. minant with First Order Decay for Steady State Flow Conditions In this problem saturated steady state water flow and single component transport of a nonlinearly adsorbing first order decaying contaminant Pola through a soil column of 1 m length for a period of 1000 d are considered Transport and reactive parameters are as followed the saturated hydraulic conductivity K 1 cm d the saturated water content 0 5 cm cm the dispersivity 1 cm the bulk density 1 5 g cm the Freundlich distribution coefficient 5 cm g the Freundlich exponent is 0 8 and the first order decay constant is 0 02 d Initially no contaminant is present in the soil The contaminant concentration in the percolating water is 1 mol kgw Profiles of Pola concentrations are shown in Figure 6 0 days 250 00 days 500 00 days 750 00 days 1000 00 days Distance cm 100 ii 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 Total concentration of Pola mol kg water Figure 6 Profiles of Pola concentrations for the example STDECAY Verification problem 4 in Jacques and Sim nek 2005 7 Note that in the manual of HP1 version 1 0 Jacques and Simunek 2005 the decay coefficient was wrongly printed as 0 2 d instead of 0 02 d 22 3 6 SEASONCHAIN First Order Decay Chain of Nonlinearly Adsorbing Contaminants During Unsteady Flow In this example we consider the transport of three non linearly adsorbing contaminant
89. mponent 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 HP1 will issue a warning when a component is present in the aqueous phase during the geochemical calculations with PHREEQC but is not transported i e when it is not defined as a component in the HP1 Components and Database Pathway dialog windows 2 7 Create the phreeqc in File 2 7 1 Options to create and modify the phreeqc in file The H1D GUI allows for three options to create the pAreeqc in file e Create and modify the phreegc in file using the HID GUI e Create the phreeqc in file usin
90. n Unselect T Level information Select Print at Regular Time Interval Time Interval 0 025 days Print Times Number of Print times 5 Button Next Print Times Button Default Button OK HP1 Print and Punch Controls Check Make GNUplot Templates Button Next Water Flow Iteration Criteria Button Next Water Flow Soil Hydraulic Model Button Next Water Flow Soil Hydraulic Parameters Qs 0 43 Ks 1 cm day Button Next Water Flow Boundary Conditions Upper Boundary Condition Constant Pressure Head 74 Lower Boundary Condition Constant Pressure Head Solute Transport General Information Stability Criteria 0 25 Number of Solutes 11 Button Next Solute Transport HP1 Components and Database Pathway Database Pathway Browse phreeqcU dat Eleven Components Total O Total H Charge Ca Cl Mg Na K C 4 U 6 and U 5 Check Create PHREEQC IN file using the HYDRUS GUI Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Define the initial condition 1001 e Rain water without U Use the pH to obtain charge balance of the solution Put C and O in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide respectively Define the boundary condition 3001 e Rain water with U Use the pH to obtain charge balance of the solution Put C and O in equilibrium with the atmospheric partial pressure of oxyge
91. n and carbon dioxide respectively solution 1001 ph 7 charge pe 15 2939 units mol kgw C 1 CO2 9 3 5 Ca 6E 6 Cl 69E 6 K 4E 6 Mg 8E 6 Na 64E 6 O 0 1 O2 g 0 68 solution 3001 rain water ph 7 charge pe 15 2939 units mol kgw C1 CO2 g 3 5 Ca 6E 6 Cl 69E 6 K 4E 6 Mg 8E 6 Na 64E 6 O 0 1 02 g 0 68 75 U 6 1E 7 Button OK Geochemical Model e Define the surface complexation assemblage for 101 nodes e Add identifier no edl e Equilibrate the exchange sites with the initial solution Surface 1 101 Hfo w 0 00287 no edl equilibrate with solution 1001 Button OK Additional Output Define the additional output to be written to selected output files selected output totals U user punch headings Adsorbed_U mol kg Percentage adsorbed U6G start 10 Usorbed mol Hfo_wOUO2 tot water bulkdensity cell no 20 PUNCH Usorbed 30 if SYS U 6 gt 0 en percentag mol Hfo0_wOUO2 tot water SXS U 6 100 else percentage 0 40 if SYS U 6 gt 0 then Kd logl0 Usorbed tot U 6 else Kd 9999 50 PUNCH percentage Kd end Button OK Button Next Solute Transport Solute Transport Parameters Bulk density 1 31 g cm Disp 1 cm cm Button Next Solute Transport Boundary conditions Upper Boundary Condition Bound Cond 3001 Soil Profile Graphical Editor Menu Conditions gt
92. nk between the definition of different materials in the HID GUI and the chemical heterogeneity in the geochemical model Thus numbering of geochemical keywords must refer to the node numbers If the material distribution is changed in the H1D GUI the user must change the numbering of the geochemical model using the editor Geochemcial Model in the HP1 Definitions dialog window When the user defines a material distribution in the HID GUI a template of it with corresponding node numbers is incorporated in the text editor when he clicks the Add button of the corresponding geochemical model Note that this template is not automatically updated when the material distribution or number of nodes are changed The numbering of the geochemical model is e 1 to number of nodes for the mobile water phase e number of nodes 1 to 2 number of nodes for the immobile water phase 10 2 7 7 Define the Output The user can define additional output using the editor Additional output in the HP1 Definitions dialog window by using the PHREEQC data blocks SELECTED_OUTPUT and USER_PUNCH Depending on the options selected in the HP1 Print and Punch Control dialog window a number of output files is created HP1 specific output files have the same structure as the selected output files of PHREEQC They are tab delineated and can be opened using ASCII text editors or EXCELL 2 8 Define the Spatial Distribution of the Initial Solutions and Temporal Va
93. o secondary master species from the primary master species N Only the secondary master species N 5 was defined as a component to be transported the Solute Transport HP1 Components dialog window HP1 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 4 4 3 Output Display results for Observation Points or Profile Information Alternatively Figure 20 can be created using information in the output file obs nod out 50 0 0014 0 0012 4 0 001 0 0008 4 0 0006 4 0 0004 4 Concentration mol kg 0 0002 0 14400 28800 43200 57600 72000 86400 Time s Figure 20 Outflow concentrations of Cl Ca Na and K for the single pulse cation exchange example The results for this example are shown in Figure 20 The concentrations for node 41 the last node are plotted against time Chloride is a conservative solute and arrives in the effluent at about one pore volum
94. ochemical model i e the cation exchange assemblage X 0 0011 moles 1000 cm and equilibrate it with the initial solution solution 1001 EXCHANGE 1 41 Layer 1G X 0 0011 equilibrate with solution 1001 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 Button Next Solute Transport Transport Parameters Bulk Density 1 5 g cm Disp 0 2 cm Button Next Solute Transport Boundary Conditions Upper Boundary Condition Concentration Flux Add the solution composition number i e 3001 for the upper boundary condition Lower Boundary Condition Zero Gradient 49 Button Next Soil Profile Graphical Editor Menu Conditions gt Profile Discretization or Toolbar Ladder Number from sidebar 41 Menu Conditions gt Initial Conditions gt Pressure Head or Toolbar red arrow Button Edit condition select with Mouse the entire profile and specify 0 cm pressure head Menu Conditions gt Observation Points Button Insert Insert a node at the bottom Menu File gt Save Data Menu File gt Exit Soil Profile Summary Button Next Close Project Run project Note This exercise will produce the following warnings Master species N 3 is present in solution n but is not transported The same warning occurs for N 0 N 3 and N 0 are tw
95. oefficient 0 01 day 4 11 2 Input Project Manager Select project TCE 2 Button Copy New Name TCE 3 Description TCE first order degradation network initial value problem MIM Button OK Main Processes Heading TCE first order degradation network initial value problem MIM Button OK Solute Transport General Information Check Dual Porosity Mobile Immobile Water Model Physical nonequilibrium Solute Transport HP1 Definitions Definitions of Solution Compositions Delete solution 1002 Add the initial solution for the immobile water phase in equilibrium with the PCE solid solution 1001 initial solution mobile phase solution 2001 initial solution immobile phase Pce 1 Pce_lg 0 solution 3001 boundary solution Button OK Geochemical Model 90 Add the PCE contamination in the top 50 cm in the immobile zone Numbers for the immobile zone starts at numbers of node 1 and end at two times the number of nodes For this project numbers for the immobile zone are thus from 102 to 202 Equilibrium_phases 102 128 PCE_lq 0 0 01 Button OK Button OK Solute Transport Transport Parameters Mass Tr 0 01 day ThImob 0 1 Button OK Soil Profile Graphical Editor Menu Conditions gt Initial Conditions gt Concentrations Concentration number 1 Button Edit Condition Select all Solution composition 1001 Menu Conditions gt Initial Conditions gt Sorbed Conc
96. of Heavy Metals Subject to Multiple Cation Exchange In this problem the transport of ten components Al Br Ca Cd Cl K Mg Na Pb and Zn through a soil column is modeled Initial and inflow concentrations of the ions are given in Table 2 The cation exchange capacity is equal to 0 011 mol 1000 cm The soil core has a length of 8 cm and is discretized into 40 cells of 0 2 cm The flow velocity is 2 cm d and the dispersivity is 2 cm Simulations were performed for 15 days The maximum time step used in HP1 was 0 015 d Selected results are present in Figure 8 through Figure 11 Verification problem 6 in Jacques and Sim nek 2005 24 Table 2 Initial and inflow concentrations for the example CATEXCH mmol I Initial pore water Initial concentrations of Inflow concentrations composition exchangeable cations Al 0 5 0 92 0 1 Ca 110 2 88 107 5 Cd 0 09 0 17 0 K 2 1 06 0 Mg 0 75 1 36 1 Na 6 0 62 0 Pb 0 1 0 34 0 Zn 0 25 0 76 0 Br 11 3 7 Cl 1107 10 pH 5 5 2 9 Calculated in equilibrium with the initial pore water composition Br is used to impose a charge balance at pH of 5 5 0 0003 Time days 2 0 cm 4 0 cm 6 0 cm 8 0 cm Total concentration of Cd mol kg water 9 12 15 3 6 Time days 2 0 cm 6 0 cm 4 0 cm 8 0 cm Total concentration of Ca mol kg water Total concentration of Zn mol kg water 0 005 D100 Listes E EEE tec T on 010
97. olutions for each node The block starts with an END keyword For each node both for the mobile and immobile aqueous phases a MIX SAVE statement is included with the following format MIX solution number solution composition water content SAVE SOLUTION solution number END where solution number 1s the solution number equal to the node number for the mobile aqueous phase and to the node number N for the immobile aqueous phase where N is the number of nodes solution composition is the solution composition number as defined in the HID GUI Soil Profile Summary Soil Profile Summary dialog window and water content is the initial water content as defined in the HID GUI either as the initial water content or calculated from the initial pressure head and soil retention parameters This block is automatically updated by the HID GUI when the project is saved This block contains the definition of the geochemical model typically using the following PHREEQC data blocks EQUILIBRIUM PHASES EXCHANGE SURFACE KINETICS and SOLID SOLUTIONS The content is defined in the editor Geochemical Model of the Solute Transport HP1 Definitions dialog window This block contains the keywords END followed by PRINT with the identifiers reset and warnings as defined in the HP1 Print and Punch Controls dialog window and the keyword TRANSPORT with cells to define the number of nodes
98. on one dimensional transport and inverse geochemical calculations Water Resources Investigations Report 99 4259 Denver Co USA Puigdom nech I J A Rard A V Plyasunov I Grenthe 1997 Temperature corrections to thermodynamic data and enthalpy calculations In Modelling in aquatic chemistry eds I Grenthe and I Puigdom nech OECD Nuclear Chemistry Paris France pp 427 493 Schaerlaekens J D Mallants J Sim nek M Th van Genuchten and J Feyen 1999 Numerical simulation of transport and sequential biodegradation of chlorinated aliphatic hydrocarbons using CHAIN 2D Hydrological Processes 13 2847 2859 Selim H M and M C Amacher 1997 Reactivity and transport of heavy metals in soils CRC Press Florida USA Seuntjens P 2000 Reactive solute transport in heterogeneous porous media Cadmium leaching in acid sandy soils Ph D University of Antwerp Belgium Sim nek J M Sejna H Saito M Sakai and M Th van Genuchten 2008 The HYDRUS 1D Software Package for Simulating the Movement of Water Heat and Multiple Solutes in Variably Saturated Media Version 4 08 HYDRUS Software Series 3 Department of Environmental Sciences University of California Riverside Riverside California USA 99 Sim nek J D Jacques N K C Twarakavi and M Th van Genuchten 2009 Selected HYDRUS modules for modeling subsurface flow and contaminant transport as influenced by biological processes at various scal
99. on of multiple cations Ca Na and K into the initially dry soil column It is vaguely based on experimental data presented by Smiles and Smith 2004 The cation exchange between particular cations is described using the Gapon exchange equation White and Zelazny 1986 For an exchange reaction on an exchange site X involving two cations N and M with charge n and m NinX Im M Mi X l nN 2 the Gapon selectivity coefficient Kay is My ux T 3 K GMN Iv Xl a T where denotes activity The activity of the exchange species is equal to its equivalent fraction The Gapon selectivity coefficients for Ca Na Ca K and Ca Mg exchange are Kacawa 2 9 Kacak 0 2 and Kgcamg 1 2 It is assumed that the cation exchange capacity c mol kg soil is constant and independent of pH Consider a soil column 20 cm long with an initial water content of 0 075 Infiltration occurs on the left side of the column under a constant water content equal to the saturated water content Consider a free drainage right boundary condition Some physical parameters of the column are bulk density 1 75 g cm dispersivity 10 cm the soil water retention characteristic and unsaturated hydraulic conductivity curve are described with the van Genuchten Mualem model with the following parameters 8 0 307 6 0 a 0 259 cm n 1 486 K 246 cm day and 0 5 The CEC is 55 meq kg soil As initial concentrations take Cl 1 mmol kg
100. onditions In Total Concentrations Ma n Liquid Phase Concentrations Mass solute Volume water solute Volur Nonequilibrium phase is initially at equilibrium with equilibrium phase 11 In case of time variable boundary conditions the boundary condition is assigned in the Variable Boundary Conditions dialog window For example Time ariable Boundary Conditions temen mius en Heb _Addline Delete Line Defaut Tin 2 9 Control Output The HID GUI allows users to specify times and locations for which output variables are to be printed into output files This is defined in the HP1 Print and Punch Controls dialog window HP1 Print and Punch Controls 9 e 2 9 1 Punch Times and Locations The Punch Times and Locations section defines how variables selected by in the PHREEQC data blocks SELECTED OUTPUT and USER PUNCH are to be printed Depending on the choice of the user data is written in a series of ASCII files with tab delimited columns 12 If the option Controlled by HYDRUS is checked punch times and locations i e observation nodes are defined using the H1D GUI e Time series at observation points o Locations of the observation points are defined in the Soil Profile Graphical Editor module which can be selected from the pre processing menu Conditions gt Observation Points Insert o Print times are defined in the Print Times dialog windo
101. ons have to be defined in the phreeqc in file e When the option In Solution Compositions is selected without the option Create PHREEQC IN file using HYDRUS GUI only solution composition numbers are defined in the H1D GUI Therefore e the phreeqc in file has to be created and modified outside the HID GUI e the composition of the boundary solutions has to be defined in pAreeqc in using specific solution composition numbers e the temporal variation of the boundary solution is defined in the HID GUI by specifying the solution composition number corresponding to the solution composition number defined in phreeqc in e the initial conditions and their spatial distribution have to be defined in the phreeqc in file 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 is a structured file which is created and can be modified using the HP1 Definitions dialog window and the H1D GUI e the composition of the boundary solutions has to be defined in pAreeqc in using specific solution composition numbers e the temporal variation of the boundary solutions is defined in the HID GUI by specifying the solution composition number corresponding to the solution composition number defined in phreegc in e the initial solutions are defined in the pAreeqc in file using specific solution composition numbers e the spatial distribution of the initial solutions is de
102. ow Soil Hydraulic Model Button Next Water Flow 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 Water Flow Boundary Conditions Upper Boundary Condition Constant Pressure Head Lower Boundary Condition Constant Pressure Head Button Next Solute Transport General Information Number of Solutes 7 Button Next Solute Transport HP1 Components and Database Pathway Add seven components Total O Total H Na K Ca Cl N 5 Check Create PHREEQC IN file using HYDRUS GUI Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Define the initial condition 1001 e K Na N 5 solution e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 to be in equilibrium with the atmospheric partial pressure of oxygen 48 Define the boundary condition 3001 e Ca Cl solution e Use pH to obtain the charge balance of the solution e Adapt the concentration of O 0 to be in equilibrium with the atmospheric partial pressure of oxygen Solution 1001 Initial condition units mmol kgw pH 7 charge Na 1 K 0 2 N 5 1 2 O 0 1 O2 g 0 68 Solution 3001 Boundary solution units mmol kgw pH 7 charge Ca 0 6 Gl 1 2 O 0 1 O2 g 0 68 Geochemical Model Define for each node 41 nodes the ge
103. r Initial Time Step 0 1 hr Minimum Time Step 0 05 hr Maximum Time Step 0 1 hr Number of Time Variable Boundary Records 4 Button Next Print Information Number of Print Times 12 Button Select Print Times Default Button Next 54 Solute Transport General Information Button Next Solute Transport HP1 Components and Database Pathway Button Next Solute Transport HP1 Definitions Definitions of Solution Compositions Add additional boundary solution compositions with numbers 3002 and 3003 Define a bottom boundary solution Solution 4001 pure water Solution 3002 Boundary solution units mmol kgw ph 7 charge Na 1 K 0 2 N 5 1 2 Ca 5E 3 Cl 1E 2 O 0 1 O2 g 0 68 Solution 3003 Boundary solution units mmol kgw ph 7 charge Na 1 K 0 8 N 5 1 8 Ca 5E 3 Cl 1E 2 O 0 1 O2 g 0 68 solution 4001 bottom boundary solution pure water Button OK Button Next Solute Transport Boundary Conditions Upper Boundary Condition Concentration Flux Lower Boundary Condition Zero Gradient Button Next Time Variable Boundary Conditions Fill in the time and the solution composition number for the top boundary Time cTop cBot 8 3001 4001 18 3002 4001 38 3001 4001 53 60 3003 4001 Soil Profile Graphical Editor Menu Conditions gt Observation Points Button Insert Insert nodes at 2 4 6 and 8 cm Menu File gt Save Data Menu
104. r _ pit O0days Odays 0 50 days 0 50 days 1 00 days 1 00 days 1 50 days 1 50 days 2 00 days 2 00 days 2 50 days 2 50 days 5 gt E eo o o o E S DES QD a amp 0L 5 3 60 i _ _ _ 1 5e 0063e 0064 5e 0066e 0067 5e 006 0 1 5e 006 3e 006 4 5e 006 6e 006 Total concentration of Cd mol kg water otavite mol 1000 cm of soil 9 0 days 0 50 days 1 00 days 1 50 days 104 2 00 days 2 50 days 20 fo Distance cm BOS pase poet TEE nndis SET are ted ess Oc a ea ee a 50 a L S O L L L L 0 10 20 30 40 50 60 70 80 90 100 Percentage Cd in solution Figure 17 Profiles of total aqueous Cd top left the amount of otavite top right and the percentage of Cd in solution bottom at selected print times during dissolution of calcite and gypsum and Cd transport 4 3 Dissolution of gypsum and calcite and transport of Cd the effect of higher Cl concentrations on the Cd mobility 4 3 1 Problem Definition Aqueous components which form strong complexes with Cd will enhance the mobility of Cd The same physical and geochemical set up as in the previous example paragraph 4 2 is used here but the composition of the inflowing water is changed after 1 day to a solution with a higher CaCl concentration 1 4 3 2 Input Project Manager x10 M Select project HP1 2
105. r adaptations the command lines can be saved to be used later on 2 41 Running a HP1 Project A HPI project is saved and executed as a regular HYDRUS 1D project After saving input data all output files out are deleted Output files with other extensions are not deleted Note that the pit files are overwritten whenever input data are saved as long as the option Make GNUplot Templates in the HP1 Print and Punch Controls dialog window is checked 2 2 Looking at Selected Numerical Results After execution of the HP1 code output variables related to the physical part of the project can be inspected using the post processing menus in the HID GUI The post processing menu shows only the total concentration of the components Concentrations are always in moles 1000 cm The user has to go to the project directory to look at the output of the geochemical variables Part of the data can be visualized using GNUPLOT if GNUPLOT templates are generated 2 13 Help File The help file of the HID GUI contains some information on HP1 and on the PHREEQC keywords identifiers and BASIC statements for the pAreeqc in file Only some basic information is included in the help file The user is referred to the PHREEQC manual Parkhurst and Appelo 17 1999 for a full description of the PHREEQC keywords identifiers and BASIC statements Not all keywords are yet documented in the help file of version 4 13 of HYDRUS 1D 18 3 Examples Installed with HP
106. riationS of the Boundary Solutions The following methods are available to define the spatial distribution of the initial solutions e Using the Soil Profile Graphical Editor module After selecting Condition gt Initial Conditions gt Concentration Concentration number 1 Edit Condition a range of nodes can be selected and a solution composition number can be assigned for the mobile water phase To assign a solution composition number for the immobile water phase Condition gt Initial Conditions gt Sorbed Concentration Concentration number 1 Edit Condition e Via the Soil Profile Summary dialog window Solution composition numbers are defined in the column Cnc Comp for the mobile water phase and in the column Im C Comp for the immobile water phase In case of a constant boundary condition the boundary condition is assigned in the Solute Transport Boundary Conditions dialog window by specifying the solution composition number Solution composition numbers 3001 and 4001 are specified in the example below Solute Transport Boundary Conditions x r Upper Boundary Condition Concentration BC Concentration Flux BC Stagnant BE for Volatile Solute Sol No Bound Cond OK t Bound Cond x Cancel Previous r Lower Boundary Condition C Concentration BC Concentration Flux BC Zero Concentration Gradient Next Sol No Bound Cond 1 ami Hep Initial C
107. s Conta Contb and Contc that are involved in a sequential first order decay chain defined as Hak conta LL kc cont Ls k conte Conta lt Contb Contec 1 Kane conta Kane contb Kane contc SoraConta SoraContb SoraContc where uw z are the first order rate constants connecting two contaminants 44 4 is the first order rate constant for Contc Ka and nr are the Freundlich isotherm parameters for the three contaminants and SoraConta SorbContb and SorcContc are the three surface species related to Conta Contb and Contc on three surfaces Sora Sorb and Sorc respectively Reaction parameters for the three contaminants are given in Table 1 Model simulations were carried out for a 1 m deep homogeneous soil profile during 1000 d assuming transient flow Upper boundary conditions were taken as daily precipitation rates representative for the Campine Region in Belgium Evaporation was neglected during the simulations The lower boundary condition was defined as free drainage A uniform initial pressure head of 60 cm was assumed for the entire soil profile For solute transport the following initial and boundary conditions were considered 1 initial concentrations equal to zero for all three contaminants 2 third type solute fluxes as the top boundary conditions with 1 0 1 and 0 mol I for Conta Contb and Contc respectively and 3 zero gradient bottom boundary condition Profile concentrations at selected t
108. s of Cd concentrations at different depths top figures and profiles of the amount of otavite bottom figures Total concentration of Cl mol kg water 0 0 5 1 1 5 2 2 5 Time days Figure 19 Time series of Cl at selected depths observation nodes for the example described in section 4 3 10 0 cm 20 0 cm 30 0 cm 40 0 cm 50 0 cm 45 infiltration front see Figure 18 Due to the high Cl concentrations solubility of Cd is increased and otavite is not formed anymore after 1 5 days 46 4 4 Transport and Cation Exchange Single Pulse 4 4 1 Problem Definition This example is adapted from Example 11 of the PHREEQC manual Parkhurst and Appelo 1999 We will simulate the chemical composition of the effluent from an 8 cm column containing a cation exchanger The column initially contains a Na K NO 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 is equal to 24 cm d 0 00027777 cm s The column is discretized into 40 finite elements i e 41 nodes The example assumes that the same solution is initially associated with each node Also we use the same exchanger composition for all nodes The initial Na K NO solution is made by using 1 x 10 M NaNO and 2 x 10 KNO M The inflowing CaCl solution has a concentr
109. s obtained by the BASIC statement cell no o The water content obtained as tot water Add meaningful headings for the punch output SELECTED OUTPUT totals Cl Ca K Na Mg S 69 USER_PUNCH headings Sorbed_Ca meq kg_soil Sorbed_Mg meq kg_soil Sorbed_Na meq kg_soil Sorbed_K meq kg_soil start 10 bd bulkdensity cell_no kg 1000cm soil 40 PUNCH mol Ca0 5G tot water bd 1000 in meq kg 50 PUNCH mol Mg0 5G tot water bd 1000 in meq kg 60 Pl H mol NaG tot water bd 1000 in meq kg 70 PUNCH mol KG tot water bd 1000 in meq kg end Button OK Button Next Solute Transport Solute Transport Parameters Bulk Density 1 75 g cm Disp 10 cm Button Next Solute Transport Boundary Conditions Upper Boundary Condition Concentration Flux Bound Cond 3001 Lower Boundary Condition Zero Gradient Button Next Soil Profile Graphical Editor Menu Conditions gt Initial Conditions gt Water content Button Edit Condition Select All Top Value 0 075 Button Edit Condition Select first node Value 0 307 Menu Conditions gt Observation Points Button Insert Insert 4 observation nodes at 3 6 9 and 12 cm Menu File gt Save Data Menu File Exit Soil Profile Summary Button Next Run Application 4 7 4 Output Explore the HYDRUS output and the GNUPLOT templates 70 Distance cm
110. t Run Application 4 1 3 Output The standard HYDRUS output can be viewed using commands in the right Post processing part of the project window Only the total concentrations of the components which were defined in the Solute Transport HP1 Components dialog window can be viewed using the GUI H1D HP1 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 Manager Directory gives the path to the project group folder Input and output files of a given project are in the folder directory project_name 36 where directory is the project group folder project_name is the project name Following HP1 output files are created for the HP1 1 project Createdfiles out Phreeqc out HPI I hse obs nod chem21 out obs nod chem4l out obs nod chem l out obs nod chem l out An ASCII text file containing a list of all files created by HP1 in addition to the output files created by the HYDRUS module of HP1 An ASCII text file which is the standard output file created by the PHREEQC module in HP1 An ASCII text file tab delimited that includes a selected output of all geochemical calculations in HP1 carried out before actual transport calculations Inspection of this file can be done with any ASCII editor or spreadsheet such as MS Excel obs nod cheml101 out A series of ASCII files tab delimited with the selected output for nod
111. tal CEC 0 0 001 0 002 0 003 0 004 Cd site over total CEC 0 years 0 70 years 0 30 years 1 00 years m 0 years 0 50 years 1 00 years 0 50 years 0 30 years 0 70 years Figure 14 Profiles of pH top left Cd top right the fraction of deprotonated cation exchange sites bottom left and the fraction of cation exchange sites with Cd bottom right at selected times for the example MCATEXCH 32 4 Step By Step Instructions for Selected Examples 4 1 Dissolution of Gypsum and Calcite 4 1 1 Problem Definition Sulfate free water is infiltrated in a 50 cm long uniform soil column under steady state saturated flow conditions The reactive minerals present in the soil column are calcite CaCO3 and gypsum CaSO 2H5O 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 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 the oxidized components of S and C Calculate the movement of the dissolution fronts of calcite and gypsum over a period of 2
112. the example is described in section 4 7 71 Figure 26 Profiles of aqueous concentration of U for the example described in section 4 8 76 Figure 27 Perchloroethylene PCE degradation pathway Figure from Schaerlaekens et al 1999 77 Figure 28 Degradation pathway of PCE using first order rate constants 78 Figure 29 Time series of Dcecis left and Vc righ at selected depths observation nodes for the example described in section 4 9 83 Figure 30 Profiles of Tce left and Eth righ at selected print times for the example described in paragraph 4 9 84 Figure 31 Outflow curves for the example described in section 4 9 84 Figure 32 Profiles of the solid phase PCE Iq left and the aqueous concentrations of Pce right at selected print times for the example described in section 4 10 87 xiv Figure 33 Outflow concentrations for the example described in section 4 10 88 Figure 34 Profiles of the solid phase PCE_lq top aqueous concentrations of Pce in the mobile right and immobile right water phases at selected print times for the example described in section 4 11 91 Figure 35 Outflow concentrations for the example described in section 4 11 91 Figure 36 Time series of Nta concentrations and biomass at selected depths observation nodes for the example described in section 4 12 96 Figure 37 Profiles of Nta concentrations and biomass at selected print times for the example described in s
113. times for the example CATEXCH 3 8 MINDIS Transport with Mineral Dissolution A 100 cm long soil column consisting of amorphous SiO2 and gibbsite Al OH 3 is leached with a solution containing 5 10 mol I Si 1 10 mol I Al and 1 10 mol I Na to obtain an inflow pH of 11 15 Initial concentrations are 1 76 10 mol T Si 8 87 10 mol I Al and 1 10 12 mol I Na corresponding to a pH of 6 33 In each 1 cm thick cell 0 015 mol amorphous SiO and 0 005 mol gibbsite is present The flow velocity is 2 cm day and the dispersivity is 1 cm Results are given in Figure 12 1 Verification problem 7 in Jacques and im nek 2005 28 20 J FREE a MED DER OS AE E NE E Distance cm 0 days 8 00 days 50 00 days 2 00 days 15 00 days 100 00 days 4 00 days 25 00 days 150 00 days Distance cm Distance cm 100 i i i i i 100 i i i i Y Y T T Y T T 0 0 0005 0 001 0 0015 0 002 0 0025 0 003 0 5e 005 0 0001 0 00015 0 0002 0 0002 Total concentration of Si mol kg water Total concentration of Al mol kg water 0 days 8 00 days 50 00 days mE 0 days 8 00 days 50 00 days 2 00 days 15 00 days 100 00 days 2 00 days 15 00 days 100 00 days 4 00 days 25 00 days 150 00 days 4 00 days 25 00 days 150 00 days 3 3 S S o o z 2 g Q R2 a a K Ei 0
114. tively a series of node numbers can be defined Print times can be linked to the specified print options in the Print Options dialog window Alternatively a print frequency can be defined 2 9 4 PHREEQC Dump The dump files created by PHREEQC give a complete geochemical state for all nodes at a given time step It is formatted as a PHREEQC input file and can thus be used to restart a HPI calculation after failure some adaptations may be necessary More information is given in the PHREEQC manual There are options to link the times when a dump file should be created to the print times defined in the Print Options dialog window 2 9 5 HP1 Output Files with Geochemical Information Following output files are created by HP1 in addition to the output files created by the regular routines of the HYDRUS program Phreeqc out the standard text output file of PHREEQC This file contains information on different calculations steps warnings and a full description of the geochemical 14 calculations The amount of information written to the pAreeqc out file can be controlled using the PHREEQC data block PRINT Specific user defined output in the pAreeqc out output file can be defined using the PHREEQC data block USER PRINT When the radio button No Printing in phreeqc out is selected in the HP1 Print and Punch Controls dialog window the output is generated only during the initialization of the project i e for the PHREEQC commands defined
115. total aqueous concentrations of Cl Na K Ca and Mg at selected print times during horizontal infiltration of multiple cations the example is described in section 4 7 71 0 5 S 1 S B8 i 8 m i E a a 154 20 i i i 20 i i 0 6 07 0 8 0 9 1 1 1 3 12 15 Sorbed Na meq kg soil Sorbed K meq kg soil 0 min 12 00 min 144 00 min 0 min 12 00 min 144 00 min 2 29 min 27 47 min 2 29 min 27 47 min 5 24 min 62 90 min 5 24 min 62 90 min 0 5 2 S 8 104 8 g m E a a 154 120 J i FE i i j 27 28 29 30 31 32 33 34 13 14 15 16 17 Sorbed Ca meq kg soil Sorbed Mg meq kg soil 0 min 12 00 min 144 00 min 0 min 12 00 min 144 00 min 2 29 min 27 47 min 2 29 min 27 47 min 5 24 min 62 90 min 524min 62 90 min Figure 25 Profiles of sorbed concentrations of Na K Ca and Mg at selected print times during horizontal infiltration of multiple cations the example is described in section 4 7 72 4 8 U Transport and Surface Complexation 4 6 1 Problem definition This exercise simulates the leaching of U under saturated steady state flow conditions U adsorbs on Fe oxides in the soil profile Consider a 50 cm deep loamy soil with a saturated hydraulic conductivity of 1 cm day Take a porosity of 0 43 a bulk densi
116. ty of 1 31 g cm and a dispersivity of 1 cm The Fe O content of the soil is 0 02 weight percentage The capacity of the surface is calculated assuming that Fe203 has 0 875 reactive sites per mole of Fe Waite et al 1994 Following elements are considered Ca Cl K Mg Na U 6 and C 4 In this geochemical transport problem that is pH sensitive also Total O and Total H need to be transported U adsorption is described by a non electrostatic surface complexation model As a consequence of this a charge on the solid surface is not balanced by counter ions in a double layer near the surface Therefore the aqueous phase will have a charge imbalance that will be of the same size but having an opposite sign as the charge on the surface The entire system i e solid surface aqueous phase will then be charged balanced Therefore also the Charge of the aqueous solution has to be transported Note that when an electrostatic surface complexation model which takes into account the composition of the double layer is used the aqueous phase will be charged balanced and so will be the solid surface and the double layer A solution composition of rain water is assumed for both initial and boundary conditions Cl 69 umol kg water Ca 6 umol kg water K 4 umol kg water Na 64 umol kg water Mg 8 umol kg water The concentration of O2 and CO are assumed to be in equilibrium with the atmospheric partial pressure of O g and CO
117. w Print Options gt T level information and or Print Options gt Print at Regular Time Interval e Profiles at specific times o Print times are defined in the Print Times dialog window Print Times Number of Print Times Select Print Times Depending on the options selected by the user a number of output files is created e Observ Nodes Printed to Different Files Time series for different observation nodes are printed into different files e Mobile and Immobile Cells in Different Files Time series and profile data for the mobile and immobile water phases are printed into different files Following files are created e f both options are unchecked o Obs node chem out for the time series o Node inf chem out for the profile data e f Observ Nodes Printed to Different Files is checked o Obs node chemx out for the time series for the observation point with a node number x One file is created for each observation point o Node inf chem out for the profile data e If Mobile and Immobile Cells in Different Files is checked o Obs node chem m out for the time series of the mobile water phase o Obs node chem im out for the time series of the immobile water phase o Node inf chem m out for the profile data of the mobile water phase o Node inf chem im out for the profile data of the immobile water phase e If both options are checked o Obs node chemxm out for the time series of the mobile water phase for the observation point with

Notes on HP1 – a software package for simulating - PC

Contents

Download Pdf Manuals

Related Search

Related Contents

Notes on HP1 &ndash; a software package for simulating - PC

Contents

Download Pdf Manuals

Related Search

Related Contents

Notes on HP1 – a software package for simulating - PC