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PFLOTRAN User Manual

1. ar Wes B 02 aq 1 78132e 4 T Al 4 SS M K Feldspar Ca 1 20644e 3 M Calcite Cu 1 e 6 T F 1 e 9 M Ferrihydrite g 5 09772e 4 T UO2 2 34845e 7 T K 1 54789e 4 T Na 2 03498e 3 a HCO3 2513053 T eal 6 97741e 4 T F 2 09491e 5 T HPO4 1 e 6 T NO3 4 69979e 3 T SO4 6 37961e 4 T Si02 aq 5 36989e 4 Ab Tracer 2 34845e 7 F if MINERALS Quartz sia em em Calcite On em o Metatorbernite 0 Me o lem i END secondary constraint SECONDARY_CONSTRAINT sec CONCENTRATIONS Ca 1 e 3 M Calcite H AE pH SO4 re M Gypsum HCO3 3 5 E C02 g el mes Z si02 aq e 4 M Quartz Tracer d 8 F MINERALS Quartz 020191875 az Calcite 0 730825 1 42 Gypsum omo le if Return to List of Keywords lt 66 gt PFLOTRAN User Manual 84 13 0 August 14 2015 4 13 Keyword DATASET Return to List of Keywords Description Specifies a data set to be associated with parameters sets in the model DATASET lt string gt Opens the card block with the name of the data set in the string NAME lt string gt Name of the data set if not included with DATASET card Note this string overwrites the name specified with the DATASET FILENAME lt string gt Name of file containing data TYPE lt string gt Reserved for future application where the data set can be a single scalar or vector value or a functional relationship The TYPE is currently fixed at HETEROGENEOU
2. Typical values are to set the write group size equal to the number of processes on a compute node typically 16 or 32 A much higher read group size is preferred e g use 512 when run ning on 512 cores so that one process reads the input file and broadcasts relevant sections Put HDF5_WRITE_GROUP_SIZE under the OUTPUT keyword 2 output options OUTPUT TIMES y 5 10 15 20 FORMAT HDF5 HDF5 WRITE GROUP SIZE 16 END and HDF5 READ GROUP SIZE in the main body of the input file HDF5 READ GROUP SIZE 1024 For more details on the SCORPIO library please see Appendix A in Sarat Sreepathi s lt admin O sarats com gt dissertation Instructions for downloading and installing the SCORPIO library for use with PFLOTRAN is provided below Note that this software is separate from PFLOTRAN and under a LGPL 1 Download source code for building the SCORPIO library svn co http ascem io secure water org ascem io scorpio DIRNAME where DIRNAME is the installation directory Default scorpio The username and password are username pflotran dev password grOundw t3r lt 20 gt PFLOTRAN User Manual 83 5 0 August 14 2015 2 Compile SCORPIO library First set the environment variable SCORPIO_DIR to a directory where you wish to install the library files Please make sure that you have the correct permis sions to write to that location For examp
3. Return to List of Keywords lt 129 gt PFLOTRAN User Manual 84 52 0 August 14 2015 4 52 Keyword SOURCE_SINK Return to List of Keywords SOURCE SINK lt name gt REGION lt region name gt name of the region the source sink term is applied to FLOW CONDITION lt condition name gt name of the flow condition TRANSPORT CONDITION lt condition name gt name of the transport condition END Example SOURCE SINK Well 2 9 1 FLOW CONDITION Injection 1 TRANSPORT CONDITION Source REGION Well 2 9 1 END Return to List of Keywords lt 130 gt PFLOTRAN User Manual 84 53 0 August 14 2015 4 53 Keyword STRATIGRAPHY STRATA Return to List of Keywords Couples material IDs and or properties with a region in the problem domain STRATIGRAPHY STRATA MATERIAL lt string gt name of the material property to be associated with a region REGION lt string gt name of region associated with a material property Optional Cards START_TIME lt float gt lt string gt Start time when STRATA card is relevant The string specifies units This keyword allows for changes in a material property at a given point in time e g due to human intrusion END_TIME lt float gt lt string gt End time when STRATA card is relevant The string spec ifies units INACTIVE Inactivates all cells in the associated REGION END Note a filename can be provided instead of a material
4. DATASET Permeability FILENAME permeability_with_white_noise_multi h5 REALIZATION_DEPENDENT Python script fragment to generate permeability field dataset name PermeabilityxX h5dset h5file create dataset dataset name data rarrayl print done with dataset name dataset name PermeabilityY h5dset h5file create dataset dataset name data rarray2 print done with dataset name lt 104 gt PFLOTRAN User Manual 84 34 0 August 14 2015 dataset name PermeabilityZ h5dset h5file create dataset dataset name data rarray3 print done with dataset name For the full permeability tensor the dataset naming convention is PermeabilityX PermeabilityY PermeabilityZ PermeabilityXY PermeabilityXZ PermeabilityYZ Return to List of Keywords lt 105 gt PFLOTRAN User Manual 84 35 0 August 14 2015 4 35 Keyword MODE Return to List of Keywords Description determines the flow mode Richards variably saturated porous media MPH MPHASE FLASH2 CO H20 TH Thermal Hydrologic IMMIS THS Immisible MODE lt option gt Option Description GENERAL Two phase air water nonisothermal variably saturated groundwater flow RICHARDS Single phase isothermal variably saturated groundwater flow using Richards equation MPHASE MPH Two phase supercritical CO2 brine energy based on variable switching for phase c
5. 2 20 bw EE a 136 4 57 Keyword UNIFORM_VELOCITY Optional se cx esk 139 4 58 Keyword USE TOUCH OPTIONS 25225 2 42 2 001 e wae s 140 4 59 Keyword VELOCITY_DATASET 22 dra ra a ewe ge 141 4 60 Keyword WALLCLOCK STOP 4 22542402 zu 48 0 Se sa eee 142 5 PFLOTRAN Regression Test Manager 143 5 1 Running the Test Manager gt s os 44 3u 444454025 aa ar ke 143 2 EL OR en en ERE mn En Ber REM NS DE nd 144 5 3 Configuration Files s pesce c soe A RAE AAA ERMA 145 E NEW TESIS i m a ea Br an Br an BS EEE 146 5 5 Updating Test Results 224244494444 43 8 As u a su a se a ne 147 6 Visualization 148 Gl CUBO re oe AR ACA ANA AAA AA 148 OA Melisa a A ORE A A kr 148 6 3 G nuplot MatPlotLi ge gal ge ae Sede Sk ee Bi EON Sok a 149 7 Benchmark Problems 150 ZA Jon Exechanse u es eede 30 RET a8 HSE EERE EES HED RES dc 150 1 2 GENERAL REACTION Example ess ess wen ner REM ann 157 721 Problem Description s sa ces Ped Sek Pe Sensor Se BSE HEE E 157 7 22 MIO RESUME s ses koa se hoe ae Moose e ee 157 723 PELOTRAN Inp t Files lt 24025 simaa hae eae a hr HR od 158 7 3 RICHARDS Mode with Tracer SX 115 Hanford Tank Farm 161 731 Problem Description e s es wea ra ee ee a GA 161 PFLOTRAN User Manual 0 0 0 August 14 2015 732 Governing Equations a oras A o 161 7 3 2 1 Semi Analytical Solution for Steady State Conditions 162 A E 162 T33 Model Parameters
6. 3 2433E 10 2 0899E 01 1 6323E 01 with effective saturation s defined by SI Sir Se 7 36 1 Slr For the supercritical CO phase the Corey curve is used defined by 2 1 112 kry 1 8 1 8 7 37 with 51 Sir ua E 138 1 Bip Sgr Shown in Figure 7 9 is a comparison of PFLOTRAN with TOUGHREACT TOUGHREACT results provided by Alt Epping and Wanner private comm The same thermodynamic database is used for both codes Only slight differences can be seen The CO aqueous and total concentrations are essentially identical for PFLOTRAN in the low pH region where supercritical CO is present with slight differences for TOUGHREACT Note that the CO aqueous concentration and mole fraction Xco although not visible in the figure obtained from PFLOTRAN is not exactly constant This is caused presumably by a change in pressure as shown in Figure 7 10 for the liquid and CO pressures in addition to the CO saturation sco lt 175 gt PFLOTRAN User Manual 87 4 1 August 14 2015 5 5 5 TOUGHREACT Sy z TOUGHREACT Xco A TOUGHREACT moo tiot T o TOUGHREACT Moo ag TOUGHREACT pH 7 PFLOTRAN sy 4 PFLOTRAN Xco PFLOTRAN mco tot Sg Xco Mco ag tot PFLOTRAN Mo aa PFLOTRAN pH 435 3 9 10 20 30 40 50 Distance m Figure 7 9 Comparison with TOUGHREACT dashed curves and
7. Some important command line arguments when running manually are e executable the path to the PFLOTRAN executable e mpiexec the name of the executable for launching parallel jobs mpiexec mpirun aprun etc e config file the path to the configuration file containing the tests you want to run e recursive search the path to a directory The test manager searches the directory and all its sub directories for configuration files lt 143 gt PFLOTRAN User Manual 85 2 0 August 14 2015 tests a list of test names that should be run e suites a list of test suites that should be run e update indicate that the the gold standard test file for a given test should be updated to the current output e new tests indicate that the test is new and current output should be used for gold standard test file e check performance include the performance metrics SOLUTION blocks in regression checks The full list of command line options and a brief description can be found by running with the help flag S python regression tests py help 5 2 Test output The test manager produces terse screen output only printing critical warnings a progress bar as each test is run and a summary of the overall test results Example results from running make test are Test log file pflotran tests 2013 05 06_13 07 05 testlog xx WARNING mpiexec was not provided on the command line All paral
8. 4 21 0 August 14 2015 Keyword Description GEOMECHANICS_CONDITION TYPE DISPLACEMENT_X DISPLACEMENT_Y DISPLACEMENT_Z FORCE_X FORCE_Y FORCE_Z END DISPLACEMENT_X DISPLACEMENT_Y DISPLACEMENT_Z Initiates a geomechanics condition entry and defines its name Specifies condition type Specifies x displacement condition type Specifies y displacement condition type Specifies z displacement condition type Specifies in x force condition type Specifies in y force condition type Specifies in z force condition type Terminates type entry Displacement in the x direction Displacement in the y direction Displacement in the z direction FORCE_X Force in the x direction FORCE_X Force in the y direction FORCE_X Force in the z direction END Terminates condition entry Example TYRE DISPLACI EM GEOMECHANICS_CONDITION ENT 27 dirichlet DISPLAC EM END ENT_Z 0 d0 Return to List of Keywords lt 82 gt PFLOTRAN User Manual 84 22 0 August 14 2015 4 22 Keyword GEOMECHANICS_GRID Return to List of Keywords Description The grid type and the format for geomechanics is specified here Only unstructured grids can be read If you need to use a structured grid generate the grid as an unstructured grid in the implicit format see GRID keyword for details of the format below GEOMECHANICS_GRID
9. 7 Benchmark Problems In this section several benchmark problems are introduced illustrating the capabilities of PFLO TRAN 7 1 Ion Exchange Voegelin et al 2000 present results of ion exchange in a soil column for the system Ca Mg Na Here PFLOTRAN is applied to this problem using the Gaines Thomas exchange model Soil column C1 with length 48 1 cm and diameter 0 3 cm was used for the simulations A flow rate of 5 6 cm min was used in the experiment The inlet solution was changed during the coarse of the experiment at 20 and 65 pore volumes with cation compositions listed in Table 2 of Voegelin et al 2000 The CEC of the soil used in the experiments was determined to have a value of 0 06 0 002 mol kg As PFLOTRAN requires the CEC in units of mol m this was obtained from the formula Ns _ Ns MsVs Zur mu in ps 1 p CEC 7 12b Using a porosity of 0 61 and solid grain density of 3 0344 g cm yielded w 71 004 mol m The results of the simulation are shown in Figure 7 4 along with data reported by Voegelin et al 2000 Self sharpening fronts can be observed at approximately 10 and 71 at pore volumes and a self broadening front from 30 55 pore volumes where agreement with experiment is not as good The input file for the simulation is listed in Table 7 1 lt 150 gt PFLOTRAN User Manual 7 1 0 August 14 2015 0 01 Cations Expl Ca Expl Mg Expl Nat PFLOTRAN Ca FPFLOTRAN Mg PFL
10. Click on Open and select geomech xmf database nN A U N e Click on Add gt Pseudocolor gt rel_disp_z and click Draw Set Auto apply to avoid clicking Draw repeatedly ON Select the domain and rotate it to a preferred angle 7 Select Window 2 and make it active 8 Click Open and select pflotran h5 or pflotran h5 This file contains all the subsurface flow data 9 Click on e g Add gt Pseudocolor gt Gas Saturation or other desired variable 10 Click on Lock view and Lock time on both windows This will sync views and times on both windows lt 148 gt PFLOTRAN User Manual 86 3 0 August 14 2015 11 After awindow pops up select Yes 12 With Window 2 active select Operators gt Slicing gt ThreeSlice 13 Double click on three slice and change x and y to appropriate values 14 Select Window 1 15 Select Controls gt Expressions 16 Click New and add a name e g disp_vector Select Vector Mesh Variable 17 Under Definition add lt rel disp x _lb_m_rb_ gt lt rel_disp_y _lb_m_rb_ gt lt rel_disp_z _lb_m_rb_ gt Apply and Dismiss 18 Click Add gt Vector gt disp vector 19 Double click Vector under pflotran geomech xmf database disp_vector 20 Select Form and set Scale to e g 0 5 Then select Rendering and change magnitude color from Default to difference select a color scheme of your choice 21 Apply and Dismiss 22 Double click Ps
11. INVERT_DIRECTION Inverts the sign of the flux For fluxes at upwind boundaries influx will be negative This has no impact on the actual flux values other than to change the sign of the flux Optional END Examples INTEGRAL FLUX flux up shaft COORDINATES 25 40 15r 002300740 33 40 202407300230 INTEGRAL_FLUX NAME inflow COORDINATES 040024070740 0 d0 T0 d0 5 00 INVERT_DIRECTION Return to List of Keywords lt 98 gt PFLOTRAN User Manual 84 33 0 August 14 2015 4 33 Keyword LINEAR_SOLVER Return to List of Keywords Description Input LINEAR_SOLVER TRAN TRANSPORT FLOW SOLVER_TYPE SOLVER KRYLOV_TYPE KRYLOV KSP KSP_TYPE NONE PREONLY DIRECT LU decomposition ITERATIVE Bi CGStab BCGS and block Jacobi preconditioning with ILU O in each block GMRES FGMRES BCGS BICGSTAB BI CGSTAB IBCGS IBICGSTAB IBI CGSTAB Improved BCGS RICHARDSON CG PRECONDITIONER_TYPE PRECONDITIONER PC PC_TYPE NONE PCNONE ILU PCILU LU PCLU BJACOBI BLOCK JACOBI ASM ADDITIVE SCHWARTZ PCASM HYPRE SHELL HYPRE OPTIONS TYPE pilut parasails boomeramg euclid BOOMERAMG CYCLE TYPE lt char gt V w BOOMERAMG MAX LEVELS lt int gt BOOMERAMG MAX ITER lt int gt BOOMERAMG TOL lt float gt BOOMERAMG TRUNCFACTOR lt float gt BOOMERAMG AGG NL lt float gt BOOMERAMG AGG NUM PATHS lt int gt BOOMERAMG STRONG THRESHO
12. PFLOTRAN User Manual 87 3 4 August 14 2015 200000 1 0 9 100000 0 8 0 40 7 100000 10 6 c D 2 2 200000 705 D 2 pe an 104 O 300000 FR EEE 10 3 400000 Pressure O mm y Saturation 0 mm y 40 2 Pressure 8 mm y 500000 Saturation 8 mm y 40 1 Pressure 80 mm y i Saturation 80 mm y 600000 i i l l 0 0 10 20 30 40 50 60 70 Height m Figure 7 6 Steady state saturation and pressure profiles for infiltration rates of 0 8 and 80 mm y The water table is located at 6 m from the bottom of the computational domain lt 164 gt PFLOTRAN User Manual 87 3 4 August 14 2015 Liquid Saturation 0 10 20 30 40 50 60 70 Height m Figure 7 7 Simulation of a tank leak with a duration of two weeks showing the saturation profile for different times indicated in the figure for an infiltration rate of 8 mm y 75 100 0 4 T T T T T T Years 2 weeks 0 35 0 5 7 1 0 0 3 L 1 5 2 0 5 0 0 25 10 A 25 50 0 2 Concentration C C 0 10 20 30 40 50 60 70 Height m Figure 7 8 The solute concentration profile corresponding to Figure 7 8 for different times indi cated in the figure for an infiltration rate of 8 mm y lt 165 gt PFLOTRAN User Manual 87 3 5 August 14 2015 7 35 PFLOTRAN Input File Listing for the PFLOTRAN input file coupling Richards mode
13. S References Balay S V Eijkhout V W D Gropp L C McInnes and B F Smith 1997 Modern Software Tools in Scientific Computing Eds Arge E Bruaset AM and Langtangen HP Birkha ser Press pp 163 202 Coats K H and A B Ramesh 1982 Effects of Grid Type and Difference Scheme on Pattern Steamflood Simulation Results paper SPE 11079 presented at the 57th Annual Fall Tech nical Conference and Exhibition of the Society of Petroleum Engineers New Orleans LA September 1982 Ebigbo A Holger Class H Helmig R 2007 CO leakage through an abandoned well problem oriented benchmarks Comput Geosciences 11 103 115 DOI 10 1007 s10596 006 9033 7 Fenghour A W A Wakeham and V Vesovic 1998 The viscosity of carbon dioxide J Phys Chem Ref Data 27 1 31 44 Goode D J 1996 Direct simulation of groundwater age Water Resources Research 32 289 296 Hammond G E P C Lichtner C Lu and R T Mills 2011 PFLOTRAN Reactive Flow amp Transport Code for Use on Laptops to Leadership Class Supercomputers Editors Zhang F G T Yeh and J C Parker Ground Water Reactive Transport Models Bentham Science Publishers ISBN 978 1 60805 029 1 Khaleel R E J Freeman 1995 Variability and scaling of hydraulic properties for 200 area soils Hanford Site Report WHC EP 0883 Westinghouse Hanford Company Richland WA Khaleel R T E Jones A J Knepp FM Mann D A Myers P M Rogers R J Serne and
14. po po Return to List of Keywords lt 70 gt PFLOTRAN User Manual 84 15 0 August 14 2015 4 15 Keyword DEBUG Return to List of Keywords Input DEBUG PRINT SOLUTION VECVIEW SOLUTION VIEW SOLUTION PRINT RESIDUAL VECVIEW RESIDUAL VIEW RESIDUAL PRINT JACOBIAN MATVIEW JACOBIAN VIEW JACOBIAN PRINT JACOBIAN NORM NORM JACOBIAN PRINT COUPLERS PRINT COUPLER PRINT JACOBIAN DETAILED MATVIEW JACOBIAN DETAILED VIEW JACOBIAN DETAILED PRINT NUMERICAL DERIVATIVES VIEW NUMERICAL DERIVATIVES END Explanation Examples PRINT RESIDUAL PRINT JACOBIAN Return to List of Keywords lt 71 gt PFLOTRAN User Manual 84 16 0 August 14 2015 4 16 Keyword EOS Return to List of Keywords The EOS keyword defines an equation of state for a simulated fluid EOS lt string gt WATER GAS Specifies the fluid for which EOS applies Optional Input DENSITY lt string gt lt optional parameters gt DENSITY CONSTANT lt float gt DENSITY EXPONENTIAL lt float gt lt float gt lt float gt ref density rho0 ref pres sure p0 compressibility p poe Po DENSITY DEFAULT Default water EOS based on International Formulation Com mittee of the Sixth International Conference on Properties of Steam 1967 ENTHALPY lt string gt lt optional parameters gt ENTHALPY CONSTANT lt float gt VISCOSITY lt string gt lt
15. 0 0873 y 1 0341 10 A 56 with mass fraction of water y The viscosity and diffusivity have the forms u y 10 1 6743 1 91 0 0758 1078 A 57 and D y 4 0213 9 1181 y 5 9703 y1 0 4043 y 0 5687 10 A 58 The mass fraction is related to mole fraction according to x21W jp Lern a A 59 where the mean formula weight W is given by W 11 Wh o t2Wrra A 60 with formula weights for water and proplyene glycol equal to Wg o 18 01534 and Wppc 76 09 kg kmol Global mass conservation satisfies the relation d with M omav A 62 In terms of mass fractions and mass density MP WM ppyidV A 63 lt 195 gt PFLOTRAN User Manual 81 7 0 August 14 2015 A 6 Mode Air Water The Air Water mode involves two phase liquid water gas flow coupled to the reactive transport mode Mass conservation equations have the form sinn spe V anz qPaT ps D p Vx ps Dyp Vas Q A 64 for liquid and gas saturation s densit diffusivity D Darcy velocity q and mole frac Lg y Pi g y y y Lg lg A Lg r E tion x The energy conservation equation can be written in the form 2 Prat V dapatla a prC T V kV Q A 65 a l g as the sum of contributions from liquid and gas fluid phases and rock with internal energy Ua and enthalpy Ha of fluid phase a rock heat capacity Cp and thermal conductivity Note
16. A 171 Then the transport equations become o En eu 2 sn V Q 2 dos A 172 The total sorbed concentrations are obtained from the equations Ta RS Sia A 173 lt 211 gt PFLOTRAN User Manual 81 9 3 August 14 2015 A 9 3 Sorption Isotherm lt Under Revision gt The distribution coefficient K r m kg is customarily defined as the ratio of sorbed to aqueous concentrations with the sorbed concentration referenced to the mass of solid as given by M3 M KP 1 A 174 2 A 174b NM i ei A 174c Cj Pw My where M W N M o W N de refers to the mass and number of moles of sorbed and aqueous solute related by the formula weight W of the jth species M refers to the mass of the solid V denotes the aqueous volume S N M mol kg represents the sorbed concentration refer enced to the mass of solid C N y V denotes molarity and m C pw represents molality where p is the density of pure water The distribution coefficient K E may be related to its dimensionless counterpart K 7 de fined by N N V 1 S Ke 23 A 175 J No N V psi Cj by writing NEM V V V Ria e A 176 j M V V V N 1 o p Kk RP A 177 psi psi with grain density ps M Vs bulk density pp 1 p ps porosity p V V and saturation S1 Vi Vp An alternative definition of the distribution coefficient denoted by R E kg m is obtained by using molalit
17. PFLOTRAN User Manual A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes Peter C Lichtner Glenn E Hammond Chuan Lu Satish Karra Gautam Bisht Benjamin Andre Richard Mills Jitu Kumar OFM Research peter lichtner O gmail com 8 SNL gehammo Osandia gov IHEG luchuancn 163 com LANL satkarra lanl gov Y LBNL gbishtO1bl gov NCAR andre ucar edu Intel rtm eecs utk edu PORNL jitul503 gmail com August 14 2015 ee Sandia Nee Alamos A Mh is Ze RA National Laboratory Fa PFLOTRAN User Manual 0 0 0 August 14 2015 TABLE OF CONTENTS 1 Introduction 11 2 Quick Start 12 2 1 Installing PELOTRAN 2 2225 2 essa tl a E dA A 12 2 2 Running on Big Iron Parallel Architectures lt lt lt 15 3 Installation 16 3 1 Compilers orses rers isete dan Aa ee ee 16 3 2 Building PEISE posse a ar Bar GD eek 16 321 MacOSX 224642434 42 443 65 Denn 17 3 2 1 1 Lion Mavericks lt Mac OS X 10 9 x 17 32 12 Yosemite Mac OS X 10 10 x canas ma e 17 322 Windows dis a a a Sad A 18 323 ORNS acter XII 2 cee a BI AAA AA AA 18 3 3 Building PELOTRAN lt n aoa moen rs OR HE OE Re a 19 3 4 Updating PFLOTRAN coser ARANA ARA 19 3 5 Parallel I O using Sarat Sreepathi s SCORPIO library with PFLOTRAN 20 3 6 Running PFLOTRAN q cs dos 2 0 0 au ee A ORE AR a 23 3 7 Multiple Realization Simulat
18. TIMESTEPPER TS_ACCELERATION 8 MAX_STEPS 100000 MAX_STEPS 1 GRID TYPE structured NXYZ 250 1 1 BOUNDS 0 d0 0 d0 0 d0 481d0 1 d0 1 d0 0 flow solvers NEWTON_SOLVER FLOW PRECONDITIONER_MATRIX_TYPE AIJ reference variables time stepping discretization lt 152 gt PFLOTRAN User Manual 87 1 0 August 14 2015 RTOL 1 ATOL 1 STOL 1 d 30 TOL_UPDATE 1 d0 NO_INFINITY_NORM NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE d 8 d 8 LINEAR_SOLVER FLOW KSP_TYPE PREONLY PC_TYPE LU KSP_TYPE FGMRES samrai PC_TYPE SHELL samrai NEWTON_SOLVER TRANSPORT PRECONDITIONER_MATRIX_TYPE AIJ RTOL 1 d 8 ATOL 1 d 8 STOL 1 d 30 NO_INFINITY_NORM NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE LINEAR_SOLVER TRANSPORT PC_IYPE LU KSP_TYPE PREONLY KSP_TYPE FGMRES samrai PC_TYPE SHELL samrai FLUID_PROPERTY DIFFUSION_COEFFICIENT 1 d 9 DIFFUSION_COEFFICIENT 9 33333e 7 transport solvers fluid properties MATERIAL_PROPERTY HD D 1 SATURATION_FUNCTION default POROSITY 0 61 TORTUOSITY 1 0 LONGITUDINAL_DISPERSIVITY 0 001 PERMEABI
19. based on the assumption that p is hydrostatic 1 e py p o Ps92 reduce to o Ot o gg 9 simUi song simUs 1 prc T V gt omh V KVT Qe ATT Un 9 sy XT sim sim V vim V losgrangDgV XE Qu A 77a k CY pi p192 A 770 In the above formulation temperature and liquid pressure are chosen to be primary variables It is ensured that complete dry out does not occur and that liquid is present at all times With this approach it is not necessary to change the primary variables based on the phases present In addition to the previously described mass and energy balance equations additional consti tutive relations are required to model non isothermal multiphase flow of water Assuming thermal equilibrium among the ice liquid and vapor phases the mole fraction of water in vapor phase is given by the relation ea A 78 Pg where p is the vapor pressure and p is the gas pressure It is assumed that p 1 atm throughout the domain Vapor pressure is calculated using Kelvin s relation which includes vapor pressure lowering due to capillary effects as follows Fe l PaT 2 A 79 Po Paul P exp nn nn where Pa is the saturated vapor pressure P is the liquid gas capillary pressure and R is the gas constant Empirical relations for saturated vapor pressure are used for both above and below freezing conditions To calculate the partition of ice liquid and
20. 1 l g is the saturation of the a th phase no a 2 l g is the molar density of the a th phase py p are the mass densities of the gas and liquid phases Qu is the mass source of H20 Xola 1 1 g is the mole fraction of H20 in the a th phase 7 is the tortuosity of the gas phase D is the diffusion coefficient in the gas phase 7 is the temperature assuming all the phases and the rock are in thermal equilibrium c is the specific heat of the rock p is the density of the rock Uala i l g is the molar internal energy of the a th phase H a L g is the molar enthalpy of the a the phase Q is the heat source V is the gradient operator V is the divergence operator The Darcy velocity for the gas and liquid phases are given as follows krok Vg V py p492 A 74a Hg krik v WV pi pa A 74b lt 197 gt PFLOTRAN User Manual 1 7 1 August 14 2015 where k is the absolute permeability k a L g is the relative permeability of the a th phase pala 1 9 is the viscosity of the a th phase pala L g is the partial pressure of the a th phase g is acceleration due to gravity and z is the vertical distance from a reference datum The constraint on the saturations of the various phases of water is given by Sp sy s 1L A 75 Furthermore neglecting the amount of air in liquid and ice phases it follows that X 0 X 0 gt X 1 1 A 76 and so Eqns A 73 A 74
21. 15 2040 N 25 30 0 35 40 0 45 50 0 60 70 80 90 100 125 150 175 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 PERIODIC TIME 0 1d SCREEN PERIODIC 50 FORMAT HDF5 MULTIPLE_FILES FORMAT TECPLOT BLOCK FLUXES lt 180 gt PFLOTRAN User Manual 87 4 2 August 14 2015 MASS_BALANCE PRINT_COLUMN_IDS PERIODIC_OBSERVATION TIMESTEP 1 fluid properties FLUID_PROPERTY LIQUID_DIFFUSION_COEFFICIENT 1 d 9 GAS_DIFFUSION_COEFFICIENT 2 13e 5 NAME flx COORDINATES 0 d0 0 d0 80 d0 1000 d0 1000 d0 80 d0 material properties MATERIAL PROPERTY aquifer ID 1 POROSITY 0 15d0 TORTUOSITY 1 d0 ROCK_DENSITY 2 84E3 SPECIFIC_HEAT 1E3 THERMAL_CONDUCTIVITY_DRY 0 5 THERMAL_CONDUCTIVITY_WET 0 5 SATURATION_FUNCTION sf PERMEABILITY PERM_X 2 d 14 PERM_Y 2 d 14 PERM_Z 2 d 14 MATERIAL_PROPERTY aquitard ID 2 POROSITY 0 15d0 TORTUOSITY 1 d0 ROCK_DENSITY 2 84E3 SPECIFIC_HEAT 1E3 THERMAL_CONDUCTIVITY_DRY 0 5 THERMAL_CONDUCTIVITY_WET 0 5 SATURATION_FUNCTION sf PERMEABILITY PERM_X 1 d 18 PERM Y 1 d 18 PERM Z 1 d 18 MATERIAL PROPERTY well ID 3 POROSITY 0 15d0 TORTUOSITY 1 d0 ROCK_DENSITY 2 84E3 SPECIFIC_HEAT 1E3 THERMAL_CONDUCTIVITY_DRY 0 5 THERMAL_CONDUCTIVITY_WET 0 5 SATURATION_FUNCTION sf PERMEABILITY PERM_X 1 d 12 PERM_Y 1 4 12 PERM Z 1 d 12 saturation functions SATURATION FUNCTION sf lt 181 gt PFLOTRAN
22. 173 80 and the empty site concentration by Ww sa gt A 160 1 30 AQ where the ion activity product Q is defined by One I 405 A 161 j The site concentration wa satisfies the relation Wa Sat Y Sia A 162 and is constant The equilibrium sorbed concentration S74 is defined as W SA o SS ie A 163 Ja a Viji 10 1 KQ Vj Q lt 210 gt PFLOTRAN User Manual 81 9 3 August 14 2015 A 9 2 3 Multirate Sorption In the multirate model the rates of sorption reactions are described through a kinetic relation given by Or e al ka Sia A 164 for surface complexes and OSa E 2 RS Sia A 165 Kl A 166 for empty sites where S 4 denotes the equilibrium sorbed concentration For simplicity in what follows it is assumed that vy 1 With each site is associated a rate constant k and site concentration wa These quantities are defined through a given distribution of sites such that Je plka dka 1 A 167 0 The fraction of sites f belonging to site a is determined from the relation ka A Ko 2 fa Hlka dka ka Aka A 168 ka Aka 2 with the property that Re A 169 Given that the total site concentration is w then the site concentration wa associated with site a is equal to O PA A 170 An alternative form of these equations is obtained by introducing the total sorbed concentra tion for the jth primary species for each site defined as Sia Y Via
23. 7 19 Ox a o 7 2 2 Simulation Results Results are shown in Figure 7 5 for the concentrations of species A B C at 5 years obtained from PFLOTRAN and a prototype code written in C based on the PETSc TS time stepping class The code uses a backward Euler TSBEULER time integrator with nodes placed at the grid cell corners The slight discrepancy between the results of the two codes may be due to the use of a finite volume cell centered grid in PFLOTRAN versus the corner node grid used in the prototype code lt 157 gt PFLOTRAN User Manual 87 2 3 August 14 2015 Concentration mol L Distance m T r A PFLOTRAN Ts O B PFLOTRAN TS S C PFLOTRAN T 5 Figure 7 5 Comparison of concentrations for species A B C plotted as a function of distance for an elapsed time of 5 years for PFLOTRAN and a prototype code based on PETSc s TS class 7 2 3 PFLOTRAN Input File Description 1D general reaction with the aqueous reaction A 2 B gt C SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT useful tranport parameters UNIFORM_VELOCITY 1 d0 0 d0 0 d0 m yr REFERENCE_DENSITY 1000 d0 CHEMISTRY PRIMARY SPECIES A ag B aq C aq GENERAL_REACTION REACTION A aq 2 B ag lt gt C aq FORWARD_RATE 5 d 8 BACKWARD_RATE 0 d0 lt 158 gt PFLOTRAN User Manual 87
24. By default if ALL or MINERALS are listed under CHEMISTRY OUTPUT the volume fractions and rates of kinetic minerals are printed To print out the saturation indices of minerals listed under the MINERAL keyword add the name of the mineral to the OUT PUT specification Saturation indices are not printed when only ALL or MINERALS are specified Outputting tens to hundreds of minerals most of which are simply considered as potential candidates for active minerals but not modeled through a kinetic precipitation dissolution reaction would overwhelm the output Return to List of Keywords lt 62 gt PFLOTRAN User Manual 84 10 0 August 14 2015 4 10 Keyword COMPUTE_STATISTICS Description COMPUTE_STATISTICS enables the calculation statistical analysis of flow veloci ties during a simulation The average maximum minimum and standard deviations velocities are computed Return to List of Keywords Input COMPUTE STATISTICS compute statistics true Explanation Example COMPUTE STATISTICS Return to List of Keywords lt 63 gt PFLOTRAN User Manual 84 11 0 August 14 2015 4 11 Keyword COZ DATABASE Return to List of Keywords Description The keyword COZ DATABASE is for specifying the path to CO database file pro viding a lookup table for CO fluid properties density viscosity fugacity and fugacity coefficient derived from the Span Wagner 1996 EOS The temperature pressure
25. FLUXES VELOCITIES MASS_BALANCE frequency of output time frequency of output time step Tecplot POINT output valid for 1D and 2D prob lems on a single processor core Tecplot BLOCK output for multi processor core runs HDFS5 output format written to a h5 file which can be read by Vislt and ParaView MAD Method of Anchored Distributions format VTK format which can be read by Vislt and Par aView time units of seconds s minutes min hours h hr days d weeks w months mo and years y yr keyword to output velocities keyword to output global mass balances and boundary fluxes both cumulative and instanta neous The output in the mass balance file refers to global mass conservation This output is described in detail for the MPHASE mode The total number of moles of the th component in phase a is given as the integral over the entire computational domain see Eqn A 19a N 2 PSaNak AV 4 2 From the governing equations Eqn A 19a the time rate of change of the total number of moles of the sth component NSS Ny 4 3 lt 120 gt PFLOTRAN User Manual 84 44 0 August 14 2015 is given by dN dN 2 4 4 dt 5 dt en gt Fi dS Q 4 5 av where the surface integral on the right hand side is over the flux flowing through the boundaries of the domain The surface averaged flux F is defined as a Fi dS 4 6 av defined as positive for fl
26. FNO_INFINITY_NORM lt 33 gt PFLOTRAN User Manual 84 4 0 August 14 2015 NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE LINEAR_SOLVER TRANSPORT PC_TYPE LU KSP_TYPE PREONLY KSP_TYPE FGMRES samrai PC_TYPE SHELL samrai fluid properties O SO O O O O O O O O O OS FLUID_PROPERTY DIFFUSION_COEFFICIENT 1 d 9 UNIFORM_VELOCITY 3 84259d 6 0 d0 0 d0 1 38333 cm h H material properties EE MATERIAL PROPERTY HD ID 1 SATURATION_FUNCTION HD POROSITY 0 262 TORTUOSITY 1 0 PERMEABILITY PERM_ISO 5 43d 13 saturation permeability functions gt SATURATION_FUNCTION HD SATURATION_FUNCTION_TYPE VAN_GENUCHTEN RESIDUAL_SATURATION 0 115 LAMBDA 0 286 ALPHA 1 9401d 4 H output zz zz en zz ze zz anne OUTPUT PERIODIC TIMESTEP 1 PERIODIC TIME 0 1 y FORMAT HDF5 FORMAT TECPLOT BLOCK VELOCITIES times TT TIME FINAL TIME 1 d0 y INITIAL 1 e 6 y MAXIMUM_TIMESTEP_SIZE 1 e 2 y H regions REGION all COORDINATES 0 d0 0 d0 0 d0 6 d0 6 d0 6 d0 lt 34 gt PFLOTRAN User Manual 84 4 0 August 14 2015 REGION Top FACE TOP COORDINATES 0 d0 0 d0 6 d0 6 d0 6 d0 6 d0 REGION Inlet FACE TOP COORDINATES 2 d0 2 d0 6 d0 4 d0 4 d0 6 d0 BLOCK 343466 REGION Bottom FACE BOTTOM COORDINATES 0 d0 0 d0 0 d0 6 d0 6 d0 0 d0 H flow condit
27. PERM ISO lt float gt Isotropic permeability values m PERM_XY lt float gt Off diagonal permeability kyy for use with MFD mimetic_unstructured grid m not currently supported PERM_XZ lt float gt m Off diagonal permeability kyz PERM_YZ lt float gt m Off diagonal permeability kyz END PERMEABILITY_POWER lt float gt see Eqn A 124 PERMEABILITY_CRIT_POR lt float gt see Eqn A 125 PERMEABILITY_MIN_SCALE_FAC lt float gt see Eqn A 126 TORTUOSITY_POWER lt float gt lt 102 gt PFLOTRAN User Manual 84 34 0 August 14 2015 MINERAL SURFACE AREA POWER toggle to update mineral surface area see MINERAL_KINETICS keyword for setting porosity or volume fraction power SECONDARY CONTINUUM Activate with MULTIPLE CONTINUUM keyword TYPE lt char gt SLAB NESTED CUBES NESTED SPHERES NUM CELLS lt int gt Number of secondary continuum grid cells LOG GRID SPACING Toggle to use logarithmic grid spacing in secondary continua applies to nested spheres and cubes only OUTER SPACING lt float gt m Outer matrix node grid spacing for logarithmic grid see Egns A 90 LENGTH lt float gt m length of SLAB type AREA lt float gt m cross section area for SLAB type MATRIX BLOCK SIZE lt float gt m matrix block size for NESTED CUBES type FRACTURE SPACING lt float gt m fracture spacing for NESTED CUBES type RADIUS lt float gt m radius for NESTED SPHERES type EPSILON lt float
28. a2 soa uon ER a 54 eS Se Se EU A 162 732 SMU Results st si 242 24 BEER re 163 732 ERLOTRAN put File lt s scs dna ee aa am We we we STR a 166 TA MPHASE s Set ce He ae rn a a ee ee ee em a 174 7 4 1 CO Sequestration 1D Example Problem and Comparison with TOUGHREACT gt e s soes a aea e e e a a R A 174 74 2 CO Sequestration in the Presence of a Leaky Well 178 8 References 185 Appendix A Governing Equations 187 A l Mods RICHARDS 22 22 AH ER een 45444444 187 A 2 Capillary Pressure Relations lt lt lt eee ee eee 187 A 2 1 Brooks Corey Saturation Function 2 188 A 2 2 Relative Permeability 5 225 us aaa sache ara 188 A23 MODO 2 4 9 244 284 coe Roe Kee chata hs 189 A 3 Mode PHASE orgs aaa Bd SC ea eh eek we he oe e 4 189 Aal Source Sink Terms lt lt sd es a eat na EM ew Rae A 190 A 3 2 Variable Switching ck ee ee aw ER RHE RH OHS 191 A 3 2 1 Gas pg T 260 Two Phase Py Ty 8 sus usas 191 A 3 2 2 Liquid py T 260 gt Two phase py Ts cc 192 A 3 2 3 Two Phase py T sy gt Liquid p T xG0 or Gas py T vto 192 A 3 3 Sequentially Coupling MPHASE and CHEMISTRY 193 A 4 Mode IMMI S 2 AA RATA 193 AS Mode MISCIBLE pr sou ri See O A A AAA 194 A 6 Mode Air Waterf apra dci va ra EIA na 196 PFLOTRAN User Manual 0 0 0 August 14 2015 A 7 Mode TH Thermal Hydrol gie lt c o c ooorcsccsress essa Dil EMO ss
29. in order to transfer data from the subsurface to geomechanics grid without interpolation the geomechanics grid is constructed such that the vertices of the geomechanics grid coincide with the cell centers of the subsurface mesh That is the dual mesh of the subsurface mesh is used for the geomechanics solve Also the geomechanics grid must be read in as an unstructured grid Even if one needs to work with a structured grid the grid must be set up in the unstructured grid format lt 219 gt PFLOTRAN User Manual 82 2 0 August 14 2015 Appendix B Method of Solution The flow and heat equations Modes RICHARDS MPHASE FLASH2 TH are solved using a fully implicit backward Euler approach based on Newton Krylov iteration Both fully implicit backward Euler and operator splitting solution methods are supported for reactive transport B 1 Integrated Finite Volume Discretization The governing partial differential equations for mass conservation can be written in the general form o As V Fj Q B 1 with accumulation A flux F and source sink Q Integrating over a REV corresponding to the nth grid cell with volume V yields d dt Jy Va Va The accumulation term has the finite volume form d Attat _ At dt At B 3 with time step At The flux term can be expanded as a surface integral using Gauss theorem V F F dS B 4 Vn OVn gt Eni Ants B 5 where the latter finite volume form is based on th
30. linkage of these process models is preset For instance SUBSURFACE_FLOW pro cesses always precede SUBSURFACE TRANSPORT processes in timestep execution Options include SUBSURFACE_FLOW lt string gt GENERAL RICHARDS MPHASE END SUBSURFACE_TRANSPORT lt string gt GLOBAL_IMPLICIT END SURFACE_FLOW lt string gt END END SUBSURFACE Opens a block of input parameters for subsurface process models this block is essentially the old PFLOTRAN input file with the exception that several of the cards 1 e flow MODE have been moved to the SIMULATION block END_SUBSURFACE Closes the subsurface block lt 26 gt PFLOTRAN User Manual 84 2 0 August 14 2015 Example SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_FLOW flow RICHARDS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT END SUBSURFAC E END_SUBSURFACI Gl lt 27 gt PFLOTRAN User Manual 84 2 2 August 14 2015 4 2 1 Keyword SUBSURFACE_FLOW SUBSURFACE_FLOW Block Required Cards MODE lt string gt Specifies the flow mode to be employed Water Modes RICHARDS single phase variably saturated flow GENERAL two phase air water energy TH variably saturated flow and energy and optional ice phase COs Related Modes MPHASE two phase supercritical CO water energy IMMISCIBLE immiscible two phase CO gt water energy MISCIBLE miscible H 0 glycol FLASH2
31. lt float gt The maximum CFL number allowed for transport Enables Courant CFL number lim iting on the transport time step DT_FACTOR lt float gt Array of floating point numbers of tfac array expert users only INITIALIZE_TO_STEADY STATE lt float gt steady state convergence relative toler ance Flag indicating that the simulation is to be initialized as steady state Warning not robust RUN_AS_STEADY_ STATE Flag requesting that a steady state solution be computed based on boundary and initial conditions at the beginning of the simulation Warning not robust MAX_PRESSURE_CHANGE lt float gt Maximum change in pressure for a time step 5 d4 Pa MAX_TEMPERATURE_CHANGE lt float gt Maximum change in temperature for a time step 5 C MAX_CONCENTRATION_CHANGE lt float gt Maximum change in pressure for a time step 1 mol L MAX_SATURATION_CHANGE lt float gt Maximum change in pressure for a time step 0 5 PRESSURE_DAMPENING_FACTOR lt float gt END lt 134 gt PFLOTRAN User Manual 84 55 0 August 14 2015 Examples TIMESTEPPER TS_ACCELERATION 8 AX_STEPS 10000 terminates simulation after 10 000 time steps AX_TS_CUTS 5 terminates simulation after 5 consecutive time step cuts END TIMESTEPPER CFL_LIMITER 1 limits time step size to enforce a CFL er dl END Return to List of Keywords lt 135 gt PFLO
32. lt string gt Filename Description Set initial conditions for flow from specified HDFS file Example regression tests default 543 543 flow in INITIALIZE FLOW FROM FILE 543 initial pressure h5 4 31 Keyword INITIALIZE TRANSPORT FROM FILE INITIALIZE TRANSPORT FROM FILE lt string gt Filename Description Set initial conditions for transport from specified HDFS file Example INITIALIZE TRANSPORT FROM FILE filename h5 Return to List of Keywords lt 97 gt PFLOTRAN User Manual 84 32 0 August 14 2015 4 32 Keyword INTEGRAL_FLUX Return to List of Keywords Description Sets up a surface through which fluxes of all primary dependent variables can be calculated Note add keyword PERIODIC_OBSERVATION to OUTPUT keyword to toggle printing of integral fluxes to a file with the suffix int dat Input INTEGRAL FLUX lt string Optional gt Opens input block and associates a name with INTE GRAL_FLUX Required NAME lt string gt Specifies a name that is associated with the integral fluxes in the int dat file This name will overwrite any name specified with the INTE GRAL_FLUX keyword Optional COORDINATES Opens a block listing coordinates x1 y1 21 2 Y2 22 defining the rectangle over which the flux is to be calculated The coordinates must form a rectangular plane that is aligned with the coordinate axes Required
33. two phase supercritical CO2 water energy Optional Cards OPTIONS MODE dependent block for defining options for each flow process model Example SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_FLOW flow ODE GENERAL OPTIONS ISOTHERMAL TWO_PHASE_ENERGY_DOF TEMPERATURE GAS_COMPONENT_FORMULA_WEIGHT 2 01588D0 MAXIMUM_PRESSURE_CHANGE 1 0D6 END 4 2 2 Keyword SUBSURFACE TRANSPORT SUBSURFACE_TRANSPORT Block Optional Cards GLOBAL_IMPLICIT Specifies fully implicit coupling of transport and reaction OPERATOR_SPLITTING not currently implemented lt 28 gt PFLOTRAN User Manual 84 2 2 August 14 2015 Example SIMULATION SIMULATION_TYPE SUBSURFACI PROCESS_MODELS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT E El lt 29 gt PFLOTRAN User Manual 4 3 0 August 14 2015 4 3 Subsurface Keyword Links Table 4 5 SUBSURFACE Keywords listed in alphabetical order Keyword Description BOUNDARY CONDITION BRINE CHARCTERISTIC CURVES CHECKPOINT CHEMISTRY MINERAL KINETICS SORPTION RADIOACTIVE DECAY REACTION GENERAL REACTION MICROBIAL REACTION REACTION SANDBOX OUTPUT COMPUTE STATISTICS CO2 DATABASE CONSTRAINT Transport required DATASET DBASE DATASET DEBUG EOS FLOW CONDITION FLUID PROPERTY GEOMECHANICS GEOMECHANICS GRID GEOMECHANICS
34. 14 2015 Appendix C Reaction Sandbox 225 CA ee RA A do 225 Cs Deere ep ara odia a aa ae a e a 225 lt 8 gt PFLOTRAN User Manual 0 0 0 August 14 2015 LIST OF FIGURES 4 1 Side set numbering of supported cell types within unstructured grid 4 2 a Example of a 5x4x3 unstructured grid problem with default decomposition across two processors Cells labelled in natural ID b ParMETIS decomposition of the domain c Representation of a global PETSc vector 4 3 a b Local and ghost cells on proc O and proc 1 with cell IDs in PETSc order c d Local PETSc Vector with cell IDs in local ghosted order 7 4 Breakthrough curves for Ca Mg and Nat compared with experimental results from Voepeti er al 2000 sas poa 308000 Shoe Sr aa A RR 7 5 Comparison of concentrations for species A B C plotted as a function of distance for an elapsed time of 5 years for PFLOTRAN and a prototype code based on PER AE A ee Bee er a 7 6 Steady state saturation and pressure profiles for infiltration rates of 0 8 and 80 mm y The water table is located at 6 m from the bottom of the computational COMM ssp ssr ee ed Mek ESE ERE VESEY SE aco erben 7 7 Simulation of a tank leak with a duration of two weeks showing the saturation profile for different times indicated in the figure for an infiltration rate of 8 mm y 7 8 The solute concentration profile corresponding to Figure 7 8 for different times indi
35. 2 3 August 14 2015 DATABASE Users lichtner pflotran pflotran dev database hanford dat OUTPUT all TOTAL LINEAR_SOLVER TRANSPORT SOLVER DIRECT END TYPE structured NXYZ 100 1 1 BOUNDS 0 d0 0 d0 0 d0 100 d0 100 d0 1 d0 END fluid properties FLUID_PROPERTY DIFFUSION_COEFFICIENT 1 d 9 END material properties MATERIAL_PROPERTY soill ID I POROSITY 0 25d0 TORTUOSITY 1 d0 ROCK_DENSITY 1650 d0 END OUTPUT TIMES y 5 FORMAT TECPLOT POINT END FINAL TIME 5 d0 y INITIAL TIMESTEP SIZE 1 d0 h MAXIMUM TIMESTEP SIZE 1 d 2 y END REGION all COORDINATES 0 d0 0 d0 0 d0 100 d0 1 d0 1 d0 END REGION west FACE west COORDINATES 0 d0 0 d0 0 d0 0 401 490 1 40 END REGION east FACE east COORDINATES 100 d0 0 d0 0 d0 100 d0 1 d0 1 d0 END lt 159 gt PFLOTRAN User Manual 7 23 August 14 2015 TRANSPORT_CONDITION initial TYPE dirichlet CONSTRAINT_LIST 0 d0 initial END TRANSPORT_CONDITION inlet TYPE dirichlet CONSTRAINT_LIST 0 d0 inlet END TRANSPORT_CONDITION outlet TYPE zero_gradient CONSTRAINT_LIST 0 d0 inlet CONSTRAINT initial CONCENTRATIONS A aq 1 d 16 T B aq 1 d 16 C ag 1 d 16 T H END CONSTRAINT inlet CONCENTRATIONS A aq 1 d0 T B aq 1 d0 C ag 1 d 16 T H initial condition INITIAL CONDITION REGION all ND EJ BOUNDARY_CONDITION
36. Cac12 aq Cai CaOH MgCO3 aq MgHCO3 MgGi MgOH Al OH 4 Al OH 3 aq Al OH 2 lt 45 gt PFLOTRAN User Manual 84 9 0 August 14 2015 AMO H3S104 H2S104 HCl aq KCl aq KOH ag NaCl aq Naco3 NaHCO3 aq NaHSi03 aq NaOH aq GAS_SPECIES CO2 g 02 9 MINERALS Quartz K Feldspar Kaolinite Gibbsite Muscovite Oligoclase Illite Albite Anorthite Brucite Magnesite Calcite Example Deactivate redox equilibrium reactions for the listed redox pairs RI EDOX_SPECIES F F H SO4 ES Acetate Ethanol aq lt 46 gt Return to List of Keywords PFLOTRAN User Manual 84 9 1 August 14 2015 4 9 1 Keyword MINERAL_KINETICS The keyword MINERAL KINETICS specifies parameters for kinetic mineral precipitation dissolution reactions based on transition state theory Return to List of Keywords MINERAL KINETICS Mineral Name lt Char gt RATE CONSTANT lt float gt mol m s Jf lt float gt lt 0 lt float gt 10 lt float gt ACTIVATION_ENERGY lt float gt kJ mol Referenced to rate constant at 25 C AFFINITY THRESHOLD lt float gt AFFINITY POWER lt float gt see Eqn A 114 TEMKIN CONSTANT lt float gt See Eqn A 114 SURFACE AREA POROSITY POWER lt float gt see Eqn A 128 SURFACE AREA VOL FRAC
37. Kco Yco Mco where it is assumed that Pat T Yoo 1 p A 29 A 30 A 31 A 3 2 3 Two Phase py T s gt Liquid p T co or Gas py T o Equilibrium in a two phase H 0 CO system is defined as the equality of chemical potentials between the two phases as expressed by the relation foo Yco Pco Py Koo co Mco where Yco TOO FR tho H20 Py and PalT sat o a Dg From these equations a Henry coefficient like relation can be written as Yoo Kco Tco gt where a el Too Teco Veo K co Mco P co Pg TCOs Koo A 32 A 33 A 34 A 35 A 36 A 37 A 38 e A phase change to single liquid or gas phase occurs if s lt 0 or sy gt 1 respectively Conversion relations between mole fraction x mass fraction w and molality m are as follows Molality mole fraction m My 0 Wn onno WH oTH 0 Wao 1 AHO zi lt 192 gt A 39 PFLOTRAN User Manual 1 4 0 August 14 2015 Mole fraction molality Ni Ni Mg o Mi Wyomi Tu A 40 N Mo N 5 m 1 Wh o Y 14H20 mu Mole fraction mass fraction i W Win Aa E ni A mo Wow A 41 N SW Wm DW Mass fraction mole fraction w A 42 M gt Win So Wa A 3 3 Sequentially Coupling MPHASE and CHEMISTRY MPHASE and CHEMISTRY may be sequentially coupled to one another by including the CHEM ISTRY keyword in th
38. M I Wood 2000 Modeling data package for S SX Field Investigation Report FIR Report RPP 6296 Rev 0 CH2M Hill Hanford Group Richland WA Lichtner P C Yabusaki S B Pruess K and Steefel C I 2004 Role of Competitive Cation Exchange on Chromatographic Displacement of Cesium in the Vadose Zone Beneath the Hanford S SX Tank Farm VJZ 3 203 219 Lichtner P C 1996a Continuum Formulation of Multicomponent Multiphase Reactive Trans port In Reactive Transport in Porous Media eds P C Lichtner C I Steefel and E H Oelkers Reviews in Mineralogy 34 1 81 Lichtner P C 1996b Modeling Reactive Flow and Transport in Natural Systems Proceedings of the Rome Seminar on Environmental Geochemistry Eds G Ottonello and L Marini Castelnuovo di Porto May 22 26 Pacini Editore Pisa Italy 5 72 Lichtner P C 2000 Critique of Dual Continuum Formulations of Multicomponent Reactive Transport in Fractured Porous Media Ed Boris Faybishenko Dynamics of Fluids in Frac tured Rock Geophysical Monograph 122 281 298 lt 185 gt PFLOTRAN User Manual 8 0 2 August 14 2015 Painter S L 2011 Three phase numerical model of water migration in partially frozen geologi cal media model formulation validation and applications Computational Geosciences 15 69 85 Peaceman D W 1977 Interpretation of Well Block Pressures in Numerical Reservoir Simula tion with Nonsquare Grid Blocks and Anisotropic Permeability
39. PFLO TRAN solid curves after an elapsed time of 0 4 y corresponding to the end of injection Reasonable agreement is obtained between the two codes lt 176 gt PFLOTRAN User Manual 87 4 1 August 14 2015 200 0 6 198 1 10 5 196 0 4 194 Fe O N 192 103 5 A a a 190 0 1 0 5 10 15 20 25 30 35 Distance m Figure 7 10 Liquid blue curve and supercritical CO red curve pressures predicted by PFLOTRAN after an elapsed time of 0 4 y corresponding to the end of injection Also shown is the CO saturation green curve lt 177 gt PFLOTRAN User Manual 87 4 2 August 14 2015 7 4 2 CO Sequestration in the Presence of a Leaky Well The simulation domain has a lateral extent of 1 000 x 1 000 m and vertical height of 160 m The leaky well is at the center of the domain and the injection well is 100 m east There are two aquifers at the top and bottom of the domain each 30 m thick and an aquitard with thickness of 100 m sandwiched between the two aquifers The leaky well is modeled as a porous medium with a higher permeability compared to the formation Parameter values used in the simulation are listed in Table 7 11 Other parameters used for characteristic curves heat conduction etc may be found in the input file listing see Table 7 4 2 The initial conditions consist of hydrostatic pressure and isothermal temperature of 34 C The initial pressure at the bottom of the domain is 3 086 x
40. POWER lt float gt see Eqn A 128 RATE_LIMITER lt float gt mol m s see Eqn A 118 IRREVERSIBLE ARMOR_MINERAL lt Char gt See Eqn A 136 ARMOR_PWR lt float gt See Eqn A 136 ARMOR_CRIT_VOL_FRAC lt float gt See Eqn A 136 PREFACTOR RATE CONSTANT lt float gt mol m s If lt float gt lt 0 lt float gt 10 lt f 0at gt ACTIVATION_ENERGY lt float gt kJ mol PREFACTOR_SPECIES lt Char gt ALPHA lt float gt BETA lt float gt ATTENUATION_COEF lt float gt END END END END lt 47 gt PFLOTRAN User Manual 84 9 1 August 14 2015 Example Mineral kinetics CHEMISTRY MINERALS Quartz Calcite Gibbsite MINERAL_KINETICS Calcite RAT Hoc CONSTANT 1 d 12 mol cm 2 sec A OUTPUT ALL Gibbsite Examples Using PREFACTOR for mineral TST kinetics see Eqn A 117 MINERAL_KINETICS Quartz RATE CONSTANT 17 99d0 mol cm 2 sec ACTIVATION_ENERGY 87 7d0 A Albite PREFACTOR RATE CONSTANT 16 56d0 mol cm 2 sec ACTIVATION ENERGY 69 8d0 PREFACTOR RATE CONSTANT 14 16d0 mol cm 2 sec ACTIVATION ENERGY 65 0d0 PREFACIOR SPECIES H ALPHA 0 457d0 BETA ATTENUATION COEF PREFACTOR RATE CONSTANT 19 6d0 mol cm 2 sec ACTIVATION_ENERGY 71 0d0 PREEACTOR SPE
41. Quick Start For those adverse to reading manuals the following is a quick start guide to getting up and running with PFLOTRAN in four easy steps On the MacOSX platform Xcode must be installed with the commandline tools Required Software Packages e Compilers compatible with Fortran 2003 gcc 4 7 x Intel 14 x x For MacOSX 10 10 x the latest Fortran compiler binaries gcc gfortran 4 9 at the time of this writing may be downloaded from the web site HPC for MacOSX e Mercurial hg version control system e CMAKE version 3 0 x needed for installing METIS and ParMETIS e Developer version of PETSc petsc dev MPI for running in parallel BLAS LAPACK libraries HDES parallel output METIS ParMETIS unstructured grids e PFLOTRAN 2 1 Installing PFLOTRAN Step 1 Installing PETSc The first step is to download the developer version of PETSc petsc dev To do this follow the directions at the PETSc Developer web site The recommended approach is to use git To compile PETSc it is first necessary to configure the makefile To this end define the environmental variables PETSC_DIR and PETSC_ARCH pointing to the directory where petsc dev is installed and an identifying name for the installation respectively E g if using the t shell on MacOSX 10 10 x and gcc 4 9 enter into the tcshrc file setenv PETSC_DIR path to petsc dev and setenv PETSC_ARCH MacOSX 10 10 x gcc4 9 Finally set the environmental va
42. Required Input Parameters TYPE lt type gt Grid type unstructured FILE lt filename gt Name of file containing grid information unstructured only Optional Input Parameters GRAVITY lt gt Specifies gravity vector for geomechanics calculations or specific body force Default 0 0 9 81 m s END lt 83 gt PFLOTRAN User Manual 84 23 0 August 14 2015 4 23 Keyword GEOMECHANICS_MATERIAL_PROPERTY Return to List of Keywords Description Specifies geomechanics material properties to be associated with a geomechanics region in the problem domain Input GEOMECHANICS_MATERIAL_PROPERTY lt char gt ID lt int gt YOUNGS_MODULUS lt float gt Pa POISSONS_RATIO lt float gt ROCK_DENSITY lt float gt kg m BIOT_COEFFICIENT lt float gt THERMAL_EXPANSION_COEFFICIENT lt float gt Pa K END Explanation The Young s modulus and Poisson s ratio for the linear elastic model rock density used in body force calculation Biot s coefficient and thermal expansion coefficient can be set here Example MATERIAL PROPERTY rock DET YOUNGS_MODULUS 1 d10 POISSONS_RATIO 0 3 ROCK_DENSITY 2200 BIOT_COEFFICIENT 1 0 THERMAL_EXPANSION_COEFFICIENT 1 d 5 END Return to List of Keywords lt 84 gt PFLOTRAN User Manual 84 24 0 August 14 2015 4 24 Keyword GEOMECHANICS_OUTPUT Return to List of Keywords De
43. Value gt ITOL_SEC ITOL_RES_SEC INF_TOL_SEC lt Value gt Checks the infinite norm of secondary continuum residual for convergence when using transport default set to 1 d 10 MAXIT lt Value gt Cuts time step if the number of iterations exceed this value MAXF lt Value gt MAX NORM lt Value gt Cuts time step if the convergence norm exceeds this value END Explanation typedef enum converged S S S S S un nn ES_CONVERGED_FNORM_ABS ES_CONVERGED_FNORM_RELATIVE ES_CONVERGED_SNORM_RELATIVE 2 IFI lt atol IIFI lt rtol F_initial 4 Newton computed step size small delta x lt stol x 5 x maximum iterations reached 1 od w gt ES_CONVERGED_ITS ES_CONVERGED_TR_DELTA diverged x ES_DIVERGED_FUNCTION_DOMAIN 1 x the new x location passed the function is not in the domain of F x ES_DIVERGED_FUNCTION_COUNT ES_DIVERGED_LINEAR_SOLVE ES_DIVERGED_FNORM_NAN the linear solve failed tou sll w lt 108 gt PFLOTRAN User Manual 84 37 0 August 14 2015 SNES_DIVERGED_MAX_IT 5 SNES_DIVERGED_LINE_SEARCH 6 x the line search failed SNES_DIVERGED_INNER 7 x inner solve failed x SNES_DIVERGED_LOCAL_MIN 8 x J T b is small implies converged to local minimum of F x SNES_CONVERGED_ITERATING 0 SNESConvergedReason Example Return to List of Keywords lt 109 gt PFLOTRAN Us
44. _ see Eqn A 127 UPDATE_PERMEABILITY Must activate update_porosity see Eqn A 124 UPDATE MINERAL SURFACE AREA see Eqn A 128 Must set SURFACE AREA VOL FRAC POWER UPDATE MNRL SURF AREA WITH POR see Eqn A 128 Must set SURFACE AREA POROSITY POWER MINIMUM POROSITY lt float gt UPDATE ARMOR MINERAL SURFACE See Eqn A 136 MAX DLNC Default 5 MAX RELATIVE CHANGE TOLERANCE Relative speciation tolerance Default 1 d 12 MAX RESIDUAL TOLERANCE Speciation tolerance Default 1 d 12 lt 59 gt PFLOTRAN User Manual 84 9 7 August 14 2015 4 9 7 Keyword OUTPUT Return to List of Keywords OUTPUT MOLALITY MOLARITY ACTIVITY COEFFICIENTS ALL Output all primary species OFF Turn off printout Species Name Primary or secondary species FREE ION Output free ion primary species concentrations TOTAL Output total primary species concentrations PRIMARY SPECIES Output primary species including pH SECONDARY SPECIES Output all secondary species concentrations GASES Output gas species MINERALS Output all kinetic mineral volume fractions and reaction rates Mineral Name Output mineral saturation index IMMOBILE pH Output pH pe Output pe Eh Output Eh V 02 Output log fo fo in bars TOTAL SORBED TOTAL SORBED MOBILE COLLOIDS KD TOTAL SORBED TOTAL BULK TOTAL SORBED MOBILE AGE Output mean solute or water age SITE DENSITY END END lt 60 gt PFLOTRAN User Manual 84 9 7 Augus
45. also MPI HDF5 ParMETIS METIS and various solver libraries such as MUMPS for sparse direct solvers Hypre for a variety of preconditioners and multi level solvers and the Trilinos multilevel solver ML For systems that do not provide specially optimized versions of these libraries we recommend using PETSc s configure to install these third party libraries If you do wish to install any of these third party libraries yourself you will need to do so before installing PETSc to that the necessary PETSc interfaces to these packages can be built The development branch of PFLOTRAN tracks the main development branch of PETSc and hence requires this petsc dev version which can be either downloaded from the PETSc web page petsc dev or installed using Mercurial following instructions on the PETSc developer web page We recommend that PETSc be obtained using the version control system Mercurial Define environment variables PETSC_DIR and PETSC_ARCH giving the location of the petsc dev source and the directory where the libraries for the particular architecture are stored after compiling and installing PETSc 3 2 1 MacOSX 3 2 1 1 Lion Mavericks lt Mac OS X 10 9 x To install ParMETIS METIS on MacOSX it is necessary to first install the latest version 3 0 x of CMAKE from e g Homebrew MacPorts or Fink To install PETSc MPI using openmpi HDF5 and ParMETIS METIS with debugging turned off configure PETSc using confi
46. and viscosity are computed as a function of temperature and pressure through an equation of state for water The quantities pp Cp and denotes the density heat capacity and thermal conductivity of the porous medium fluid system The internal energy and enthalpy of the fluid U and H are obtained from an equation of state for pure water These two quantities are related by the thermodynamic expression U H 2 A 71 Thermal conductivity is determined from the equation Somerton et al 1974 K Kdry Al VS51 Ksat Kary A 72 where Kary and ksa are dry and fully saturated rock thermal conductivities A 7 1 Ice Model In PFLOTRAN the formulation used to model ice and water vapor involves solving a modified Richards equation coupled with an energy balance equation This formulation is different from Painter 2011 where a multiphase approach was used and mass balance for air was also solved for In this formulation the movement of air is not tracked and hence the mass balance for air is not considered The balance equations for mass and energy involving three phases liquid gas ice for the water component are given by i Ot l smX sg Xi sim Xi V X vm XI ngv V PSgTgNngD VXI Qu A 73a o at LO s mU SgNgUg simU 1 0 prerT V vin H P UgNg Ha V kVT Qe A 73b where the subscripts l i g denote the liquid ice and gas phases respectively amp is the porosity Sala
47. are three known comparisons absolute for absolute dif ferences c g relative for relative differences 6 c g g and percent for specifying a percent difference 8 100 c g g In addition there are two optional sections in configuration files The section default test criteria specifies the default criteria to be used for all tests in the current file Criteria specified in a test section override these value A section name suites defines aliases for a group of tests suites serial test 1 test 2 test 3 parallel test 4 test 5 test 6 Common test suites are standard and standard_parallel used by make test and do main specific test suites geochemistry flow transport mesh et cetra 5 4 Creating New Tests We want running tests to become a habit for developers so that make pflotran is always followed by make test With that in mind ideal test cases are small and fast and operate on a small subsection of the code so it is easier to diagnose where a problem has occurred While it may will be necessary to create some platform specific tests we want as many tests as possible to be platform independent and widely used There is a real danger in having test output become stale if 1t requires special access to a particular piece of hardware operating system or compiler to run The steps for creating new regression tests are e Create the PFLOTRAN
48. datum ENTHALPY Enthalpy at datum CONSTRAINT_LIST END Specifies list of concentration constraints for solute transport Terminates condition entry lt 75 gt PFLOTRAN User Manual 84 17 0 August 14 2015 Examples FLOW_CONDITION initial TYPE PRESSURE hydrostatic PRESSURE END 1956741 84 200 meter piezometric head FLOW_CONDITION source TYPE RATE volumetric_rate RATE 10 m 3 hr TRANSPORT_CONDITION initial TYPE zero_gradient CONSTRAINT_LIST Quid Ol mimi tiai END TRANSPORT CONDITION source TYPE dirichlet CONSTRAINT LIST 0 d0 well END FLOW_CONDITION East TYPE PRESSURE seepage PRESSURE conductance CYCETG DATUM file river_scope3 datum GRADIENT PRESSURE file river_scope3 gradient CONDUCTANCE 1 d 12 PRESSURE 101325 d0 END 2002997732298 lt 76 gt Return to List of Keywords PFLOTRAN User Manual 84 18 0 August 14 2015 4 18 Keyword FLUID PROPERTY Return to List of Keywords Description Assign diffusion coefficients and temperature dependence Input FLUID PROPERTY PHASE lt name gt LIQUID PHASE GAS PHASE Default LIQUID PHASE DIFFUSION COEFFICIENT lt float gt m s Default 0 x 107 m s DIFFUSION ACTIVATION ENERGY lt float gt kJ mo1 Default O kJ mol END Explanation Read in reference diffusion coe
49. input file and get the simulation running correctly e Tell PFLOTRAN to generate a regression file by adding a regression block to the input file e g REGRESSION CELLS NE 3978 CELLS PER PROCESS 4 END lt 146 gt PFLOTRAN User Manual 85 5 0 August 14 2015 Add the test to the configuration file e Refine the tolerances so that they will be tight enough to identify problems but loose enough that they do not create a lot of false positives and discourage users and developers from running the tests e Add the test to the appropriate test suite Add the configuration file input file and gold file to revision control Guidelines for setting tolerances go here once we figure out what to recommend 5 5 Updating Test Results The output from PFLOTRAN should be fairly stable and we consider the current output to be correct Changes to regression output should be rare and primarily done for bug fixes Updating the test results is simply a matter of replacing the gold standard file with a new file This can be done with a simple rename in the file system mv test_l regression test 1 regression gold Or using the regression test manager python regression tests py executable src pflotran pflotran config file my_test cfg tests test 1 update Updating through the regression test manager ensures that the output is from your current exe cutable rather than a stale file Please documen
50. kmol m q Darcy flux m s 1 k intrinsic permeability m k relative permeability yy viscosity Pa s P pressure Pa Wi formula weight of water kg kmol g gravity m s and z the vertical component of the position vector m Supported relative permeability functions k for Richards equation include van Genuchten Books Corey and Thomeer Corey while the saturation functions include Burdine and Mualem Water density and viscosity are computed as a function of temperature and pressure through an equation of state for water The source sink term Qu kmol m s has the form Qu Ze l Tss A 3 where qm denotes a mass rate in kg m s and r denotes the location of the source sink A 2 Capillary Pressure Relations Capillary pressure is related to saturation by various phenomenological relations one of which is the van Genuchten 1980 relation s i 2 A 4 De where pe represents the capillary pressure Pa and the effective saturation se is defined by S Sp Se A 5 So Sr where s denotes the residual saturation and sy denotes the maximum saturation The inverse relation is given by e 1 n De Pe Se el A 6 e The quantities m n and p are impirical constants determined by fitting to experimental data lt 187 gt PFLOTRAN User Manual 81 2 3 August 14 2015 A 2 1 Brooks Corey Saturation Function The Brooks Corey saturation function is a limiting form
51. line search information print line search method options cubic quadratic basic basic nonorms lt delta0 gt draws line graph of the residual norm conver gence using X11 lt 23 gt PFLOTRAN User Manual 83 8 0 August 14 2015 Examples Moran np er pilortran output prefix path to prefix 3 7 Multiple Realization Simulation Mode To launch 1000 realizations on 100 processor groups using 10 000 processor cores mpirun np 10000 pflotran stochastic num_realizations 1000 num_groups 100 Each processor group will utilize 100 processor cores and run 10 realizations apiece num_realizations num_groups one after another Thus 100 realizations are executed simultaneously with each processor group simulating a single realization on 100 processor cores at a time Each processor group continues to run realizations until its allocation of 10 is completed To simulate a specific realization without running in multi realization stochastic mode use mpirun np 10000 pflotran realization_id lt integer gt where lt integer gt specifies the realization id 3 8 Multiple Simulation Mode To run multiple input decks simultaneously create a file e g filenames in containing the list of filenames that are to be run siml in sim2 in sim100 in where simn in is the usual PFLOTRAN input file The names may be arbitrarily chosen Then launch the run as mpirun n XXX pflotran pflotranin file
52. mo y MAXIMUM_TIMESTEP_SIZE lt value gt Unit s m h d mo y MAXIMUM_TIMESTEP_SIZE lt value gt Unit s m h d mo y AT lt Value gt Unit s m h d mo y STEADY STATE END Explanation Example TIME FINAL_TIME 100 h INITIAL TIMESTEP SIZE 1 d 3 h MAXIMUM TIMESTEP SIZE 1 d0 h END Ability to change maximum time step size at select times during simulation TIME FINAL TIME 100 y INITIAL TIMESTEP SIZE 1 5 AXIMUM TIMESTEP SIZE 1 y AXIMUM TIMESTEP SIZE 1 d AXIMUM TIMESTEP SIZE 10 y at 11 y END Return to List of Keywords lt 133 gt PFLOTRAN User Manual 84 55 0 August 14 2015 4 55 Keyword TIMESTEPPER Description the keyword TIMESTEPPER controls time stepping Return to List of Keywords Input TIMESTEPPER FLOW TRANSPORT Must include one of FLOW or TRANSPORT NUM_STEPS_AFTER_CUT lt int gt Number of time steps after a time step cut that the time step size is held constant 5 MAX_STEPS lt int gt Maximum time step after which the simulation will be terminated 999999 TS_ACCELERATION lt int gt Integer indexing time step acceleration ramp expert users only 5 MAX_TS_CUTS lt int gt Maximum number of consecutive time step cuts before the simulation is terminated with plot of the current solution printed to a XXX_cut_to_failure tec file for debugging 16 CFL_LIMITER
53. name V nspec v n name n n 1 nspec log K 1 Ntemp w Surface Complexes gt name nspec v gt site v n name n n 1 nspec 1 log K 1 Niemp 2 w Note that chemical reactions are not unique For example given a particular mineral reaction gt YmA Mm A 201 j and equally acceptable reaction is the scaled reaction Y iting LM A 202 j with scale factor fm corresponding to a different choice of formula unit A different scale factor may be used for each mineral The scaled reaction corresponds to Si Aj Mm A 203 J with Min fmMm Vim fmVjm In addition mineral molar volume V m formula weight Wm equilibrium constant Km and the kinetic rate constant km are scaled according to A Vm fmVm A 204a Wa EAN A 204b log K fmlog Km A 204c lt 217 gt PFLOTRAN User Manual 1 12 0 August 14 2015 The saturation index SI transforms according to O O Sin A 205 Consequently equilibrium is not affected as is to be expected However a more general form for the reaction rate is needed involving Temkin s constant see Eqn A 114 in order to ensure that the identical solution to the reactive transport equations is obtained using the scaled reaction Thus 1t is necessary that the following conditions hold VI Vind A 206 Vimlm VYimIm A 207 This requires that the reaction rate Im transform as i II A 208 fm which guarantees that mineral volume fraction
54. of the van Genuchten relation for p p gt 1 with the form A Se E A 7 De pe pls A A 8 with A mn and inverse relation A 2 2 Relative Permeability Two forms of the relative permeability function are implemented based on the Mualem and Burdine formulations The quantity n is related to m by the expression 1 1 m 1 Fi n A 9 n 1 m for the Mualem formulation and by 2 2 m 1l n A 10 n 1 m for the Burdine formulation For the Mualem relative permeability function based on the van Genuchten saturation function is given by the expression ky Vee 1 E ae A 11 The Mualem relative permeability function based on the Brooks Corey saturation function is defined by A se platens A 12 5 242 on p A A 13 c For the Burdine relative permeability function based on the van Genuchten saturation function is given by the expression ee efi or bo A 14 The Burdine relative permeability function based on the Brooks Corey saturation function has the form med e A 15 0430 2 A 16 lt 188 gt PFLOTRAN User Manual 1 3 0 August 14 2015 A 2 3 Smoothing At the end points of the saturation and relative permeability functions it is sometimes necessary to smooth the functions in order for the Newton Raphson equations to converge This is accom plished using a third order polynomial interpolation by matching the values of the function to be fit capi
55. outlet TRANSPORT_CONDITION outlet REGION east ND EJ BOUNDARY_CONDITION inlet TRANSPORT_CONDITION inlet REGION west STRATA REGION all MATERIAL soill END END_SUBSURFACE TRANSPORT_CONDITION initial lt 160 gt PFLOTRAN User Manual 87 3 2 August 14 2015 7 3 RICHARDS Mode with Tracer SX 115 Hanford Tank Farm 7 3 1 Problem Description The saturation profile is computed for both steady state and transient conditions in a 1D vertical column consisting of a layered porous medium representing the Hanford sediment in the vicinity of the S SX tank farm The transient case simulates a leak from the base of the SX 115 tank This problem description is taken from Lichtner et al 2004 7 3 2 Governing Equations The moisture profile is calculated using parameters related to the Hanford sediment at the S SX tank farm based on the Richards equation for variably saturated porous media The Hanford sed iment is composed of five layers with the properties listed in Tables 7 7 and 7 8 The governing equations consist of Richards equation for variably saturated fluid flow given by o gP V ap Q 29 and solute transport of a tracer o Tid V go ystDVC Qe 7 21 In these equations y denotes the spatially variable porosity of the porous medium assumed to con stant within each stratigraphic layer s gives the saturation state of the porous medium p represents the fluid density in general a function of pressur
56. property name from which material IDs are read on a cell by cell basis In this case there is no need for the REGION keyword Examples Assign hanford_unit material properties to the region source_zone STRATA MATERIAL hanford_unit REGION source_zone Assign material properties through material IDs read from an HDF5 formatted file In this case there is no need to specify a region as material IDs are assigned to the entire grid on a cell by cell basis STRATA MATERIAL field_material_ids h5 For a detailed example on creating the h5 file see the PFLOTRAN wiki Strata lt 131 gt PFLOTRAN User Manual 84 53 0 August 14 2015 Evolving strata MATERIAL PROPERTY soill IB A PERMEABILITY ERMETSO I d 12 as MATERIAL PROPERTY soil2 MDEA PERMEABILITY PBERMENSO SPAS A END STRATA REGION all ATERIAL soill START TIME 0 d0 y END TIME 25 00 y END STRATA REGION all ATERIAL soil2 START_TIME 25 d0 y ND TIME 50 d0 y E E ND Return to List of Keywords lt 132 gt PFLOTRAN User Manual 84 54 0 August 14 2015 4 54 Keyword TIME Return to List of Keywords Description the keyword TIME controls the simulation time Input TIME FINAL_TIME lt Value gt Unit s m h d mo y INITIAL_TIMESTEP_SIZE lt Value gt Unit s m h d
57. range in the default lookup table is 7 0 375 C and P 0 01 1250 bars This keyword is required for MPHASE FLASH2 and IMMIS modes Input CO2_DATABASE Path Database Name The default database file is pflotran dev database co2_data0 dat Return to List of Keywords lt 64 gt PFLOTRAN User Manual 84 12 0 August 14 2015 4 12 Keyword CONSTRAINT Return to List of Keywords Description The keyword CONSTRAINT sets up fluid compositions based on various constraint conditions chosen by the user Use SECONDARY_CONSTRAINT for constraining secondary continua initial concentrations Input CONSTRAINT SECONDARY_CONSTRAINT constraint_name CONC CONCENTRATIONS Primary Species Name Concentration_Value Constraint Name mineral gas END MNRL MINERALS mineral name volume fraction surface area mt END END Explanation The variable Constraint is chosen from the following list F FREE Free ion species concentration T TOTAL Total aqueous concentration TOTAL_SORB Total aqueous and sorbed concentration P pH pH L LOG Log base 10 of free ion concentration M MINERAL MNRL Mineral equilibrium constraint G GAS Gaseous species constraint bars SC CONSTRAINT SUPERCRIT CO2 Supercritical CO EOS Z CHG Charge balance Example CONSTRAINT initial CONCENTRATIONS lt 65 gt PFLOTRAN User Manual 84 12 0 August 14 2015
58. saturated permeability ksa Data taken from Khaleel and Freeman 1995 Khaleel et al 2001 and Pruess et al 2002 Formation ps c Kan Bae Sip a m Rest gem Jkg K Wm Bas m BF 2 8 800 05 2 0 2585 0 0774 1 008e 3 0 6585 1 240e 12 HF 2 8 800 05 2 0 3586 0 0837 9 408e 5 0 4694 3 370e 13 PP 2 8 800 0 5 2 0 4223 0 2595 6 85le 5 0 4559 3 735e 14 URG 2 8 800 0 5 2 0 2625 0 2130 2 966e 5 0 3859 1 439e 13 MRG 2 8 800 05 2 0 1643 0 0609 6 340e 5 0 3922 2 004e 13 7 3 4 Simulation Results The calculations are carried out for an isothermal system using Richards equation First the steady state saturation profile is obtained without the tank leak present Then using the steady state profile as the initial condition the tank leak is turned on This can be easily accomplished using CHECK POINTING and RESTART keywords The results for the steady state saturation and pressure profiles are shown in Figure 7 6 for infiltration rates at the surface of 0 8 and 80 mm y The mean infiltration rate at the Hanford site is approximately 8 mm y A 1D column 68 m heigh with the water table located at a height of 6 m from the bottom is used in the simulation A uniform grid spacing of 0 5 m is used to discretize Richards equation Shown in Figure 7 7 is the saturation at different times following a two week leak releasing 60 000 gallons from the SX 115 tank at a depth of 16 m In the simulation a release rate of 1 87 x 107 kg s is used lt 163 gt
59. that Pa Ua Ha A 66 Pa Thermal conductivity is determined from the equation Somerton et al 1974 K Kary T Sil Esat u Kary A 67 where Kary and ksa are dry and fully saturated rock thermal conductivities A 7 Mode TH Thermal Hydrologic The current implementation of the TH mode applies to mass and energy conservation equations which are solved fully coupled The fluid density only a function of T and P Future generaliza tions of the TH mode will include multicomponent variable density fluids The TH equations may be coupled to the reactive transport mode see Section A 9 TH mode applies to single phase variably saturated nonisothermal systems with incorporation of density variations coupled to fluid flow The governing equations for mass and energy are given by psp V pq Qu A 68 and 9 ap PSP 1 p ppepT V pqH kVT Qe A 69 The Darcy flow velocity q is given by q mV P Wogz A 70 Here y denotes porosity s saturation p mixture density of the brine q Darcy flux k intrinsic permeability k relative permeability yu viscosity P pressure g gravity and z the vertical com ponent of the position vector Supported relative permeability functions k for Richards equation lt 196 gt PFLOTRAN User Manual 1 7 1 August 14 2015 include van Genuchten Books Corey and Thomeer Corey while the saturation functions include Burdine and Mualem Water density
60. that is responsible for reading a configu ration file identifying the tests declared in the file running PFLOTRAN on the appropriate input files and then comparing the results to aknown gold standard output file 5 1 Running the Test Manager The test manager can be run in two ways either as part of the build system using make or manually There are two options for calling the test manager through make make check and make test The check target runs a small set of tests that verify that PFLOTRAN is built and running on a given system This would be run by user to verify that their installation of PFLOTRAN is working The test target runs a fuller set of regression tests intended to identify when changes to the code cause significant changes to PFLOTRAN s results Calling the test manager through make relies on make variables from PETSc to determine the correct version of python to use if PFLOTRAN was build with MPI and optional configurations such as unstructured meshes The version of python used to call the test manager can be changed from the command line by specifying python cd S PELOTRAN_DEV src pflotran make PYTHON opt local bin python3 3 check To call the test manager manually cd PFLOTRAN_DEV regression_tests python regression tests py executable src pflotran pflotran config file shortcourse copper_leaching cu_leaching cfg tests cu_leaching
61. the well radius and o refers to the skin thickness factor For a rectangular grid block of area A Ax Ay r can be obtained from the relation Te Alm A 28 See Peaceman 1977 and Coats and Ramesh 1982 for more details A 3 2 Variable Switching In PFLOTRAN a variable switching approach is used to account for phase changes enforcing local equilibrium According to the Gibbs phase rule there are a total of N 1 degrees of freedom where Nc denotes the number of independent components This can be seen by noting that the intensive degrees of freedom are equal to Nin No Np 2 where Np denotes the number of phases The extensive degrees of freedom equals Next Np 1 This gives a total number of degrees of freedom Naot Nint Next Nc 1 independent of the number of phases Np in the system Primary variables for liquid gas and two phase systems are listed in Table A 1 The conditions for phase changes to occur are considered in detail below A 3 2 1 Gas py T vto gt Two Phase py T s Peat L Pal Poet 1 or equivalently 24 9 gt 7 Pg Pg e gas gt 2 ph z o lt 1 lt 191 gt PFLOTRAN User Manual 1 3 2 August 14 2015 A 3 2 2 Liquid 7 T vco gt Two phase p T s e liq gt 2 ph zho gt Co The equilibrium mole fraction v is given by MCO2 ZI gt Wio Mco 14 0 00 MU eq Teco where the molality at equilibrium is given by eq 1 Pest COP p
62. to a tracer is given below Note that the stratigraphic zone specification in REGION is grid independent as is the grid size specification in keyword GRID Therefore to change the grid spacing only the line NXYZ 1 1 136 needs to be changed Also note that lines beginning with are read as a comment as is input following Note that the input file looks for the RESTART file for the transient run in the subdirectory ss sx115 restart chk PFLOTRAN input file sx115 in Description 1D test problem for tracer transport for Hanford SX 115 waste tank SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_FLOW flow MODE RICHARDS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT END SUBSURFACE CHEMISTRY PRIMARY_SPECIES Tracer OUTPUT all FREE_ION CHECKPOINT 100000 RESTART ss sx115 restart chk 0 d0 FOVERWRITE_RESTART_TRANSPORT WALLCLOCK_STOP 11 75 TIMESTEPPER FLOW MAX_STEPS 1 TS_ACCELERATION 8 INITIALIZE_TO_STEADY_STATE 1 d0 END NEWTON_SOLVER FLOW RTOL 1 d 12 RTOL 1 d 20 ATOL 1 d 12 STOL 1 e 60 DTOL 1 e4 ITOL_UPDATE 1 d0 NO_INFINITY_NORM NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE END lt 166 gt PFLOTRAN User Manual 87 3 5 August 14 2015 LINEAR_SOLVER FLOW KSP_TYPE GMRES PC_TYPE NONE KSP_TYPE PREONLY PC_TYPE LU SOLVER GMRES END NEWTON_SOLVER TRANSPORT RTOL 1 d 12 ATOL 1 d 12 STOL 1 e 60 DTOL 1 e4 ITOL_U
63. 0 e Thermodynamic inhibition 1 Q K A 10 Tracer Mean Age PFLOTRAN implements the Eulerian formulation of solute age for a nonreactive tracer following Goode 1996 PFLOTRAN solves the advection diffusion dispersion equation for the mean age given by o ZpSAC V aac sDV AC psC A 198 where A denotes the mean age of the tracer with concentration C Other quantities appearing in the age equation are identical to the tracer transport equation for a partially saturated porous medium with saturation state s The age and tracer transport equations are solved simultaneously for the age concentration a AC and tracer concentration C The age concentration a satisfies the usual advection diffusion dispersion equation with a source term on the right hand side The mean tracer is calculated in PFLOTRAN by adding the species Tracer_Age together with Tracer to the list of primary species lt 215 gt PFLOTRAN User Manual 1 11 0 August 14 2015 PRIMARY_SPECIES racer Tracer Age including sorption through a constant K4 model if desired SORPTION ISOTHERM REACTIONS racer TYPE LINEAR DISTRIBUTION COEFFICIENT 500 kg water m 3 bulk Tracer Age IYPE LINEAR DISTRIBUTION COEFFICIENT 500 kg water m 3 bulk and specifying these species in the initial and boundary CONSTRAINT condition as e g CONSTRAINT initial CONCENTRATION
64. 0 August 14 2015 4 59 Keyword VELOCITY_DATASET Return to List of Keywords Description Set time dependent velocity for transport mode Input VELOCITY_DATASET UNITS cm h CYCLIC INTERPOLATION step default INTERPOLATION linear VELOCITY Time velx vely velz END END Explanation Example lt ELOCITY_DATASET UNITS cm h CYCLIC cycles the data set using last time as offset INTERPOLATION STEP interpolation method step default VELO Cit time velx vely velz time units time unit in velocity units 0 d0 3858890 02d0 Odo Trdo 138393930000 OCIO 24 d0 5838840 0 070 40 END er linear Return to List of Keywords lt 141 gt PFLOTRAN User Manual 84 60 0 August 14 2015 4 60 Keyword WALLCLOCK STOP Return to List of Keywords WALLCLOCK STOP lt real gt lt char gt Explanation Specifies a wall clock time at which the simulation will shut down gracefully gen erating a restart file 1f specified The option is especially useful when there is an upper limit on wall clock time that can be requested e g on a supercomputer and it is not certain 1f the run will be completed within that time Example WALLCLOCK STOP 9 5 h Return to List of Keywords lt 142 gt PFLOTRAN User Manual 85 1 0 August 14 2015 5 PFLOTRAN Regression Test Manager The test manager for PFLOTRAN is a python program
65. 0 0 d0 200 d0 PRESSURE 3 086d7 3 086d7 TEMPERATURE 33 6d0 CONCENTRATION 0 d0 ENTHALPY 0 d0 0 d0 FLOW_CONDITION side UNITS Pa C M yr TYPE PRESSURE hydrostatic TEMPERATURE zero_gradient CONCENTRATION zero_gradient ENTHALPY dirichlet IPHASE 1 PRESSURE 3 086d7 3 086d7 TEMPERATURE 33 6d0 CONCENTRATION 0 d0 ENTHALPY 0 d0 0 d0 FLOW_CONDITION source UNITS Pa C M yr TYPE RATE mass_rate TEMPERATURE dirichlet CONCENTRATION dirichlet ENTHALPY dirichlet RATE LIST TIME_UNITS d DATA_UNITS kg s lt 183 gt PFLOTRAN User Manual 87 4 2 August 14 2015 0 0 1 47833 8 87 kg s 6 1000 0 0 TEMPERATURE 33 6d0 CONCENTRATION 0 d0 ENTHALPY 0 d0 0 d0 condition couplers INITIAL_CONDITION FLOW_CONDITION initial REGION all ND EJ BOUNDARY_CONDITION north FLOW_CONDITION side REGION north ND EJ BOUNDARY_CONDITION south FLOW_CONDITION side REGION south ND EJ BOUNDARY_CONDITION east FLOW_CONDITION side REGION east ND ty BOUNDARY CONDITION west FLOW CONDITION side REGION west ND E SOURCE_SINK FLOW_CONDITION source REGION inj_well END stratigraphy couplers STRATA REGION upper MATERIAL aquifer END STRATA REGION middle MATERIAL aquitard END STRATA REGION lower MATERIAL aquifer END STRATA REGION well MATERIAL well END END_SUBSURFACE lt 184 gt PFLOTRAN User Manual 8 0 2 August 14 2015
66. 10 Pa at 3 000 m depth At the lateral boundaries hydrostatic boundary conditions are imposed on the system The boundaries at the top and bottom of the domain are no flow boundary conditions CO is injected at a constant rate of 8 87 kg s for the duration of the simulation of 1000 days and at a constant temperature of 33 6 C The computational domain was discretized into 200 x 200 x 32 grid blocks with spacing Ar Ay 5 m and Az 5 m The total number of degrees of freedom are 3 840 000 The problem was run on 512 processes on the supercomputer Yellowstone at the NCAR Wyoming Supercomputing Center Table 7 11 Model parameters Unit Permeability m Porosity Depth m Aquifer DO Nets 0 15 0 30 130 160 Aquitard AS 0 15 30 130 Leaky well 1 107 0 15 0 160 Results of the simulation for an elapsed time of 250 days are shown in Figure 7 11 for liquid pressure and saturation of supercritical CO Supercritical CO2 proceeds up the leaky well until it ponds at the top of the domain where a closed boundary is imposed The leakage of CO through the leaky well as a function of time is shown in Figure 7 12 This is defined as the CO mass flow midway between the top and bottom domain divided by the injection rate The maximum value in the leak occurs at approximately 800 d The leak begins at approximately 50 d The results can be compared to Ebigo et al 2007 Figure 8 It should be noted that the leakage rate is highly sensitive to the la
67. ARD_RATE 0 d0 Return to List of Keywords lt 54 gt PFLOTRAN User Manual 84 9 5 August 14 2015 4 9 5 Keyword MICROBIAL_REACTION Specifies parameters for microbially mediated reactions Return to List of Keywords MICROBIAL_REACTION REACTION lt string gt Reaction equation The rate constant is multiplied by the Monod expressions for electron donor and acceptor for select species on the left side of the equation The reaction may be inhibited by any species in the system RATE CONSTANT lt float gt Rate constant for the reaction MONOD lt string gt lt float gt Specifies the Monod equation for the electron donor and acceptor named by the string and the half saturation constant INHIBITION Specifies inhibition based on species concentration and an inhibition constant s Three types of inhibition are currently supported MONOD INVERSE_MONOD and THRESHOLD Monod Inhibition INHIBITION SPECIES NAME lt string gt TYPE MONOD Specifies the type of inhibition to be Monod The reac tion proceeds as long as the species concentration is well below the half saturation constant inhibition C Cin concentration INHIBITION_CONSTANT lt float gt Half saturation constant Inverse Monod Inhibition INHIBITION SPECIES NAME lt string gt TYPE INVERSE_MONOD Specifies the type of inhibition to be in verse Monod The reaction proceeds as long as the species con centration is w
68. BOUNDARY CONDITION Description The BOUNDARY_CONDITION keyword couples conditions specified under the FLOW_CONDITION and or TRANSPORT_CONDITION keywords to aREGION in the problem domain The use of this keyword enables the use reuse of flow and transport conditions and regions within multiple boundary and initial conditions and source sinks in the input deck Return to List of Keywords Input BOUNDARY_CONDITION boundary_condition_name FLOW CONDITION flow_condition_name TRANSPORT CONDITION transport condition name REGION region name END Explanation Keyword Description BOUNDARY CONDITION Defines the beginning of a boundary condition entry and the name of the boundary condition FLOW CONDITION Defines the name of the flow condition to be linked to this boundary condition TRANSPORT CONDITION Defines the name of the transport condition to be linked to this boundary condition REGION Defines the name of the region to which the conditions are linked END Terminates the boundary condition entry lt 37 gt PFLOTRAN User Manual 84 5 0 August 14 2015 Examples BOUNDARY_CONDITION river FLOW_CONDITION river_stage TRANSPORT_CONDITION river_chemistry R D EGION river_bank m Z UNDARY_CONDITION recharge FLOW CONDITION infiltration flux TRANSPORT CONDITION infiltration chemistry R D EGION ground surface mi Return to List of Keywords lt 38 gt
69. CIES H ALPHA 0 5720 BETA ATTENUATION_COEF A END Return to List of Keywords lt 48 gt PFLOTRAN User Manual 84 9 2 August 14 2015 4 9 2 Keyword SORPTION The keyword SORPTION specifies parameters for ion exchange and surface complexation reactions Return to List of Keywords SORPTION SURFACE_COMPLEXATION_RXN EQUILIBRIUM MULTIRATE_KINETIC KINETIC SITE FRACTION lt float gt Continuation line RATE RATES lt float gt l s Continuation line A MULTIRATE SCALE FACTOR lt float gt MINERAL Mineral Name SITE Name Site Density mol m COMPLEXES Complex Name END COMPLEX KINETICS COMPLEX name FORWARD RATE CONSTANT lt float gt Vs BACKWARD RATE CONSTANT lt float gt 1 s If value lt 999 calculate backward rate constant from expression ky Kegky where Keq is the corresponding equilibrium constant of the reaction END END COLLOID Name SITE Name Site Density mol m COMPLEXES Surface_Complex Name END END END lt 49 gt PFLOTRAN User Manual 84 9 2 August 14 2015 ION_EXCHANGE_RXN MINERAL Mineral Name CEC lt float gt mol m CATIONS Exchange reactions must be written in terms of a single reference cation which must appear first in the list of cations see A 140 Cation Name Selectivity_Coefficient END END END ISOTHERM_REACTIONS Species_Name TYPE LINEAR LANGMUIR FREUNDLICH D
70. EE E EEan a e ER Ea EEE E ER e Emen aea EEEE Ee ere a jea Eee em ea m e e a CHEMISTRY OPERATOR_SPLIT PRIMARY SPECIES Ca H CO2 aq Tracer SECONDARY_SPECIES OH HCO3 C03 CaHCO3 CaCO3 aq GAS_SPECIES CO2 g MINERALS Calcite I MINERAL_KINETICS Calcite RATE_CONSTANT 1 e 8 mol m s DATABASE Users lichtner flotran database hanford dat LOG_FORMULATION lt 32 gt PFLOTRAN User Manual 84 4 0 August 14 2015 ACTIVITY_COEFFICIENTS INEWTON ITERATION MOLAL OUTPUT Al H reference variables gt gt REFERENCE_POROSITY 0 25d0 H time stepping TIMESTEPPER TS_ACCELERATION 8 MAX_STEPS 100000 H discretization GRID TYPE structured NXYZ 666 BOUNDS 0 d0 0 d0 0 d0 1 d0 1 d0 1 d0 HDXYZ 1 1 1 flow solvers e a O O O SS NEWTON_SOLVER FLOW PRECONDITIONER_MATRIX_TYPE AIJ RTOL 1 d 8 ATOL 1 d 8 STOL 1 d 30 ITOL_UPDATE 1 d0 FNO_INFINITY_NORM NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE LINEAR_SOLVER FLOW KSP_TYPE PREONLY PC_TYPE LU KSP_TYPE FGMRES samrai PC_TYPE SHELL samrai transport solvers SS je e R e NEWTON_SOLVER TRANSPORT PRECONDITIONER_MATRIX_TYPE AIJ RTOL 1 d 12 ATOL 1 d 12 STOL 1 d 30
71. ENUCHTEN MAX CAPILLARY PRESSURE 1 PERMEABILITY FUNCTION MUALE d6 lt 41 gt PFLOTRAN User Manual 84 7 0 August 14 2015 PHASE LIQUID LIQUID RESIDUAL SATURATION 0 d0 0 5d0 PERMEABILITY_FUNCTION MUALEM_VG_GAS PHASE GAS LIQUID_RESIDUAL_SATURATION 0 d0 GAS_RESIDUAL_SATURATION 1 d 40 0 5d0 CHARACTERISTIC_CURVES cc2 SATURATION_FUNCTION BROOKS_COREY LIQUID_RESIDUAL_SATURATION 0 2d0 LAMBDA 0 7d0 ALPHA 9 869d 6 AX_CAPILLARY_PRESSURE 1 d8 SMOOTH E PERMEABILITY FUNCTION BURDIN PHASE LIQUID LIQUID RESIDUAL SATURATION 0 2d0 LAMBDA 0 7d0 PERMEABILITY_FUNCTION BURDINE_BC_GAS PHASE GAS LIQUID_RESIDUAL_SATURATION 0 2d0 GAS_RESIDUAL_SATURATION 1 d 5 LAMBDA 0 7d0 lt 42 gt Return to List of Keywords PFLOTRAN User Manual 84 8 0 August 14 2015 4 8 Keyword CHECKPOINT Return to List of Keywords Description Checkpoint files enable the restart of a simulation at any discrete point in simulation where a checkpoint file has been printed When the CHECKPOINT card is included in the input deck checkpoint files are printed every N time steps where N is the checkpoint frequency and at the end of the simulation should the simulation finish or the be shut down properly mid simulation using the WALL_CLOCK_STOP card Checkpoint files are named pflotran chkN
72. Ergo Goe sender ee le 98 Keyword LINEAR SOLVER lt oo lt i2 iron ms 2 454404 99 Keyword MATERIAL PROPERTY 2 2 244 2202 42 4 gama a 102 Keyword MODE ss he 42 eb Se AS a a ah 106 Keyword MULTIPLE CONTINUUM 2244 8 42482445 484 688404 107 Keyword NEWTON SOLVER 2 2 0 20 42444 Sud dad ae oe 108 Keyword NONUNIFORM VELOCITY z 5224s se 22 0044 110 Keyword NUMERICAL_JACOBIAN_FLOW 2 22H een 112 Keyword NUMERICAL_JACOBIAN_RXN 2 113 Keyword NUMERICAL JACOBIAN MULTI COUPLE 114 Keyword OBSERVATION 6 sus sois drid nu rear gg eS 115 Keyword ORIGIN ORIG sssaaa 2 0 0 50 Au due heut eH 117 Keyword QUIIBUT sas sa eh ee are na are ne a 118 Keyword OVERWRITE RESTART FLOW PARAMS 123 Keyword OVERWRITE RESTART TRANSPORT 123 Keyword OVERWRITE RESTART TRANSPORT 123 Keyword PROC opresor rieron ira Ee Bee Bar RR a 124 Keyword REGION u 225 deh ea dan Epa dee a So 125 Keyword RESTART i coes desees rea es ar A EE EE HOSS 127 Keyword SATURATION FUNCTION 2 ca aa AA 128 lt 4 gt PFLOTRAN User Manual 0 0 0 August 14 2015 4 52 Keyword SOURCE SINK ces spa da wen be SRS a aed S 130 4 53 Keyword STRATIGRAPHY STRATA css zus a ea wur ze au 131 4 54 Keyword TIME an SH Eau IPEA a dd 133 4 55 Keyword TIMESTEPPER ss ss srs 2 2 0 u Re eM hau ns 2 134 4 50 Keyword TRANSPORT CONDITION 2 4
73. ION MUALEM_VG_LIQ M 0 6585d0 LIQUID_RESIDUAL_SATURATION 0 0774 END CHARACTERISTIC_CURVES HF SATURATION_FUNCTION VAN_GENUCHTEN M 0 46944d0 ALPHA 9 40796d 5 LIQUID_RESIDUAL_SATURATION 0 08366d0 PERMEABILITY_FUNCTION MUALEM_VG_LIQ M 0 46944d0 LIQUID_RESIDUAL_SATURATION 0 08366d0 END CHARACTERISTIC_CURVES PP SATURATION_FUNCTION VAN_GENUCHTEN M 0 45587d0 ALPHA 6 85145d 5 LIQUID_RESIDUAL_SATURATION 0 25953d0 PERMEABILITY_FUNCTION MUALEM_VG_LIQ M 0 45587d0 LIQUID_RESIDUAL_SATURATION 0 25953d0 END lt 168 gt PFLOTRAN User Manual 87 3 5 August 14 2015 CHARACTERISTIC_CURVES URG SATURATION_FUNCTION VAN_GENUCHTEN M 0 38594d0 ALPHA 2 96555d 5 LIQUID_RESIDUAL_SATURATION 0 21295d0 PERMEABILITY_FUNCTION MUALEM_VG_LIQ M 0 38594d0 LIQUID_RESIDUAL_SATURATION 0 21295d0 END CHARACTERISTIC_CURVES MRG SATURATION_FUNCTION VAN_GENUCHTEN M 0 39217d0 ALPHA 6 34015e 5 LIQUID RESIDUAL SATURATION 0 06086d0 PERMEABILITY FUNCTION MUALEM VG LIQ M 0 39217d0 LIQUID_RESIDUAL_SATURATION 0 06086d0 OUTPUT SCREEN PERIODIC 10 MASS_BALANCE TIMES y 0 0383562 0 5 1 0 1 5 2 0 5 0 10 0 25 50 75 100 FORMAT TECPLOT POINT VELOCITIES PRINT_COLUMN_IDS PERIODIC_OBSERVATION TIMESTEP 1 END FINAL_TIME 100 d0 y INITIAL_TIMESTEP_SIZE 1 d 6 y MAXIMUM_TIMESTEP_SIZE 1 d 2 y MAXIMUM_TIMESTEP_SIZE 1 d0 y at 10 y MAXIMUM TIMESTEP SIZE 10 d0 y at 100 y END reg
74. ISTRIBUTION COEF KD lt float gt kg water m bulk see Eqn A 182 LANGMUIR_B lt float gt see Eqn A 183 FREUNDLICH N lt float gt see Eqn A 184 END END JUMPSTART_KINETIC_SORPTION NO_CHECKPOINT_KINETIC_SORPTION NO_RESTART_KINETIC_SORPTION END Example Linear sorption distribution coefficient and mean age of a tracer SORPTION ISOTHERM_REACTIONS Tracer TYPE LINEAR DISTRIBUTION_COEFFICIENT 500 kg water m 3 bulk Tracer_Age TYPE LINEAR DISTRIBUTION_COEFFICIENT 500 kg water m 3 bulk Y lt 50 gt PFLOTRAN User Manual 84 9 2 August 14 2015 Example Ion exchange SORPTION ION_EXCHANGE_RXN CEC 0 11 eg msbulk CATIONS Na 1m Catt 0 158439 K 0r T 99526 lt 51 gt PFLOTRAN User Manual 84 9 3 August 14 2015 4 9 3 Keyword RADIOACTIVE_DECAY_REACTION Specifies parameters for radioactive decay reaction This reaction differs from the GEN ERAL_REACTION in that only one reactant species may be specified with a unit stoichiom etry 1 e the rate is always first order and the reactant species is decayed in both the aqueous and sorbed phases Return to List of Keywords RADIOACTIVE_DECAY_REACTION REACTION lt string gt Reaction equation Only one reactant species may be listed on the left side of the equation 1 e or on the right side with a negative stoichiometry The reactant s stoichi
75. K temperature M mol L concentration KJ mol enthalpy CYCLIC INTERPOLATION step linear SYNC_TIMESTEP_WITH_UPDATE TYPE PRESSURE dirichlet hydrostatic zero_gradient conductance seepage RATE mass_rate volumetric_rate scaled_volumetric_rate specifies an injection extraction rate in mass kg s volume m s and a volu metric injection extraction rate m s that is scaled across a well screen weighted as a function of the interfacial area and permeability of neighboring cells in x y FLUX dirichlet neumann mass_rate hydrostatic conductance zero_gradient production_well seepage volumetric volumetric_rate equilibrium lt 73 gt PFLOTRAN User Manual 84 17 0 August 14 2015 TEMPERATURE dirichlet CONCENTRATION dirichlet SATURATION dirichlet ENTHALPY H dirichlet END TIME not currently supported IPHASE lt int gt DATUM x Y zZ FILE file_name GRADIENT GRAD PRESSURE E FILE file_name FLUX TEMPERATURE CONCENTRATION H ENTHALPY END TEMPERATURE TEMP lt float gt ENTHALPY lt float gt PRESSURE lt float gt RATE lt float gt FLUX VELOCITY VEL lt float gt CONCENTRATION SATURATION lt float gt CONDUCTANCE lt float gt lt float gt END Explanation IPHASE Phases present 1 H20 2 SC CO 3 H20 SC CO lt 74 gt hydrostatic hydrostatic hydrostatic zero_gradient zero_gradient zero_gradient CO concentrati
76. Keywords are in boldface with optional modifying keywords in square brackets and user entries in typewriter font Unless otherwise specified units in the input file are assumed to be as listed in Table 4 4 Table 4 4 Units Quantity Units Pressure Pascal Pa absolute Temperature Celcius C Distance meter m Volume meter m Time second s Velocity meter second m s Concentration molarity M or molality m see MOLAL keyword Enthalpy kiloJoule mole kJ mol Mass kilogram kg Rate kilogram second kg s or cubic meter second m s Surface Site Density mole meter mol m 4 2 Input Deck Specification PFLOTRAN input files are divided into blocks based on the process models employed Process models are defined within the SIMULATION block which for convenience should be located at lt 25 gt PFLOTRAN User Manual 84 2 0 August 14 2015 the top of the input file but this is not required Keywords for subsurface processes are listed in Table 4 5 At present manual pages and keywords for surface processes is still under development Keywords within the SIMULATION block include SIMULATION Opens the SIMULATION block SIMULATION_TYPE lt string gt Defines the domain to be modeled and the types of process models employed Options include SUBSURFACE SURFACE_SUBSURFACE HYDROGEOPHYSICS PROCESS_MODELS Opens a block for defining all process models employed At this point the ordering and
77. LD lt float gt BOOMERAMG GRID SWEEPS ALL lt float gt BOOMERAMG GRID SWEEPS DOWN lt float gt lt 99 gt PFLOTRAN User Manual 84 33 0 August 14 2015 BOOMERAMG_GRID_SWEEPS_UP lt float gt BOOMERAMG_GRID_SWEEPS_COARSE lt float gt BOOMERAMG_RELAX_TYPE_ALL lt Value gt BOOMERAMG_RELAX_TYPE_DOWN lt Value gt BOOMERAMG_RELAX_TYPE_UP lt Value gt BOOMERAMG_RELAX_TYPE_COARSE lt Value gt BOOMERAMG RELAX WEIGHT ALL lt Value gt BOOMERAMG RELAX WEIGHT LEVEL lt Value gt BOOMERAMG OUTER RELAX WEIGHT ALL lt Value gt BOOMERAMG OUTER RELAX WEIGHT LEVEL lt Value gt BOOMERAMG NO CF lt Value gt BOOMERAMG MEASURE TYPE lt Value gt BOOMERAMG COARSEN TYPE lt Value gt BOOMERAMG INTERPOLATION TYPE BOOMERAMG INTERP TYPE lt Value gt BOOMERAMG NODAL COARSEN lt Value gt BOOMERAMG NODAL RELAXATION lt Value gt ATOL lt float gt Absolute tolerance b Az lt RTOL lt float gt Relative tolerance b Az b Axo lt DTOL lt float gt Divergence tolerance b Ax b Axo gt O MAXIT lt int gt Maximum number of linear solver iterations LU ZERO PIVOT TOL lt float gt Specifies zero pivot tolerance for ILU LU precondi tioners END Explanation LINI Examples EAR_SOLVER FLOW LINI SOLV ER DIREC EAR SOLVER TRANSPORT LINI SOLV ER ITERATIVE EAR_SOLVER FLOW S
78. LITY PERM_ISO 5 43d 13 material properties SATURATION_FUNCTION HD SATURATION_FUNCTION_TYPE VAN_GENUCHTEN RESIDUAL_SATURATION 0 115 LAMBDA 0 286 ALPHA 1 9401d 4 SATURATION_FUNCTION default OUTPUT TIMES s 10307 1 33498 2 41228 6 PERIODIC_OBSERVATION TIMESTEP 1 PERIODIC TIMESTEP 1 PERIODIC TIME 0 04 y SCREEN PERIODIC 10 lt 153 gt output PFLOTRAN User Manual 87 1 0 August 14 2015 FORMAT HDF5 FORMAT TECPLOT POINT VELOCITIES TIME FINAL_TIME 41228 6 s NITIAL_TIMESTEP_SIZE 1 s MAXIMUM_TIMESTEP_SIZE 20 s MAXIMUM_TIMESTEP_SIZE 1 s at 10200 s MAXIMUM_TIMESTEP_SIZE 20 s at 10350 s MAXIMUM_TIMESTEP_SIZE 1 s at 33300 s MAXIMUM_TIMESTEP_SIZE 20 s at 33600 s regions REGION all COORDINATES 0 d0 0 d0 0 d0 0 481d0 1 d0 1 d0 REGION west FACE WEST COORDINATES Oy G8 Os Oy Le es REGION east FACE EAST COORDINATES 0 481 0 0 0 481 1 1 OBSERVATION REGION east skip FLOW_CONDITION west TYPE FLUX neumann FLUX 0 317098d 7 1 m y FLUX 1 5855d 9 5 cm y FLUX file 200w_recharge_1951 2000_daily dat noskip FLOW_CONDITION Initial TYPE PRESSURE hydrostatic DATUM 0 d0 0 d0 0 d0 PRESSURE 101325 d0 FLOW_CONDITION west TYPE PRESSURE hydrostatic DATUM 0
79. LOTRAN is straightforward Besides PETSc third party libraries commonly installed are e MPI message passing interface OpenMPI or MPICH e HDFS5 required for parallel I O and reading HDF5 formatted input files e Metis and ParMetis graph partitioning libraries required for unstructured grids e Hypre which provides a variety of preconditioners and multilevel solves PETSc can be used to download compile and install all of these third party libraries during compilation of PETSc as explained below so that the user does not have to do this themselves individually for each library 3 1 Compilers The installation of PFLOTRAN on MacOSX requires compiler versions 4 7 or later for gfortran and gcc to be compatible with Fortran 2003 For MacOSX compilers can be obtained from several sources including MacPorts and the web site High Performance Computing for MacOSX 3 2 Building PETSc The first step to building PFLOTRAN is to configure and build the PETSc toolkit This requires at minimum working installations of C and Fortran 95 compliant compilers For users looking for lt 16 gt PFLOTRAN User Manual 83 2 1 August 14 2015 an open source compiler we recommend the gcc and gfortran compilers that are part of the GNU Compiler Collection GCC version 4 7 x or later Users may also wish to install MPI and other libraries from source or via a package manager but the PETSc configure script can be used not only to install PETSc but
80. ME lt float gt lt unit gt output the results at observa tion points and mass balance output at specified output times PERIODIC_OBSERVATION TIMESTEP lt integer gt output the results at observa tion points and mass balance output at specified time steps NO_PRINT_INITIAL the initial state of the system will not be printed to the output file if this card is activated NO PRINT FINAL the final state of the system will not be printed to the output file if this card is activated PRINT_COLUMN_IDS print column numbers in observation and mass balance output files FORMAT lt file format gt specify the snapshot in time file type File formats available are TECPLOT POINT TecPlot point format requires a single processor BLOCK TecPlot block format FEBRICK TecPlot finite element HDF5 SINGLE FILE produces single HDFS file pflotran h5 MULTIPLE FILES TIMES PER FILE produces a separate HDFS file for number of times specified by TIMES PER FILE default 1 MAD not supported VTK VTK format VOLUME Output cell volume PERMEABILITY Output cell permeability POROSITY Output cell porosity MINERAL_POROSITY Output cell porosity derived from mineral volume fractions EFFECTIVE_POROSITY Output cell effective porosity GENERAL mode only FLUXES Output interface fluxes lt 118 gt PFLOTRAN User Manual 84 44 0 August 14 2015 VELOCITY AT FACE Output interface velocities Structured grid velocity outputted at internal faces on
81. MECHANICS_REGION all lt 87 gt PFLOTRAN User Manual 84 27 0 August 14 2015 4 27 Keyword GRID Required Return to List of Keywords Description this keyword defines the descritization scheme the type of grid and resolution and the geometry employed in the simulation GRID Required Input Parameters TYPE lt type gt lt symmetry gt Grid type structured structured_mimetic unstructured Symmetry type cartesian default cylindrical spherical NXYZ lt gt of grid cells in x y z directions structured only FILE lt filename gt Name of file containing grid information unstructured only BOUNDS lt x_min y_min z_min gt lt x_max y_max z_max gt END DXYZ Specifies grid spacing of structured cartesian grid see examples below lt dx gt lt dy gt lt dz gt END Optional Input Parameters GRAVITY lt gt Specifies gravity vector Default 0 0 9 8068 m s ORIGIN lt gt Coordinate of grid origin Default 0 0 0 INVERT_Z Inverts the z axis Default positive z points upward FILE Read from file MAX_CELLS_SHARING_A_VERTEX STENCIL_WIDTH STENCIL_TYPE BOX STAR lt 88 gt PFLOTRAN User Manual 84 27 1 August 14 2015 END The following two types of unstructured grid formats implicit and explicit are currently supported by PFLOTRAN 4 27 1 Implicit Unstructured Grids In this format the grid is defin
82. N Specifies rate constants and stoichiometry for a general kinetic homogeneous aqueous for ward backward reaction It does not apply to reactions containing a solid phase however Return to List of Keywords GENERAL_REACTION REACTION lt string gt Reaction equation The forward rate is applied to reaction quo tient of species on left side of reaction The reverse or backward rate is applied to the right side Reactions can also be irreversible if one of the rate constants is zero FORWARD RATE lt float gt rate constant for n order forward reaction kg D mol 1 sec BACKWARD RATE lt float gt rate constant for n order reverse reaction kg D mol 0 sec END Examples GENERAL REACTION REACTION Tracer lt gt Tracer2 FORWARD_RATE 1 7584d 7 half life at 0 125 y BACKWARD_RATE 0 d0 CHEMISTRY PRIMARY SPECIES A ag B ag C aa GENERAL REACTION REACTION A aq lt gt B ag Calculating forward rate from half life forward rate 1n 0 5 half life 1 sec FORWARD RATE 1 75836d 9 1 s half life 12 5 yrs BACKWARD_RATE 0 d0 GENERAL REACTION REACTION B aq lt gt C ag FORWARD_RATE 8 7918d 10 1 s half life 25 yrs BACKWARD_RATE 0 d0 GENERAL_REACTION Note that C aq decays with no daughter products REACTION C ag lt gt FORWARD RATE 4 3959d 9 1 s half life 5 yrs BACKW
83. NICS_BOUNDARY CONDITION Defines the beginning of a geomechan ics boundary condition entry and the name of the geomechanics boundary condition GEOMECHANICS_CONDITION Defines the name of the geomechanics condition to be linked to this geome chanics boundary condition REGION Defines the name of the region to which the conditions are linked END Terminates the geomechanics boundary condition entry Example GEOMECHANICS_BOUNDARY_CONDITION bottom lt 79 gt PFLOTRAN User Manual 4 20 0 August 14 2015 END EOMI EOMI ECHANICS RI EGION bottom ECHANICS CONDITION z disp zero lt 80 gt Return to List of Keywords PFLOTRAN User Manual 84 21 0 August 14 2015 4 21 Keyword GEOMECHANICS_CONDITION Return to List of Keywords Description Condition coupler between regions and geomechanics boundary conditions Since the geomechanics is solved in a quasi steady manner initial conditions are not needed Input GEOMECHANICS_CONDITION geomechanics_condition_name TYPE DISPLACEMENT X dirichlet DISPLACEMENT_Y dirichlet DISPLACEMENT_Z dirichlet FORCE_X dirichlet FORCE Y dirichlet FORCE Z dirichlet END DISPLACEMENT X lt float gt DISPLACEMENT Y lt float gt DISPLACEMENT Z lt float gt FORCE X lt float gt FORCE Y lt float gt FORCE Z lt float gt END Explanation lt 8l gt PFLOTRAN User Manual
84. OLVI ER GMRES PRECONDITIONER TLU lt 100 gt PFLOTRAN User Manual 84 33 0 August 14 2015 Advanced PETSc options LINEAR_SOLVER FLOW KSP TREYPE TBCGS BC TYBE ASM LINEAR SOLVER TRANSPORT KSP TYPE PCNONE BC TYPE EO U_ZERO_PIVOT_TOL 1d 15 Return to List of Keywords lt 101 gt PFLOTRAN User Manual 84 34 0 August 14 2015 4 34 Keyword MATERIAL_PROPERTY Return to List of Keywords Description Specifies material properties to be associated with a region in the problem domain Input MATERIAL PROPERTY lt char gt ID lt int gt SATURATION FUNCTION lt char gt ROCK DENSITY lt float gt kg m SPECIFIC HEAT lt float gt J kg K LONGITUDINAL DISPERSIVITY lt float gt m TRANSVERSE DISPERSIVITY lt float gt not implemented m THERMAL CONDUCTIVITY DRY lt float gt W m K THERMAL CONDUCTIVITY WET lt float gt W m K PORE COMPRESSIBILITY lt float gt not implemented bart THERMAL EXPANSITIVITY lt float gt not implemented C POROSITY lt float gt porosity filename TORTUOSITY lt float gt PERMEABILITY ISOTROPIC Toggles on isotropy Default ANISOTROPIC Toggles on anisotropy VERTICAL_ANISOTROPY_RATIO lt float gt PERM_X lt float gt Diagonal permeability k m PERM_Y lt float gt Diagonal permeability k m PERM_Z lt float gt Diagonal permeability k m
85. OTRAN Nat 0 009 o 0 008 o o q A 0 006 0 005 0 004 0 003 Concentration mol kg H O 0 002 0 001 10 20 30 OSD ye 40 50 60 Pore Volume 70 80 Figure 7 4 Breakthrough curves for Ca Mg and Nat compared with experimental results from Voegelin et al 2000 Description 1D ion exchange problem SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT END SUBSURFACE m s UNIFORM_VELOCITY 5 69333e 4 0 d0 0 d0 CHECKPOINT 100 WALLCLOCK_STOP 11 75 chemistry CHEMISTRY OPERATOR_SPLIT PRIMARY_SPECIES Na K Cat Mg H HCO3 Cl Tracer lt 151 gt PFLOTRAN User Manual 7 1 0 August 14 2015 SECONDARY_SPECIES OH CO3 co2 aq CaOH CaCO3 aq CaHCO3 CaCl MgCO3 aq MgHCO3 MgCl HCl aq KC1 aq NaCl aq NaOH aq GAS_SPECIES CO2 g MINERALS Halite MINERAL_KINETICS Halite RATE_CONSTANT 1 e 30 if SORPTION TON_EXCHANGE_RXN MINERAL Halite CEC 71 004 mol m 3 CATIONS Na 7 94328 Catt 1 Mg 1 44544 DATABASE Users lichtner projects parallel repository pflotran database hanford dat LOG_FORMULATION ACTIVITY_COEFFICIENTS NEWTON_ITERATION MOLAL OUTPUT All REFERENCE_POROSITY 0 61d0
86. OUTPUT GEOMECHANICS MATERIAL PROPERTY GEOMECHANICS REGION GEOMECHANICS CONDITION GEOMECHANICS BOUNDARY CONDITION GEOMECHANICS STRATA GRID required lt 30 gt PFLOTRAN User Manual 4 3 0 August 14 2015 IMMOBILE_DECAY_REACTION INITIAL_CONDITION INITIALIZE_FLOW_FROM_FILE INITIALIZE_TRANSPORT_FROM_FILE INTEGRAL_FLUX LINEAR_SOLVER MATERIAL_PROPERTY MODE MULTIPLE_CONTINUUM NEWTON_SOLVER NONUNIFORM_VELOCITY NUMERICAL_JACOBIAN_FLOW NUMERICAL_JACOBIAN_RXN NUMERICAL_JACOBIAN_MULTI_COUPLE OBSERVATION ORIG ORIGIN OUTPUT OVERWRITE_RESTART_TRANSPORT PROC optional REGION RESTART SATURATION_FUNCTION SOURCE_SINK STRATIGRAPHY STRATA TIME TIMESTEPPER TRANSPORT_CONDITION UNIFORM_VELOCITY USE_TOUCH_OPTIONS VELOCITY_DATASET optional WALLCLOCK_STOP lt 31 gt PFLOTRAN User Manual 84 4 0 August 14 2015 4 4 Example Input File Description 3D infiltration problem using Richards model with calcite dissolution or denotes following text a comment SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_FLOW flow MODE RICHARDS SUBSURFACE_TRANSPORT transport GLOBAL_IMPLICIT END SUBSURFACE SUBSURFACE block ends with END_SUBSURFACE debugging gt gt EEN PE gt 22323 3 gt 23 DEBUG MATVIEW_JACOBIAN VECVIEW_RESIDUAL VECVIEW SOLUTION chemistry S 2 E D E E O E
87. PDATE 1 d 4 NO_INFINITY_NORM NO_PRINT_CONVERGENCE PRINT_DETAILED_CONVERGENCE END LINEAR_SOLVER TRANSPORT KSP_TYPE GMRES PC_TYPE NONE KSP_TYPE PREONLY PC_TYPE LU SOLVER GMRES END TYPE structured ORIGIN 0 d0 0 d0 0 d0 NXYZ 1 1 136 BOUNDS 0 d0 0 d0 0 d0 1 d0 1 d0 68 d0 FLUID_PROPERTY DIFFUSION_COEFFICIENT 1 d 9 END MATERIAL_PROPERTY Backfill ED POROSITY 0 2585d0 TORTUOSITY 0 5d0 SATURATION FUNCTION BF PERMEABILITY PERM X 1 24e 12 PERM Y 1 24e 12 PERM Z 1 24e 12 END MATERIAL PROPERTY Hanford Fine Sand Ea POROSITY 0 3586 TORTUOSITY 0 5d0 SATURATION FUNCTION HF PERMEABILITY PERM X 3 37028e 13 PERM Y 3 37028e 13 PERM Z 3 37028e 13 END MATERIAL PROPERTY Plio Pleistocene ID 3 POROSITY 0 4223d0 lt 167 gt PFLOTRAN User Manual 87 3 5 August 14 2015 TORTUOSITY 0 5d0 SATURATION_FUNCTION PP PERMEABILITY PERM_X 3 73463e 14 PERM_Y 3 73463e 14 PERM_Z 3 73463e 14 END MATERIAL_PROPERTY Upper Ringold Gravel ID 4 POROSITY 0 2625d0 TORTUOSITY 0 5d0 SATURATION_FUNCTION URG PERMEABILITY PERM_X 1 4392e 13 PERM_Y 1 4392e 13 PERM_Z 1 4392e 13 END MATERIAL_PROPERTY Middle Ringold Gravel IDAS POROSITY 0 1643 TORTUOSITY 0 5d0 SATURATION_FUNCTION MRG PERMEABILITY PERM_X 2 00395e 13 PERM_Y 2 00395e 13 PERM_Z 2 00395e 13 CHARACTERISTIC_CURVES BF SATURATION_FUNCTION VAN_GENUCHTEN M 0 6585d0 ALPHA 1 008d 3 LIQUID_RESIDUAL_SATURATION 0 0774 PERMEABILITY_FUNCT
88. PFLOTRAN Reaction networks developed within the reaction sandbox can leverage existing biogeochemical capability within in PFLOTRAN e g equilibrium aqueous complexation mineral precipitation dissolution etc or function independently Please note that although the reaction sandbox facilitates the in tegration of user defined reactions the process still requires a basic understanding of PFLOTRAN and its approach to solving reaction through the Newton Raphson method For instance One must understand the purpose and function of the rt_auxvar and global_auxvar objects C 2 Implementation The core framework of reaction sandbox leverages Fortran 2003 object oriented extendable de rived types and methods and consists of two modules Reaction_Sandbox_module reaction_sandbox F90 Reaction_Sandbox_Base_class reaction_sandbox_base F90 To implement a new reaction within the reaction sandbox one creates a new class by extending the Reaction_Sandbox_Base_class and adds the new class to the Reaction_Sandbox_module The following steps illustrate this process through the creation of the class Reaction_Sandbox_Example_class that implements a first order decay reaction 1 Copy reaction_sandbox_template F90 to a new filename e g reaction_sandbox_example F90 2 Replace all references to Template template with the new reaction name Template Example template gt example 3 Add necessary variables to the module and or the exte
89. PFLOTRAN User Manual 84 6 0 August 14 2015 4 6 Keyword BRINE BRINE lt float gt MOLAL MASS MOLE Description Units refer to concentration of an NaCl brine in molality mass fraction or mole fraction with equal concentration of Nat and CI Return to List of Keywords Example BRINE 4 d0 MOLAL Return to List of Keywords lt 39 gt PFLOTRAN User Manual 84 7 0 August 14 2015 4 7 Keyword CHARACTERISTIC_CURVES Description Specifies relative permeability and saturation functions and parameters to be associ ated with a material property Note this keyword is currently only supported for GENERAL and RICHARDS modes keyword SATURATION_FUNCTION should be used in all other flow modes Return to List of Keywords Input CHARACTERISTIC_CURVES lt string gt SATURATION_FUNCTION lt string gt VAN_GENUCHTEN BROOKS_COREY ALPHA lt float gt Pa M lt float gt LIQUID_RESIDUAL_SATURATION lt float gt MAX_CAPILLARY PRESSURE lt float gt Pa Default 10 Pa END PERMEABILITY FUNCTION MUALEM M LIQUID RESIDUAL SATURATION END PERMEABILITY FUNCTION BURDINE LAMBDA LIQUID RESIDUAL SATURATION END PERMEABILITY FUNCTION MUALEM VG GAS M LIQUID RESIDUAL SATURATION GAS RESIDUAL SATURATION END PERMEABILITY FUNCTION BURDINE BC GAS LAMBDA LIQUID RESIDUAL SATURATION GAS RESIDUAL SATURATION END END lt 40 gt PFLOTRAN U
90. REGION HF MATERIAL Hanford Fine Sand END STRATA REGION BF MATERIAL Backfill END skip STRATA REGION all lt 172 gt PFLOTRAN User Manual 87 3 5 August 14 2015 MATERIAL Middle Ringold Gravel END noskip CONSTRAINT well CONCENTRATIONS Tracer 1 d0 T END CONSTRAINT infiltration CONCENTRATIONS Tracer 1 d0 T END CONSTRAINT initial CONCENTRATIONS Tracer 1 d 16 T END END_SUBSURFACE lt 173 gt PFLOTRAN User Manual 87 4 1 August 14 2015 7 4 MPHASE 7 4 1 CO Sequestration 1D Example Problem and Comparison with TOUGHREACT In this example problem involves sequentially coupling of MPHASE and CHEMISTRY The chem ical system consists of four primary species and 5 secondary species Supercritical CO is injected into a well located at the west boundary Dirichlet pressure boundary conditions are imposed at the east boundary The problem definition with associated parameters is given in Table 7 9 Table 7 9 Problem definition and parameters used in the 1D CO sequestration example Description Symbol Value Domain l 100 m Permeability k 10715 m Porosity p 0 12 Tortuosity a 1 Injection Rate co 5 x 107 kg s duration 0 4 y Characteristic Curves modified van Genuchten see Eqns 7 34 7 38 A 0 6 a 1 9 210 Pas Spl 0 Sra 0 I 10 Pa Rock Density Pr 2650 kg m Rock Specific Heat Cs 1000 J kg K Rock Thermal Conductivity et dey 0 5 W m K The PFLOTRAN initial aqueous so
91. S name concentration constraint constraint species H e M Calcite Ca 1 20644e 3 T Cu 1 e 8 T g 5 09772e 4 M Dolomite UO2 2 4830E 11 At K 1 54789e 4 Al Nat 1 03498e 3 Z HCO3 3 5 COZTo er 6 97741e 4 T F 2 09491e 5 T HPO4 1 e 8 M Fluorapatite NO3 4 69979e 4 At SO4 6 37961e 4 al Tracer 1 e 7 F Tracer2 1 e 7 F MINERALS mineral vol frac area Calcite 0 1 S Metatorbernite 0 ls END TRANSPORT_CONDITION TIME_UNITS h CONSTRAINT_LIST O name of constraint I name of constraint 2 name_of constraint lt 137 gt PFLOTRAN User Manual 84 56 0 August 14 2015 END TRANSPORT CONDITION CONSTRAINT LIST 0 h name of constraint 1 h name of constraint 2 h name of constraint Return to List of Keywords lt 138 gt PFLOTRAN User Manual 84 57 0 August 14 2015 4 57 Keyword UNIFORM_VELOCITY Optional Return to List of Keywords Description Input UNIFORM_VELOCITY vix vly vlz m s Explanation Set uniform velocity for transport mode Example UNIFORM VELOCITY 3 84259d 6 0 d0 0 d0 1 38333 cm h Return to List of Keywords lt 139 gt PFLOTRAN User Manual 84 58 0 August 14 2015 4 58 Keyword USE TOUCH OPTIONS Return to List of Keywords Description Input USE TOUCH OPTIONS use touch options true Explanation Example Return to List of Keywords lt 140 gt PFLOTRAN User Manual 84 59
92. S Tracer 1 e 8 F Tracer_Age 1 e 16 F Output is given in terms of a and C from which the mean age A can be obtained as A a C A 11 Thermodynamic Database PFLOTRAN reads thermodynamic data from a database that may be customized by the user Re actions included in the database consist of aqueous complexation mineral precipitation and disso lution gaseous reactions and surface complexation lon exchange reactions and their selectivity coefficients are entered directly from the input file A standard database supplied with the code is referred to as hanford dat and is found in the database directory in the PFLOTRAN mercurial repository This database is an ascii text file that can be edited by any editor and is equivalent to the EQ3 6 database data0 com V8 R6 CII GEMBOCHS V2 EQ8 data0 com V8 R6 THERMODYNAMIC DATABASE generated by GEMBOCHS V2 Jewel src R5 03 dec 1996 14 19 25 The database provides equilibrium constants in the form of log K values at a specified set of temperatures listed in the top line of the database A least squares fit is used to interpolate the log K values between the database temperatures using a Maier Kelly expansion of the form c c log K c InT co aT 4 7 73 A 199 lt 216 gt PFLOTRAN User Manual 1 11 0 August 14 2015 with fit coefficients c The thermodynamic database stores all chemical reaction properties equi librium constant log K reaction stoichiometry Vi
93. S by default Other types report an unsupported error message REALIZATION DEPENDENT Toggle that causes PFLOTRAN to load the data set based on the realization ID For instance if the data set is tied to PERMEABILITY within a MATE RIAL PROPERTY and the realization ID is 99 PFLOTRAN searches for an HDF5 data set labeled PERMEABILITY99 For POROSITY POROSITY99 Examples Reading heterogeneous permeability and porosity for the Hanford unit for realization ID 99 The name of the data sets within the HDFS file are PERMEABILITY99 and POROS ITY99 respectively DATASET perm FILENAME hanford_unit h5 REALIZATION_DEPENDENT END DATASET poros FILENAME hanford_unit h5 REALIZATION_DEPENDENT END MATERIAL_PROPERTY hanford_unit POROSITY DATASET poros PERMEABILITY DATASET perm lt 67 gt PFLOTRAN User Manual 84 13 0 August 14 2015 END Return to List of Keywords lt 68 gt PFLOTRAN User Manual 84 14 0 August 14 2015 4 14 Keyword DBASE_FILENAME Return to List of Keywords Keyword DBASE_FILENAME allows the user to define input parameters through an exter nal database stored in an ASCII text or HDFS file These parameters can be realization dependent where an array of values is provided and indexed by the realization id DBASE_FILENAME lt string gt The path filename of the external database to be empl
94. SS Microbe_D 1 d 1 TION END CONSTRAINT biomass CONCENTRATIONS Aa Andi ai Bacq Indy AO gE lt gt 1 5 C ag A is the donor B is the acceptor Ces lt 56 gt the product and inhibits when too high PFLOTRAN User Manual 84 9 5 August 14 2015 IMMOBILE Microbe_D 1 d0 END Return to List of Keywords lt 57 gt PFLOTRAN User Manual 84 9 6 August 14 2015 4 9 6 Keyword REACTION_SANDBOX Specifies parameters for user defined reactions Return to List of Keywords REACTION_SANDBOX Opens the reaction sandbox block Terminate with END CLM CN Block for specifying CLM CN reaction parameters Examples REACTION_SANDBOX CLM CN POOLS SOM1 12 d0 Tigi REACTION UPSTREAM POOL Litl DONNSTREAM POOL SOM1 TURNOVER TIME 20 h RESPIRATION FRACTION 0 39d0 N INHIBITION 1 d 10 Return to List of Keywords lt 58 gt PFLOTRAN User Manual 84 9 6 August 14 2015 OPERATOR_SPLITTING Toggles operator splitting mode Default implicit not cur rently implemented GEOTHERMAL_HPT Use high pressure and temperature thermodynamic database DATABASE Path Database_Name LOG_FORMULATION NO_CHECKPOINT_ACT_COEFS ACTIVITY_COEFFICIENTS LAG NEWTON TIMESTEP NEWTON_ITERATION ACTIVITY_H2O ACTIVITY_WATER MOLAL MOLALITY NO_BDOT UPDATE_POROSITY see Eqn A 123 UPDATE_TORTUOSITY
95. STRAINT keyword Local equilibrium is assumed between phases for modeling multiphase systems with PFLO TRAN The multiphase partial differential equations for mass and energy conservation solved by PFLOTRAN have the general form q e Y soma V I Qi A 19a for the th component where the flux F is given by F Qual PSDoMo VER A 19b lt 189 gt PFLOTRAN User Manual 1 3 1 August 14 2015 and o En 2 Scala 1 one V gt nt vr A 19c for energy In these equations a designates a fluid phase a l sc at temperature T and pressure P with the sums over all fluid phases present in the system and source sink terms Q and Qe described in more detail below Species are designated by the subscript 1 H20 CO y denotes the porosity of the porous medium sa denotes the phase saturation state x denotes the mole fraction of species 2 satisfying ade A 20 the quantities Na Ha Ua refer to the molar density enthalpy and internal energy of each fluid phase respectively and q denotes the Darcy flow rate for phase a defined by pa a Q where k refers to the intrinsic permeability ka denotes the relative permeability 4a denotes the fluid viscosity W_ denotes the formula weight g denotes the acceleration of gravity and z desig nates the vertical of the position vector The mass density p is related to the molar density by the expression Pa Wana A 22 where
96. SURE 101325 d0 PRESSURE 1 4e5 200 meter piezometric head 200x997 32x9 81 END FLOW_CONDITION source TYPE RATE mass_rate RATE LIST TIME_UNITS s DATA_UNITS kg s 0 0 187e 4 1 21293e6 0 TRANSPORT_CONDITION initial TYPE zero_gradient CONSTRAINT_LIST 0 d0 initial END TRANSPORT_CONDITION boundary TYPE zero_gradient CONSTRAINT_LIST 0 d0 initial END TRANSPORT_CONDITION infiltration TYPE dirichlet CONSTRAINT_LIST 0 d0 infiltration END TRANSPORT_CONDITION source TYPE dirichlet CONSTRAINT_LIST 0 d0 well lt 171 gt PFLOTRAN User Manual 87 3 5 August 14 2015 initial condition INITIAL_CONDITION FLOW_CONDITION initial TRANSPORT_CONDITION initial REGION all END top boundary condition BOUNDARY_CONDITION top FLOW_CONDITION initial FLOW_CONDITION infiltration TRANSPORT_CONDITION initial REGION top END bottom boundary condition BOUNDARY_CONDITION bottom FLOW_CONDITION water_table TRANSPORT_CONDITION initial REGION bottom ND EJ well source sink skip SOURCE_SINK well FLOW_CONDITION source TRANSPORT_CONDITION source REGION well END noskip infiltration source sink skip SOURCE_SINK infil FLOW_CONDITION infiltration TRANSPORT_CONDITION infiltration REGION top END noskip STRATA REGION MRG MATERIAL Middle Ringold Gravel END STRATA REGION URG MATERIAL Upper Ringold Gravel END STRATA REGION PP MATERIAL Plio Pleistocene END STRATA
97. T K 1 d 10 T Ca 530 3 L Mg l e 16 T H 4 6 pH HCO3 3 5 G CO2 g ETS 3 d 4 Z Tracer 9 4d 3 T CONSTRAINT Inlet2 CONCENTRATIONS Na 4 6d 3 T K 1 d 10 T Ca 1 d 16 T Mg 2 4e 3 T H 4 6 pH HCO3 3 5 G CO2 g Cl 3 d 4 Z Tracer 9 AIF3 ArT CONSTRAINT Inlet3 CONCENTRATIONS Na 4 65d 3 T K 1 d 10 T Ca 5 2d 3 T Mg 4 55e 3 T H 4 6 pH HCO3 3 5 G CO2 g Cl 3 d 4 Z Tracer 9 4d 3 T END_SUBSURFACE lt 156 gt PFLOTRAN User Manual 87 2 3 August 14 2015 7 2 GENERAL REACTION Example 7 2 1 Problem Description A single irreversible reaction is considered of the form A 2B gt C 7 13 for flow in a fully saturated 1D column of length 100 m with a Darcy velocity of 1 m y diffusion coefficient of 107 m s and porosity equal to 0 25 The conservation equation for advection diffusion and reaction is given by o Zr V F guR 1 A B C 7 14 with stoichiometric coefficients va 1 vp 2 and vo 1 The flux F consists of contribu tions from advection and diffusion F qC pDVCi 7 15 The forward reaction rate is based on a elementary aqueous reaction R kCt or 7 16 Dividing through by porosity assuming y constant the transport equation becomes Ci DE V vC DV VC nk Or 0 7 17 with average pore velocity e 7 18 p Initial and boundary conditions imposed on the solution are given by C x t 0 Cy 7 19a ae 7 19b OC 0
98. TRAN User Manual 84 56 0 August 14 2015 4 56 Keyword TRANSPORT CONDITION Return to List of Keywords Description Specifies a geochemical solution composition based on various user defined con straints with minerals gases pH charge balance free ion and total concentrations Input TRANSPORT CONDITION Name TYPE dirichlet dirichlet zero gradient equilibrium neumann mole mole rate zero gradient CONSTRAINT LIST time constraint name END CONSTRAINT constraint name END Explanation Example TRANSPORT CONDITION Initial TYPE dirichlet zero gradient CONSTRAINT LIST 0 d0 initial END TRANSPORT_CONDITION U_source TYPE dirichlet CONSTRAINT_LIST 0 d0 U_source 336000 d0 Initial END the units for time are seconds by default CONSTRAINT U_source CONCENTRATIONS name concentration constraint constraint species H 30 pH Ca 1 20644e 3 T lt 136 gt PFLOTRAN User Manual 84 56 0 August 14 2015 cu 1 e 8 T g 5 09772e 4 T UO2 ESO al K 1 54789e 4 al Nat 1 03498e 3 Al HCO3 3 5 G Coz a Elis 6 97741e 4 Z F 2 09491e 5 T HPO4 1 e 8 M Fluorapatite NO3 4 69979e 4 4 S04 6 37961e 4 a Tracer 1 e0 F Tracer2 1 e0 F MINERALS mineral vol frac area Calcite omi di Metatorbernite 0 i end of minerals END end of constraint CONSTRAINT initial CONCENTRATION
99. TRAN on Windows see instructions on the PFLOTRAN wiki https bitbucket org pflotran pflotran dev wiki Home 3 2 3 ORNL s Jaguar XT4 5 config configure py PETSC_ARCH cray xt4 pgi_fast N configModules PETSc Configure optionsModule PETSc compilerOptions A known levell dcache size 65536 known levell dcache linesize 64 known levell dcache assoc 2 known memcmp ok 1 known sizeof char 1 known sizeof void p 8 known sizeof short 2 known sizeof int 4 known sizeof long 8 N known sizeof long long 8 known sizeof float 4 known sizeof double 8 lt 18 gt PFLOTRAN User Manual 83 4 0 August 14 2015 known sizeof size_t 8 known bits per byte 8 known sizeof MPI_Comm 4 known sizeof MPI_Fint 4 known mpi long double 0 with batch 1 with shared libraries 0 with dynamic 0 with cc ce with cxx CC with fc ftn COPTFLAGS tp barcelona 64 fastsse Mipa fast CXXOPTFLAGS tp barcelona 64 fastsse Mipa fast FOPTFLAGS tp barcelona 64 fastsse with debugging 0 with blas lib sci with lapack lib sci with x 0 with mpi dir SMPICH DIR download hypre 1 download parmetis 1 with hdf5 1 with hdf5 dir HDF5_DIR known mpi shared 0 The user wi
100. User Manual 7 4 2 August 14 2015 SATURATION_FUNCTION_TYPE BROOKS_COREY RESIDUAL SATURATION LIQUID PHASE 0 2 RESIDUAL SATURATION GAS PHASE 0 05 LAMBDA 2 0 ALPHA 1d 4 MAX CAPILLARY PRESSURE 5 0d5 regions REGION all COORDINATES 0 d0 0 d0 0 d0 1000 d0 1000 d0 160 d0 END REGION upper COORDINATES 0 d0 0 d0 130 d0 1000 d0 1000 d0 160 d0 END REGION middle COORDINATES 0 d0 0 d0 30 d0 1000 d0 1000 d0 130 d0 END REGION lower COORDINATES 0 d0 0 d0 0 d0 1000 d0 1000 d0 30 d0 END REGION top FACE TOP COORDINATES 0 d0 0 d0 160 d0 1000 d0 1000 d0 160 d0 END REGION bottom FACE BOTTOM COORDINATES 0 d0 0 d0 0 d0 1000 d0 1000 d0 0 d0 END REGION west FACE WEST COORDINATES 0 d0 0 d0 0 d0 0 d0 1000 d0 160 d0 END REGION east FACE EAST COORDINATES 1000 d0 0 d0 0 d0 1000 d0 1000 d0 160 d0 END REGION south FACE SOUTH lt 182 gt PFLOTRAN User Manual 87 4 2 August 14 2015 COORDINATES 0 d0 0 d0 0 d0 1000 d0 0 d0 160 d0 END REGION north FACE NORTH COORDINATES 0 d0 1000 d0 0 d0 1000 d0 1000 d0 160 d0 END REGION well COORDINATES 500 d0 500 d0 0 d0 500 d0 500 d0 160 d0 END REGION inj_well COORDINATES 400 d0 500 d0 0 d0 400 d0 500 d0 30 d0 END flow conditions FLOW_CONDITION initial UNITS Pa C M yr TYPE PRESSURE hydrostatic TEMPERATURE dirichlet CONCENTRATION dirichlet ENTHALPY dirichlet IPHASE 1 DATUM 0 d
101. ZA aX As A 140 with valencies z 2 of cations A and A respectively The reference cation is denoted by A and Ai 1 represents all other cations The corresponding mass action equation is given by CO ESOO a A 141 Kj ke T Xe i 4 Using the Gaines Thomas convention the equivalent fractions X are defined by So E E E ge A 142 gt aSr Wa l with NL A 143 k The site concentration wa is defined by We Y 225 A 144 k where wa is related to the cation exchange capacity Qa CEC by the expression Wa 1 p ps Qa A 145 with solid density p and porosity y lt 208 gt PFLOTRAN User Manual 81 9 2 August 14 2015 An alternative form of reactions A 140 often found in the literature is 1 1 1 1 A X A A Aj A 146 Zj i i Zj 2 2 obtained by dividing reaction A 140 through by the product z z In addition the reaction may be written in reverse order The mass action equations corresponding to reactions A 146 have the form y T 7 de KT Zj X Zj a Zi The selectivity coefficients corresponding to the two forms are related by the expression Re A 148 and similarly for k k When comparing with other formulations it is important that the user determine which form of the ion exchange reactions are being used and make the appropriate transformations For equivalent exchange z z 2 an explicit expression exists for the sorbed
102. a yer Inu B 15b B 2 1 Example To illustrate the logarithmic update formulation the simple linear equation T T0 B 16 is considered The residual function is given by R z t0 B 17 with Jacobian IR due a B 18 Ox In the linear formulation the Newton Raphson equations are given by J x R B 19 dz 1 Lg B 20 q 0x To B 21 lt 221 gt PFLOTRAN User Manual 82 2 2 August 14 2015 In the logarithmic formulation the Jacobian is given by OR sau B 22 Olnz i and the Newton Raphson equations are now nonlinear becoming Jing B 23 with the solution update Ing Ine lne B 24 or git gimit B 25 It follow that r ln tl 2 zp B 26 with the solution inet e B 27 q and thus i a g exp 7 B 28 Given that a solution x exists it follows that lim gt x B 29 1 00 i fn ep B 30 io lim exp A 41 B 31 i gt 00 q lim z gt zo B 32 1 00 B 2 2 Multirate Sorption The residual function incorporating the multirate sorption model can be further simplified by solv ing analytically the finite difference form of kinetic sorption equations This is possible when these equations are linear in the sorbed concentration Sja and because they do not contain a flux term Thus discretizing Eqn A 173 in time using the fully implicit backward Euler method gives t At t Sia an Sia zo hei B 33 Solving
103. ached to a mineral surface Colloids may be generated through nucleation of minerals in solution although this effect is not included currently in the code Three separate reactions may take place involving competition between mobile and immobile colloids and mineral surfaces gt XP Y Aj gt Sp A 185 J gt Xm Aj gt SR A 186 J gt XE Y Ay gt Sk A 187 J lt 213 gt PFLOTRAN User Manual 81 9 5 August 14 2015 with corresponding reaction rates 17 I m and where the superscripts s m and im denote min eral surfaces and mobile and immobile colloids respectively In addition reaction with minerals Ms may occur according to the reaction yA Ma A 188 j The transport equations for primary species mobile and immobile colloids read es V Q S vl R Y Vils A 189 t j j k s s e VS de A 190 SE T A 191 A i A 192 where q denotes the colloid Darcy velocity which may be greater than the fluid velocity q For conditions of local equilibrium the sorption reaction rates may be eliminated and replaced by al gebraic sorption isotherms to yield 2 losti Y valpas s Y Si V a Y vak vjs A 193 k s k S In the kinetic case either form of the primary species transport equations given by Eqn A 189 or A 193 can be used provided it is coupled with the appropriate kinetic equations Eqns A 190 A 192 The mobile case leads to additional equations tha
104. and initial conditions source sinks observation points etc Although a region may be defined though the use of I J K indices using the BLOCK keyword the user is encouraged to define regions either through COORDINATES or lists read in from an HDFS file in order to minimize the dependence of the input file on grid resolution In the case of the FILE keyword a list of grid cell ids is read from an HDFS file where the region name defines the HDFS data set It should be noted that given a region defined by a plane or point shared by two grid cells e g a plane defining the surface between two grid cells PFLOTRAN will select the upwind cell s as the region Input REGION region_name FILE file name LIST to be implemented FACE face name BLOCK il i2 31 32 kl k2 COORDINATE x y z COORDINATES xl yl zl x2 y2 22 END END Explanation Keyword REGION begins a region entry with name region_name Keyword BLOCK defines a volumetric planar or point region through IJK indices il 12 j1 j2 k1 k2 Keyword COORDINATE defines a point region through coordinates in 3D space Keyword COORDINATES Defines a volumetric planar or point region between two points in space Keyword FILE Defines an HDFS5 file within which a dataset named region name contains a list of grid cells corresponding to a region lt 125 gt PFLOTRAN User Manual 84 49 0 August 14 2015 Keyword FACE Defines the face of the grid cell to which
105. are specified by a character A test is declared as a section in the configuration file It is assumed that there will be a PFLOTRAN input file with the same name as the test section The key value pairs in a test section define how the test is run and the output is compared to the gold standard file calcite kinetics look for an input file named calcite kinetics in np 2 timeout 30 0 concentration 1 0e 10 absolute e np N optional indicates a parallel test run with N processors Default is serial If mpiexec in not provided on the command line then parallel tests are skipped e timeout N optional indicates that the test should be allowed to run for N seconds before it is killed Default is 60 0 seconds e TYPE TOLERANCE COMPARISON indicates that data in the regression file of type TYPE should be compared using a tolerance of TOLERANCE Know data types are listed below The data types and default tolerances are e time 5 percent e concentration 1 x 107 absolute e generic 1 x 107 absolute e discrete O absolute lt 145 gt PFLOTRAN User Manual 85 4 0 August 14 2015 rate 1 x 10 absolute volume_fraction 1x 107 absolute e pressure 1 x 10712 absolute e saturation 1 x 1071 absolute residual 1 x 101 absolute The default tolerances are deliberately set very tight and are expected to be overridden on a per test or per configuration file basis There
106. arten 65 K yword DATASET se lt see areg Os ER EOE Ba EW A HW A 67 Keyword DBASE FILENAME sussa are a ala r pra S 80H weh Ha 69 Key ora DEBUG css un ee a nn a A A 71 Keyword BOS ss ag ag go dc ae en re RI E 72 Keyword FLOW CONDITION 2 5 ss 2 0 0 34 Ro due Bee O SS 73 Keyword PLUID PROPERTY sussa seres a rose are sanas 77 Keyword GEOMECHANICS 2 664064 252 Eee a 78 Keyword GEOMECHANICS BOUNDARY CONDITION 79 Keyword GEOMECHANICS_CONDITION 22 22 22 020 81 Keyword GEOMECHANICS GRID y 22x oes we Su bee Ber EY ash a 83 Keyword GEOMECHANICS MATERIAL PROPERTY 84 Keyword GEOMECHANICS OUTPUT cccvesesgeshw 2 4 dig a 85 Keyword GEOMECHANICS REGION occ 24 22 2484 e444 86 lt 3 gt PFLOTRAN User Manual 0 0 0 August 14 2015 4 26 4 27 4 28 4 29 4 30 4 31 4 32 4 33 4 34 4 35 4 36 4 37 4 38 4 39 4 40 4 41 4 42 4 43 4 44 4 45 4 46 4 47 4 48 4 49 4 50 4 51 Keyword GEOMECHANICS_STRATA 2 2 2 2 nr on een 87 Keyword GRID Required so 2 02 pr 24 db a 88 427 21 Implicit Unstmietvred GAS ss s pe Se air ade 89 427 2 Explicit Unstr ct red Grids lt ss a sos anhand 90 Keyword IMMOBILE DECAY REACTION 0 42 434 ate 2 2 er E 95 Keyword INTIMAL CONDITION ss ss e sas dos wa a wa ws ae sus 96 Keyword INITIALZE FLOW_FROM FILE a 2 22 804 ee ge gas 97 Keyword INITIALIZE_TRANSPORT_FROM_FILE 97 Keyword INTEGRAL FLUX e sose koe e
107. boundary conditions are connected where face_name is one of WEST EAST NORTH SOUTH BOTTOM TOP structured grids only Keyword END Ends the region entry can be one of END Examples REGION source_zone BLOCK Ss is Gas END REGION source zone BLOCK 3752215167 225 END REGION west_boundary BLOCK ISO 1 FACE WEST END REGION source zone COORDINATES BONS ANG ee AOE ar is aa END REGION river_boundary FILE regions h5 FACE EAST REGION well COORDINATE 50 10 10 END REGION well COORDINATE 50 10 10 END REGION west_boundary COORDINATES Om 20 0 oles Able ALG FACE WEST END Return to List of Keywords lt 126 gt PFLOTRAN User Manual 84 50 0 August 14 2015 4 50 Keyword RESTART Return to List of Keywords Description The RESTART card defines a checkpoint file from which the current simulation should be restarted If a time is specified after the file name the initial simulation time is set to that time Input RESTART lt restart file name gt lt restart time gt lt time units gt Explanation Keyword RESTART defines the checkpoint filename to be read in to restart a simulation at the specified time Examples restart the simulation from the end of the previous simulation but set the time back to 0 RESTART restart chk 0 d0 y restart the program running f
108. cated in the figure for an infiltration rate of 8mm y 7 9 Comparison with TOUGHREACT dashed curves and PFLOTRAN solid curves after an elapsed time of 0 4 y corresponding to the end of injection Reasonable agreement is obtained between the two codes o oo en 7 10 Liquid blue curve and supercritical CO red curve pressures predicted by PFLO TRAN after an elapsed time of 0 4 y corresponding to the end of injection Also shown is the CO gt saturation green curve scenes e RE RIA RSA 7 11 Left pressure right supercritical CO saturation for an elapsed time of 250 days 7 12 Leakage rate relative to injection rate 2 62224 bebe Ew eee ew a A 1 Node configuration for secondary 8 continua nodes 1 l M associ ated with the nth primary e continuum node sac nn A 2 Control volumes in DCDM multiple continuum model with fracture aperture 26 and matrix block Size d s e ee eRe ERAS RRS Oo mS lt 9 gt 164 165 176 PFLOTRAN User Manual 0 0 0 August 14 2015 LIST OF TABLES 2 1 Options for configuring petsc dev 2 zer use een en er 13 2 2 Compile options for PFLOTRAN 2 4 2 24 2 24 eed arar AA 14 2 3 Available modes in PFLOTRAN 2 2 22 22 84 8 Han He HH 14 4 A UWS sao cd ede ee a A A A oe ae ae 25 4 5 SUBSURFACE Keywords listed in alphabetical order 30 4 6 Side set node ordering uke ou RR AA ARA A OR RAR 90 7 7 Stratigraphic sequ
109. checkpointing values with values read in from the input file on restart 4 46 Keyword OVERWRITE RESTART TRANSPORT Return to List of Keywords OVERWRITE RESTART TRANSPORT Overwrites checkpointing values with values read in from the input file on restart 4 47 Keyword OVERWRITE RESTART TRANSPORT Return to List of Keywords OVERWRITE RESTART TRANSPORT overwrite restart transport true Overwrites checkpointing values with values read in from the input file on restart Return to List of Keywords lt 123 gt PFLOTRAN User Manual 84 48 0 August 14 2015 4 48 Keyword PROC Return to List of Keywords PROC lt int int int gt Description The number of processor to be employed in each direction x y and z structured grids only Default let PETSc decide Warning the product of the integers must be equal to the number of processor employed Examples PROC 100 10 10 10 000 processes PROC 2 2 2 2x2x2 decomposition PROC 1 1 8 Force decomposition in z direction only 1x 1x8 decomposition Return to List of Keywords lt 124 gt PFLOTRAN User Manual 84 49 0 August 14 2015 4 49 Keyword REGION Return to List of Keywords Description The REGION keyword defines a set of grid cells encompassed by a volume or intersected by a plane or point or a list of grid cell ids The REGION name can then be used to link this set of grid cells to material properties strata boundary
110. concentra tions given by Wa KFUM j Nit a ki VIM l where my denotes the kth cation molality This expression follows directly from the mass action equations and conservation of exchange sites Q A 149 In the more general case z z it is necessary to solve the nonlinear equation X Xp 1 A 150 Aj for the reference cation mole fraction X From the mass action equation Eqn A 141 it follows that Xe Zi 2j x ko 2 A 151 koa Defining the function FAP XP X X 1 A 152 if its derivative is given by df 1 Esa a E 1 FR Bike 0 o 5 A 153 The reference mole fraction is then obtained by Newton Raphson iteration Ar pa Gor BILDER ax dX x J A 154 lt 209 gt PFLOTRAN User Manual 1 9 2 August 14 2015 The sorbed concentration for the 7th cation appearing in the accumulation term is given by Bere A 155 Zj with the derivatives for j l E a E A 156a Om my y axe l a 1 Se E A 156b 200 mS 20 1 and for 7 1 oles Wey X 2 X I Adel A 157a Om 2m Y XP l Sa 229 1 jad A 157b mj Ser l A 9 2 2 Surface Complexation Surface complexation reactions are assumed to have the form Va gt Xa gt VjiAj gt Si A 158 j for the th surface complex gt S on site a and empty site gt x As follows from the corresponding mass action equation the equilibrium sorption concentration Sid is given by Wo K iQ Beer A 159
111. config configure py with cc mpicc with fc mpif90 with cxx mpicxx with clanguage c with blas lapack dir BLAS_LAPACK_LIB_DIR with shared libraries 0 with debugging 0 download hdf5 yes download parmetis yes download metis yes lt 15 gt PFLOTRAN User Manual 83 2 0 August 14 2015 3 Installation The source code for PFLOTRAN can be downloaded from the bitbucket org web site using Mer curial hg hg clone https bitbucket org pflotran pflotran dev This requires first creating a free account on bitbucket It should be possible to build and run PFLOTRAN on essentially any system with modern C and Fortran 2003 standard or later compilers and an available implementation of the Mes sage Passing Interface MPI system that has been built with Fortran bindings Besides these re quirements the major third party library required is the open source library PETSc the Portable Extensible Toolkit for Scientific Computation that provides the parallel framework on which PFLOTRAN is built Most of the work involved in building PFLOTRAN lies in building PETSc PETSc uses a sophisticated Python based build tool BuildSystem to perform extensive platform discovery and configuration as well as automatic download and build for any of the open source third party libraries that PETSc can use The PFLOTRAN makefiles use the information generated by BuildSystem as part of the PETSc build process once PETSc is built building PF
112. d0 0 d0 0 d0 PRESSURE 101425 d0 END lt 154 gt flow conditions PFLOTRAN User Manual 87 1 0 August 14 2015 FLOW_CONDITION east TYPE PRESSURE hydrostatic DATUM 0 d0 0 d0 0 d0 PRESSURE 101325 d0 END TRANSPORT_CONDITION Initial TYPE dirichlet CONSTRAINT_LIST 0 d0 Initial TRANSPORT_CONDITION east TYPE dirichlet CONSTRAINT_LIST 0 d0 Initial TRANSPORT_CONDITION west TYPE dirichlet CONSTRAINT_LIST 0 d0 nlet1 10307 1 Inlet2 33498 2 Inlet3 NITIAL CONDITION Initial FLOW_CONDITION Initial TRANSPORT_CONDITION Initial REGION all BOUNDARY_CONDITION FLOW_CONDITION west TRANSPORT_CONDITION west REGION west END BOUNDARY_CONDITION FLOW_CONDITION east TRANSPORT_CONDITION east REGION east END STRATA MATERIAL HD REGION all transport constraints CONSTRAINT Initial CONCENTRATIONS Na 4 65d 3 T K 2 d 4 T Cat 520 3 T Mg 4 55e 3 T H 4 6 pH HCO3 35 G Cla 1 d 3 Z Tracer 4 65d 3 T A MINERALS CO2 g transport conditions couplers stratigraphy lt 155 gt PFLOTRAN User Manual 87 1 0 August 14 2015 Halite 0 91 je CONSTRAINT Inlet1 CONCENTRATIONS Na 1 d 16
113. e MPHASE input file and adding the requisite associated keywords At the end of an MPHASE time step the quantities p T s q and q are passed to the reactive trans port equations These quantities are interpolated between the current time tmpy and the new time tmpH At py The reactive transport equations may need to sub step the MPHASE time step i e Atrr lt Aturn Coupling also occurs from the reactive transport equations back to MPHASE This is through changes in material properties such as porosity tortuosity and permeability caused by mineral precipitation and dissolution reactions see A 9 1 2 In addition coupling occurs through consumption and production of H O and CO by mineral precipitation dissolution reac tions occurring in the reactive transport equations This effect is accounted for by passing the reaction rates Ry o and Rco given by S Vimlm A 43 back to the MPHASE conservation equations A further constraint on the reactive transport equations for aqueous CO is that it must be in equilibrium with supercritical CO in regions where 0 lt s lt 1 This is accomplished by S placing the CO mass conservation equations in those regions with the constraint Mco Meo A 4 Mode IMMIS The IMMIS mode applies to multiple completely immiscible phases The code PIMS parallel immiscible multiphase flow simulator is a simplified version of the MPHASE mode in which the dependency on thermodynamic relat
114. e and temperature C denotes the solute concen tration D denotes the diffusion dispersion coefficient 7 represents tortuosity Q and Qc denote source sink terms and q denotes the Darcy velocity defined by Kia kx q Ve p92 7 22 with saturated permeability ksa relative permeability k fluid viscosity u pressure p formula weight of water W acceleration of gravity g and height z Van Genuchten capillary properties are used for relative relative permeability according to the relation my 2 Bes 1 z E o l 1 23 where seg is related to capillary pressure P by the equation s 1 al Ph 7 24 where seg is defined by se 1 25 1 sr and where s denotes the residual saturation The quantity n is related to m by the expression 1 1 m l n 7 26 n l m The capillary pressure P and fluid pressure p are related by the constant gas pressure p3 P p p 7 27 where py 101 325 Pa is set to atmospheric pressure lt 161 gt PFLOTRAN User Manual 87 3 3 August 14 2015 7 3 2 1 Semi Analytical Solution for Steady State Conditions For steady state conditions the saturation profile satisfies the equation d Ple 0 7 28 dz or assuming an incompressible fluid de de 7 29 where q denotes infiltration at the surface Thus the pressure is obtained as a function of z by solving the ODE dp ge dz Ksat kr di using Eqns 7 23 and 7 24 to express the relative permeability
115. e code is designed to run on massively parallel computing architectures as well as workstations and laptops e g Hammond et al 2011 Parallelization is achieved through domain decomposition using the PETSc Portable Extensible Toolkit for Scientific Computation libraries for the parallelization framework Balay et al 1997 PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 218 processor cores with problem sizes up to 2 billion degrees of freedom Written in object oriented Fortran 90 the code requires the latest compilers compatible with Fortran 2003 At the time of this writing this requires for example gcc 4 7 x or Intel 13 x x or later As a requirement of running problems with a large number of degrees of freedom PFLOTRAN allows reading input data that would be too large to fit into memory if allocated to a single processor core The current limitation to the problem size PFLOTRAN can handle is the limitation of the HDF5 file format used for parallel IO to 32 bit integers Noting that 2 4 294 967 296 this gives an estimate of several billion degrees of freedom for the maximum problem size that can be currently run with PFLOTRAN Hopefully this limitation will be remedied in the near future Currently PFLOTRAN can handle a number of subsurface processes involving flow and trans port in porous media including Richards equation two phase flow involving supercritical CO and multicompon
116. e mesh in Natural ID Cells after ParMETIS decomposition in Natural ID PETSc ID Figure 4 2 a Example of a 5x4x3 unstructured grid problem with default decomposition across two processors Cells labelled in natural ID b ParMETIS decomposition of the domain c Representation of a global PETSc vector lt 91 gt PFLOTRAN User Manual 84 27 2 August 14 2015 Local cells in PETSc ID Local cells in PETSc ID Local cells in local ID Local cells in local ID Figure 4 3 a b Local and ghost cells on proc O and proc 1 with cell IDs in PETSc order c d Local PETSc Vector with cell IDs in local ghosted order lt 92 gt PFLOTRAN User Manual 84 27 2 August 14 2015 Format of unstructured grid file Implicitly defined grid type H hexahedron T tetrahedron W wedge P pyramid I vertn H 8 I vertn T 4 vertn W 6 I vertn P 5 I num cells num vertices integers type vertl vert2 vert3 vertn for cell 1 integers type vertl vert2 vert3 vertn for cell 2 type vertl vert2 vert3 vertn for cell num cells xcoord ycoord zcoord coordinates of vertex 1 real xcoord ycoord zcoord coordinates of vertex 2 real xcoord ycoord zcoord coord
117. e two point flux approximation where the sum over n involves nearest neighbor grid cells connected to the nth node with interfacial area Anw The discretized flux has the form for fluid phase a AA nn dn dn 2 with perpendicular distances to interface nn from nodes n and n denoted by d and d respec tively Upstream weighting is used for the advective term F a dele PsaTaDa B 6 Din nta Inn gt 0 ee B 7 A Inn lt 0 Depending on the type of source sink term the finite volume discretization has the form Q dV QjnVn B 8 Va for reaction rates that are distributed continuously over a control volume or for a well with point source Q Q r ro Q dV Qin B 9 Va lt 220 gt PFLOTRAN User Manual 82 2 1 August 14 2015 B 2 Fully Implicit Newton Raphson Iteration with Linear and Logarithm Update In a fully implicit formulation the nonlinear equations for the residual function R given by R x 0 B 10 are solved using an iterative solver based on the Newton Raphson equations Me R B 11 at the th iteration Iteration stops when R 2 B 12 or if ataa B 13 However the latter criteria does not necessarily guarantee that the residual equations are satisfied The solution is updated from the relation et pO 4 fg B 14 For the logarithm of the concentration with a In y the solution is updated according to ny Iny 6iny B 15a or yD Z
118. ed by i nodal set for each control volume and 11 coordinates of cell nodes or cell vertices Control volumes in an implicit unstructured grid can be comprised of the following cell types 1 tetrahedron 11 pyramid 111 wedge iv hexadron and v a mix of above mentioned four cell types The local number of cell nodes and faces is shown in Figure 4 1 while Table 4 6 summarizes the side set node order for the four supported cell types Tetrahedron Pyramid 5 Figure 4 1 Side set numbering of supported cell types within unstructured grid lt 89 gt PFLOTRAN User Manual 84 27 2 August 14 2015 Table 4 6 Side set node ordering Elementtype Side Node order Tetrahedron 1 1 2 4 2 2 34 3 1 4 3 4 1 3 2 Pyramid 1 1 2 5 2 2 3 5 3 3 4 5 4 4 1 5 5 1 4 3 2 Wedge 1 1 2 5 4 2 2 3 6 5 3 3 1 4 6 4 1 3 2 5 4 5 6 Hexahedron 1 1 2 6 5 2 2 3 7 6 3 3 4 8 7 4 4 1 5 8 5 1 4 3 2 6 5 6 7 8 4 27 2 Explicit Unstructured Grids The explicit unstructured grid format comprises of information about 1 cells id x y z and volume and ii cell connections upstream and downstream cell ids centroid and area of side joining cells CELLS NUM_CELLS CELL ID X Y Z VOLUME CONNECTIONS NUM_CONNECTIONS CELL_ID_UP CELL_ID_DOWN FACE_X FACE_Y FACE_Z AREA lt 90 gt PFLOTRAN User Manual 84 27 2 August 14 2015 Cells with default decomposition after reading th
119. ell above the half saturation constant inhibition concentration Cin concentration INHIBITION_CONSTANT lt float gt Half saturation constant Threshold Inhibition INHIBITION SPECIES NAME lt string gt TYPE THRESHOLD lt float gt Specifies the type of inhibition to be thresh old and the scaling factor to be applied Inhibition is calculated based on the following equation inhibition 0 5 arctan concentration Cin X f 7 Inhibition is above and below C when the sign of C is negative or positive respectively INHIBITION_CONSTANT lt float gt Threshold concentration END BIOMASS SPECIES NAME lt string gt Specifies biomass species lt 55 gt PFLOTRAN User Manual 84 9 5 August 14 2015 YIELD lt float gt Biomass yield END END Examples CHEMISTRY PRIMARY_SPECIES A ag B aq C aa MICROBIAL REACTION REACTION A ag 2 B ag RATE CONSTANT 1 d 12 MONOD A aq 1 d 5 MONOD B aq 1 d 4 INHIBITION SPECIES NAME TYPE MONOD C aq INHIBITION CONSTANT 6 d 4 lt gt SCA ag A is the donor Bis the acceptor is the product and inhibits when too high CHEMISTRY PRIMARY_SPECIES A ag B aa C aa IM OBILE SPECIES icrobe D MICROBIAL REAC REACTION A aq 2 B aq RATE_CONSTANT 1 d 12 ONOD A ag L d 5 ONOD B aq 1 d 4 INHIBITION C ag 6 d 4 BIOMA
120. ence used in the calculations after Ward et al 1996 162 7 8 Parameters for material and thermal properties for intrinsic rock density ps heat A 2 A 3 A 4 A 5 A 6 capacity c thermal conductivity x porosity y residual water saturation s van Genuchten parameters a and A and vertical water saturated permeability ksa Data taken from Khaleel and Freeman 1995 Khaleel et al 2001 and Pruess et al QOO 322 Seay EAN a AAA AR 163 Problem definition and parameters used in the ID CO sequestration example 174 Initial concentration of primary and secondary species Mineral reactions are not CONSIDERO sae io o E EEE E 175 Model parameters lt es See ed peris ee o e a RE a 178 Input file for 3D CO sequestration example problem with a leaky well 180 Cho iceof primary V riables nde nes AA A a a 191 DCDM geometrie parameters o aa Da TO EER a a ad EE 202 Independent and dependent nested cube parameters 2 224 sussa 3 45 gt 203 Definition of symbols used in modeling microbial reactions 215 Format of thermodynamic database sas we a 4 Sau ana wa a dar 217 Pit coefficients Tor log K of reaction A 212 ve ss Are ee 219 lt 10 gt PFLOTRAN User Manual 1 0 0 August 14 2015 1 Introduction PFLOTRAN solves a system of generally nonlinear partial differential equations describing multi phase multicomponent and multiscale reactive flow and transport in porous materials Th
121. ent phases e g an aqueous electrolyte solution or gas phase but is assumed to be species independent Dispersivity currently must be described through a diagonal dispersion tensor The Darcy velocity q for phase a is given by kk A a fado A 107 with bulk permeability of the porous medium k and relative permeability ka fluid viscosity Ha pressure pa density po and acceleration of gravity g The diffusivity dispersivity tensor D is the sum of contributions from molecular diffusion and dispersion which for an isotropic medium has the form En Da rD I apul 4 ar ar A 108 v with longitudinal and transverse dispersivity coefficients az ar respectively 7 refers to tortu osity and Dm to the molecular diffusion coefficient Currently only longitudinal dispersion is implemented in PFLOTRAN The porosity may be calculated from the mineral volume fractions according to the relation p 1 5 qm A 109 The temperature dependence of the diffusion coefficient is defined through the relation Dali Din exp E z Os 7 A 110 with diffusion activation energy Ap in kJ mol The quantity D denotes the diffusion coefficient at the reference temperature To taken as 25 C and the quantity R denotes the gas constant 8 317 x 107 kJ mol K The temperature T is in Kelvin lt 204 gt PFLOTRAN User Manual 1 9 1 August 14 2015 The quantity Q denotes a source sink term Q Y Err A 111 n P where qm de
122. ent reactive transport including aqueous complexing sorption and mineral pre cipitation and dissolution Reactive transport equations are solved using a fully implicit Newton Raphson algorithm Operator splitting is currently not implemented In addition to single contin uum processes a novel approach is used to solve equations resulting from a multiple interacting continuum method for modeling flow and transport in fractured media This implementation is still under development Finally an elastic geomechanical model is implemented A novel feature of the code is its ability to run multiple input files and multiple realizations simultaneously for example with different permeability and porosity fields on one or more pro cessor cores per run This can be extremely useful when conducting sensitivity analyses and quan tifying model uncertainties When running on machines with many cores this means that hundreds of simulations can be conducted in the amount of time needed for a single realization Additional information can be found on the PFLOTRAN wiki home page which should be consulted for the most up to date information Questions regarding installing PFLOTRAN on workstations small clusters and super computers and bug reports may be directed to pflotran dev at googlegroups dot com For questions regarding running PFLOTRAN con tact pflotran users at googlegroups dot com lt ll gt PFLOTRAN User Manual 82 1 0 August 14 2015 2
123. er Manual 84 38 0 August 14 2015 4 38 Keyword NONUNIFORM VELOCITY Return to List of Keywords NONUNIFORM VELOCITY lt file name gt Explanation Name of HDFS file for specifying nonuniform velocities including boundary velocities Only applies to structured grids The velocity must be specified in SI units m s Internal velocities are specified for each cell corresponding to the downwind face and read in separately for vz Vy and v Boundary velocities are read in at all cells for each boundary condition cells not in boundary condition region are ignored but need a value to be read nonetheless A boundary condition may not wrap around a comer Corner cells should be mapped to multiple boundary conditions with their boundary faces residing in different regions Below is an example python script for generating an HDFS velocity file Python script for generating an HDF5 velocity file read by PFLOTRAN import sys import math from h5py import import numpy import random filename velocity h5 ASE File filename mode w nx 100 ny 2 nz 2 nxXny nxx xny n nx ny nz larray numpy zeros n 14 add cell ids to file for i in range n jarrayli i l dataset_name Cell Ids h5dset h5file create_dataset dataset name data iarray rarray numpy zeros n 8 x velocity for i in range n rarray i 3 171e 8 dataset name Interna
124. eters a 20 lm ly where lm de notes the matrix block size and ly refers to the fracture spacing two of which are independent The fracture matrix interfacial area Anm per unit volume is equal to N Alm y Ap A 95 where the number density N 3 V of secondary continua of type is equal to Na 1 Va EB V ve qe Marae and AS and V refer to the area and volume of each geometric type as listed in Table A 2 The primary secondary coupling term can then be written in the form ap Ao KaM BAAR us EBRnM ma _ mB OB een dn da Im Tu Anm Va 2 dn dm Tr Tu Va dl lt 202 gt PFLOTRAN User Manual 1 9 0 August 14 2015 Table A 3 Independent and dependent nested cube parameters Independent Dependent Eq ly 2 lp l la eE Ea l 28 lp lm UE ll SeA 20 ly E L y lee Im by 20 26 Im ta L Las ly lim F 20 1 2 n 00 m Im 1 26 1 ea A 9 Mode Reactive Transport Keyword CHEMISTRY The governing mass conservation equations for the geochemical transport mode for a multiphase system written in terms of a set of independent aqueous primary or basis species with the form O o a OS wy SUZ V DOF Qs vimln E A 98 and gt Yn _ 77 i for minerals with molar volume Vm mineral reaction rate 1 and mineral volume fraction Pm referenced to an REV Sums over a in Eqn A 98 are over all fluid phases in the system The quantity Y7 denotes the total concentration of the jth prima
125. eudocolor gt rel disp z Select e g hot_desaturated for color table Set opacity to 50 Apply and Dismiss 23 Next for mesh movement click Operators gt Transforms gt Displace After a window pops up dismiss it 24 Double click Displace change Displacement multiplier to e g 10000 Click on Dis placement Variable gt Vectors gt disp vectors Dismiss the window saying no data etc Apply and Dismiss 25 Finally click the play button to watch movie Rotate the domain to a convenient angle before doing so 6 3 Gnuplot MatPlotLib e For 1D problems or for plotting PFLOTRAN observation integral flux and mass balance output the opensource software packages gnuplot and matplotlib are recommended e With gnuplot and matplotlib it is possible to plot data from several files in the same plot To do this with gnuplot it is necessary that the files have the same number of rows e g time history points The files can be merged during input by using the paste command as a pipe e g plot lt paste filel dat file2 dat using 1 n1x n2 plots the product of variable in file 1 in column n1 times the variable in file 2 in column n2 of the merged file e When using gnuplot it is possible to number the output file columns with PRINT COLUMN IDS added to the OUTPUT keyword This is only useful however with FORMAT TECPLOT POINT output option lt 149 gt PFLOTRAN User Manual 87 1 0 August 14 2015
126. expansion The following governing equations are used V lo pb 0 ing A 213a o tr Que B p pp I a T TI A 213b BS 5 Vu a Vula A 2130 u x u x onT A 213d on z t z onI A 213e where u is the unknown displacement field o is the Cauchy stress tensor A u are Lam parameters Young s modulus and Poisson s ratio can be related to these two parameters b is the specific body force which is gravity in most cases n is the outward normal to the boundary I Also u is the prescribed values of u on the Dirichlet part of the boundary I and t is the prescribed traction on T Additionally 3 is the Biot s coefficient a is the coefficient of thermal expansion p T are the fluid pressure and temperature obtained by solving subsurface flow problem Also p and To are set to initial pressure and temperature in the domain is the strain tensor and tr is the trace of a second order tensor 2 is the domain and I is the identity tensor Note that stress is assumed positive under tension The effect of deformation on the pore structure is accounted for via Po TIO do A 214 Note that the above equations are solved using the finite element method Galerkin finite element with the displacements solved for at the vertices Since the flow equations are solved via the finite volume method with unknowns such as pressure and temperature solved for at the cell centers
127. f equations is equal to number of phases plus one which is equal to the number of unknowns p T s1 Sn 1 A 5 Mode MISCIBLE The miscible mode applies to a mixture of water and proplyene glycol PPG In terms of molar density for the mixture 7 and mole fractions x i 1 water i 2 PPG the mass conservation equations have the form O ay Pres V anzi pDnVzi Qi A 48 with source sink term It should be noted that the mass and mole fraction formulations of the conservation equations are not exactly equivalent This is due to the diffusion term which gives an extra term when transformed from the mole fraction to mass fraction gradient The molar density n is related to the mass density by n Wo A 49 and Winx pyi A 50 It follows that WinV x pVy pyiV ln W A 51 The second term on the right hand side is ignored lt 194 gt PFLOTRAN User Manual 1 6 0 August 14 2015 Simple equations of state are provided for density g cm viscosity Pa s and diffusivity m s The density is a function of both composition are pressrue with the form o plan p plu Po 3E P po A 52 P po ply po 1 B p po A533 with the compressibility 6 y given by 10 B D A 54 p Op P po 4 49758 x 1012 5 x 101 yy A 55 and the mixture density at the reference pressure py taken as atmospheric pressure is given by ply Po 0 0806 0 203 y
128. fficient D and diffusion activation energy Ap Temperature dependence of diffusion coefficient is calculated from the expression D T D exp FG 4 1 where D2 is the reference diffusion coefficient at temperature Ty 25 C and Ap denotes the diffusion activation energy Example FLUID PROPERTY DIFFUSION COEFFICIENT 1 d 9 ES DIFFUSION ACTIVATION ENERGY 12 6 kJ mol Return to List of Keywords lt 71 gt PFLOTRAN User Manual 84 19 0 August 14 2015 4 19 Keyword GEOMECHANICS Return to List of Keywords Description This keyword is required when using geomechanics All the geomechanics part should go in this card GEOMECHANICS Required Input Parameters Allthe geomechanics keywords should go here END lt 78 gt PFLOTRAN User Manual 84 20 0 August 14 2015 4 20 Keyword GEOMECHANICS_BOUNDARY_CONDITION Return to List of Keywords Description The GEOMECHANICS_BOUNDARY_CONDITION keyword couples condition specified under the GEOMECHANICS_CONDITION keyword to a REGION in the problem do main The use of this keyword enables the use reuse of geomechanics conditions and regions within multiple geomechanics boundary conditions the input deck Input GEOMECHANICS_BOUNDARY_CONDITION geomechanics_boundary_condition_name GEOMECHANICS_CONDITION GEOMECHANICS_condition_name REGION region_name END Explanation Keyword Description GEOMECHA
129. for 94 yields Sh Ass t At __ ja a a j Da S A PER From this expression the reaction rate can be calculated as gt At gt k Q J amp a e t Al 14 k At asia Sja 32a lt 222 gt PFLOTRAN User Manual 82 3 1 August 14 2015 The right hand side of this equation is aknown function of the solute concentration and thus by sub stituting into Eqn A 172 eliminates the appearance of the unknown sorbed concentration Once the transport equations are solved over a time step the sorbed concentrations can be computed from Eqn B 34 B 3 Operator Splitting Operator splitting involves splitting the reactive transport equations into a nonreactive part and a part incorporating reactions This is accomplished by writing Eqns A 98 as the two coupled equations 0 ay Do V aa 8aDaV U Qj B 36 and d a as e gt 8 07 2 Vimlm 5 B 37 The first set of equations are linear in Y for species independent diffusion coeffients and solved over over a time step At resulting in Wi The result for W is inverted to give the concentrations Cj by solving the equations u O Y Cr B 38 where the secondary species concentrations C are nonlinear functions of the primary species concentrations C With this result the second set of equations are solved implicitly for C at t At using Y for the starting value at time t B 3 1 Constant K4 As a simple example of operator splitting consider a single c
130. g configure py with debugging 0 with shared libraries 0 with x 0 download openmpi download hdf5 1 download metis 1 download parmetis 1 followed by make all and make test Note that ParMETIS METIS is only needed for using the unstructured grid capability in PFLOTRAN HDFS5 is recommended for large problems for use with Visit for parallel visual ization 3 2 1 2 Yosemite Mac OS X 10 10 x Special considerations are required to install PETSc and PFLOTRAN on Yosemite MacOSX 10 10 x It is necessary to install gcc 4 9 from Homebrew lt 17 gt PFLOTRAN User Manual 83 2 3 August 14 2015 other installations such as HPC MacOS X are not bug free at the time of this writing 10 23 14 The following steps are required 1 install Homebrew standard location usr local must be clean to avoid collisions 2 install gcc need version 4 9 x brew install gcc 3 install cmake need version 3 0 x brew install cmake 4 configure PETSc using the Mac c and c compilers clang clang and gfortran installed from Homebrew cd petsc dev configure with cc clang with cxx clang with fc gfortran download mpich 1 download hdf5 1 download metis 1 download parmetis 1 with debugging 0 5 make all make test Notes At the time of this writing 10 23 14 openmpi did not compile HDF5 did not compile using gcc 4 9 installed from Homebrew 3 2 2 Windows To install PETSc and PFLO
131. gt Volume fraction of the primary continuum fracture in REV APERTURE lt float gt Fracture aperture if specified overrides epsilon applicable for nested cubes only AREA SCALING FACTOR lt float gt Factor multiplying primary secondary con tinua coupling term default set to 1 END END Explanation Example MATERIAL PROPERTY Hanford EDP SATURATION_FUNCTION sf1 BOROS TEY 0 332 TORTUOSTIY 1 PERMEABILITY ERM X 1 d 12 ERMSY MTONI ERM_2 1 d 12 oo to o mm END MATERIAL PROPERTY soill ED 1 SATURATION FUNCTION sf1 POROSTINY 0 1 lt 103 gt PFLOTRAN User Manual 84 34 0 August 14 2015 TORTUOSTLA 1 PERMEABILITY PERM_X 1 d 13 PERMA eas PERM Z 1 d 13 SECONDARY CONTINUUM TYPE SLAB ENGTH 50 AREA 2500 NUM_CELLS 10 EPSILON 0 02 END Example reading from a file for multiple realization simulation mpirun np 10000 pflotran stochastic num_realizations 1000 num_groups 100 PFLOTRAN input file material properties RIAL_PROPERTY rock MATI IUBI ak POROS ETY OTSO Tdo TORTUOS TEY das ROCK DENSITY 2 65d3 PECIFIC HEAT 1 d3 ERMAL CONDUCTIVITY DRY ERMAL CONDUCTIVITY WET ATURATION FUNCTION sf2 ERMEABILITY ANISOTROPIC default is ISOTROPIC DATASET Permeability ES 2m9 AS WENN
132. h MPI support e g mpicc lt 22 gt PFLOTRAN User Manual 83 6 0 August 14 2015 3 6 Running PFLOTRAN PFLOTRAN can be run from the command line as mpirun np 10 pflotran options A number of command line options are available Option Description pflotranin lt string gt input_prefix lt string gt output prefix lt string gt screen output off realization id lt integer gt multisimulation stochastic help log_summary snes_converged_reason on_error_abort options_left snes SNGS monitor linesearch monitor snes view snes Snes snes snes snes_monitor_lg_residualnorm ksp monitor lg residualnorm Is type newtonls _type newtontr tr delta specify input file Default pflotran in specify input file prefix and path default pflotran specify output file prefix and path to prefix directory which must already exist default pflotran turn off screen output run specified realization ID run multiple input files in one run Monte Carlo multiple realization run PETSc print list of command line options print out run performance print the reason for convergence divergence af ter each solve aborts run on hitting NaNs lt int gt verbose for debugging lists any PETSc objects that have not been freed print to screen function norm with each iteration print to screen
133. hanges see Sections 7 4 and A 3 FLASH2 Two phase supercritical CO2 brine energy based on the flash method for phase changes with a persistent set of unknowns TH Thermal Hydrologic coupled groundwater flow IMMIS IMS THS Immissible CO water energy MIS Missible H O glycol fluid Examples PROCESS_MODELS SUBSURFACE_FLOW flow ODE RICHARDS PROCESS_MODELS SUBSURFACE_FLOW flow ODE TH Return to List of Keywords lt 106 gt PFLOTRAN User Manual 84 36 0 August 14 2015 4 36 Keyword MULTIPLE CONTINUUM Return to List of Keywords Description This keyword initiates the multiple continuum formulation implemented currently only for heat equation The properties of the secondary continuum can be specified under the MATERIAL PROPERTY keyword MULTIPLE CONTINUUM Activate multiple continuum model for heat and single solute transport equation Return to List of Keywords lt 107 gt PFLOTRAN User Manual 84 37 0 August 14 2015 4 37 Keyword NEWTON_SOLVER Return to List of Keywords Description Input NEWTON_SOLVER TRAN TRANSPORT tran_solver DEFAULT flow_solver INEXACT_NEWTON NO_PRINT_CONVERGENCE NO_INF_NORM NO_INFINITY_NORM NO_FORCE_ITERATION PRINT_DETAILED_CONVERGENCE ATOL lt Value gt RTOL lt Value gt STOL lt Value gt DTOL lt Value gt ITOL INF_TOL ITOL_RES INF_TOL_RES lt Value gt ITOL_UPDATE INF_TOL_UPDATE lt
134. inates of vertex num_vertices real I Explicitly defined grid Format of explicit unstructured grid file id id_up_ id dn integer l x Yr Z area volume real definitions tdo td of grid cell id up id of upwind grid cell in connection id dn id of downwind grid cell in connection x coordinate of cell center I y_ y coordinate of cell center z coordinate of cell center volume_ volume of grid cell CELLS lt integer gt integer cells N id_1 x_1 y z_1 volume_l id_2 x_2 y_2 z_2 volume_2 id N xN y_N z_N volume_N CONNECTIONS lt integer gt integer connections M daup i Mid onna y zo areas id up 2 iddn 2 x 2 y 2 2 2 area 2 id_up_M id_dn_M x_M y_M z_M area_M lt 93 gt PFLOTRAN User Manual 84 27 2 August 14 2015 Examples GRID TYPE structured cylindrical NXYZ 512 1 32 DXYZ 2 40 Lido 2240 END GRID TYPE structured NoYz 5127 1032 BOUNDS ORTO OR Ra o EAT END By using the BOUNDS keyword the model domain is specified in a grid independent fashion and as a result the grid spacing may be changed by modifying the keyword NXYZ only Return to List of Keywords Return to List of Keywords lt 94 gt PFLOTRAN User Manual 84 28 0 August 14 2015 4 28 Keyword IMMOBILE_DECAY_REACTION Return to List of Keywords Description Specifies parameters f
135. ion Mode aoaaa 24 3 8 Multiple Simulation Mode a 2 2A eee a rar rasa des 24 4 Creating the Input File PFLOTRAN Keywords 25 41 Conventions and Notation u wu un eee be Rew REM an nad 25 4 2 Input Deck Specification sos ir u Le RAR A O ag 25 4 2 1 Keyword SUBSURFACE PLOW 2 0 4 1 00 Se Re e 28 4 2 2 Keyword SUBSURFACE_TRANSPORT aaa 28 4 3 Subsurface Keyword Links 2 bas ea Se eR ee ae aaa 30 44 Example Input File 22 055 254 zur ph ORR RA EEL ES ERE 32 PFLOTRAN User Manual 0 0 0 August 14 2015 4 5 4 6 47 4 8 4 9 4 10 4 11 4 12 4 13 4 14 4 15 4 16 4 17 4 18 4 19 4 20 4 21 4 22 4 23 4 24 4 25 Keyword BOUNDARY CONDITION 22 224 des 2 2 eu da S 37 Keyword BRINE gt gt pes eee ra Pre es teit e Br Br ea 39 Keyword CHARACTERISTIC CURVES 000000024 2 2 a mea Bud 4445 40 Keyword CHECKPOINT ass 234 AR AAA A A TA 43 Keyword CHEMISTRY E 44 491 Keyword MINERAL_KINETICS lt lt 0 wa was a ema 47 4 9 2 Keyword SORPTION 4 adm RRA ehe 49 4 9 3 Keyword RADIOACTIVE DECAY REACTION 52 4 9 4 Keyword GENERAL REACTION 54 4 9 5 Keyword MICROBIAL_REACTION 55 4 9 6 Keyword REACTION SANDBOX 58 497 Keyword OUTPUT 4 2 624 32 net 2 sem SHEE HDS 60 Keyword COMPUTE STATISTIOS ice ieee est satin ine Aa A 63 Keyword COZ DATABASE amp 2 2 2 20 za neh 68 A 64 KW CONSTRAINT aora
136. ion shown in Figure A 2 with fracture nodes designated by the subscript n and matrix nodes by m the integrated finite volume form of the heat transport equation for the nth fracture control volume is given by ea Patan pala O o CTA 010570 Kun a 2 dada Ha ny d Tan Tone Ad de o Som 8 En Taml q 0 A 87 2 dn a Bim nM a where V denotes the fracture volume and k k va N 0 C T5 ai p C T o At gt da dy Tom Ta Af w Kae E Sn a a Ton Tom Au 0 A 87b n TUM for the mth matrix node with volume V The matrix node designated by M refers to the outer most node in contact with the fracture see Figure A 1 More than one type of matrix geometry is included in the above equations as indicated by the sum over in Eqn A 87a where Ng denotes the number of different secondary continua However it should be noted that the current imple mentation in PFLOTRAN only allows coupling to a single secondary continuum N 1 The fracture volume V is related to the REV volume V by Ve Ea Vi A 88 Thermal conductivity at the interface between two control volumes is calculated using the har monic average iy d dy l A 89 diky dy Ky Kw lt 200 gt PFLOTRAN User Manual 1 8 0 August 14 2015 18 LB Figure A 1 Node configuration for secondary 5 continua nodes 1 l M associated with the nth primary a continu
137. ions FLOW_CONDITION Inlet TYPE FLUX neumann FLUX 0 317098d 6 10 m y FLOW_CONDITION Initial TYPE PRESSURE hydrostatic DATUM 0 d0 0 d0 6 d0 PRESSURE 101325 d0 H transport conditions TO TRANSPORT CONDITION Inlet TYPE dirichlet CONSTRAINT LIST 0 d0 Inlet TRANSPORT_CONDITION Initial TYPE dirichlet CONSTRAINT_LIST 0 d0 Initial lt 35 gt PFLOTRAN User Manual 84 4 0 August 14 2015 TRANSPORT_CONDITION Outlet TYPE zero_gradient CONSTRAINT_LIST 0 d0 Initial couplers ee ae n a r E m a e m ae E a e ae n e E a e e BOUNDARY_CONDITION Inlet FLOW_CONDITION Inlet TRANSPORT_CONDITION Inlet REGION Inlet BOUNDARY_CONDITION Outlet FLOW_CONDITION Initial TRANSPORT_CONDITION Outlet REGION Bottom INITIAL_CONDITION Initial FLOW_CONDITION Initial TRANSPORT_CONDITION Initial REGION all stratigraphy STRATA MATERIAL HD REGION all transport constraints CONSTRAINT Initial CONCENTRATIONS Ca 1 d 4 M Calcite H 8 d0 pH CO2 aq 1 d 2 G CO2 g Tracer 1 d 8 T MINERALS vol frac area Calcite 0 75 1 42 CONSTRAINT Inlet CONCENTRATIONS Ca 1 d6 T H 3 40 pH CO2 aq 1 d 3 GCO2 g Tracer 1d 0 T END_SUBSURFACE lt 36 gt PFLOTRAN User Manual 84 5 0 August 14 2015 4 5 Keyword
138. ions A E E E E REGION all COORDINATES 0 d0 0 d0 0 d0 1 d0 1 d0 136 d0 END REGION MRG COORDINATES 0 d0 0 d0 0 d0 1 d0 1 40 20 d0 END REGION URG COORDINATES 0 d0 0 d0 20 d0 1 d0 1 40 23 d0 END REGION PP COORDINATES 0 d0 0 d0 23 d0 1 d0 1 40 29 d0 lt 169 gt PFLOTRAN User Manual 87 3 5 August 14 2015 END REGION HF COORDINATES 0 d0 0 d0 1 d0 1 d0 END REGION BF COORDINATES 0 d0 0 d0 1 d0 1 d0 REGION west FACE WEST COORDINATES 0 d0 0 d0 0 d0 1 40 END REGION east FACE EAST COORDINATES 1 d0 0 d0 1 00 1 90 END REGION north FACE NORTH COORDINATES 0 d0 1 d0 1 d0 1 d0 END REGION south FACE SOUTH COORDINATES 0 d0 0 d0 1 d0 0 d0 END REGION top FACE TOP COORDINATES 0 d0 0 d0 1 d0 1 d0 END REGION bottom FACE BOTTOM COORDINATES 0 d0 0 d0 1 d0 1 d0 END REGION well COORDINATES 1 d0 1 40 1 d0 1 40 29 d0 52 d0 52 d0 68 d0 0 d0 68 d0 0 d0 68 d0 0 d0 68 d0 0 d0 68 d0 68 d0 68 d0 52 d0 52 d0 lt 170 gt PFLOTRAN User Manual 87 3 5 August 14 2015 FLOW_CONDITION initial TYPE PRESSURE hydrostatic A DATUM 0 d0 0 d0 6 d0 PRESSURE 101325 d0 END FLOW_CONDITION infiltration TYPE FLUX neumann FLUX 2 53678e 8 0 08 m yr FLUX 2 53678e 9 0 08 m yr FLUX 2 53678e 10 8 mm yr FLUX 0 d0 END FLOW_CONDITION water_table TYPE PRESSURE hydrostatic DATUM 0 d0 0 d0 6 d0 PRES
139. ions have been removed since for immiscible systems the solubility is identically zero for each component In this case the number of components is equal to the number of phases or degrees of freedom associated with each node for an isothermal system The immiscible property removes the variable switching strategy used in MPHASE which may be the most numerically difficult part of PFLOTRAN and may cause problems for multi level solvers lt 193 gt PFLOTRAN User Manual 1 5 0 August 14 2015 The governing equations solved by PIMS are given by o Ai PPasa TV Pada Qos A 44 where the subscript a denotes an immiscible phase In this equation is porosity Sa Pa refer to the ath phase saturation and density respectively q is the Darcy velocity of the ath phase given by kka x du Oda A 45 with permeability k relative permeability ka fluid viscosity jo and Qa is the source sink term The selection of primary variables are pressure p and n 1 independent phase saturation variables Sy Q 1 n 1 with y Sa 1 A 46 a 1 The mass conservation equations are coupled to the energy balance equation given by lo gt SapaUa 1 ACT V X pada Ha EVT E O A 47 a where Ua Ha denote the internal energy and enthalpy of the ath fluid phase denotes the thermal conductivity of the bulk porous medium p C denote the rock density and heat capacity and T refers to the temperature Thus the number o
140. k as a function of pressure For the special case of zero infiltration it follows that 7 30 p z po pg z 20 7 31 with p z9 po The saturation profile is obtained from Eqns 7 24 and A 4 7 3 2 2 Watertable The position of the watertable is defined by vanishing of the capillary pres sure Fila 0 7 32 where zw denotes the height of the watertable For the case with no infiltration at the surface it follows that eat 7 33 pg with the boundary condition p zo po and zo denotes the datum If po is set equal to p then Zwt Zo Or the height of the watertable is equal to the datum The same holds true also with constant nonzero infiltration 7 3 3 Model Parameters Model parameters used in the simulations are listed in Tables 7 7 and 7 8 Although not needed here thermal properties are also listed Diffusivity was set to 107 m s and tortuosity was set to one Table 7 7 Stratigraphic sequence used in the calculations after Ward et al 1996 Formation Abbrev Thickness m Backfill BF 16 0 Hanford Fine Sand HF 23 0 Plio Pleistocene PP 6 0 Upper Ringold Gravel URG 3 0 Middle Ringold Gravel MRG 20 0 lt 162 gt PFLOTRAN User Manual 87 3 4 August 14 2015 Table 7 8 Parameters for material and thermal properties for intrinsic rock density ps heat capac ity c thermal conductivity x porosity p residual water saturation s van Genuchten parameters a and and vertical water
141. l Velocity X h5dset h5file create dataset dataset name data rarray lt 110 gt PFLOTRAN User Manual 84 38 0 August 14 2015 y velocity for i in range n rarray lil 0 dataset name Internal Velocity Y h5dset h5file create dataset dataset name data rarray z velocity dataset name Internal Velocity 2 h5dset h5file create dataset dataset name data rarray west boundary velocity i 0 for index in range n rarraylindex 0 for k in range nz for j in range ny index kx nx ny J nx i rarray index 3 171e 8 dataset name West h5dset h5file create dataset dataset name data rarray east boundary do gt mal for index in range n rarray index 0 for k in range nz for j in range ny index kx nx ny J nx i rarray index 3 171e 8 dataset name East h5dset h5file create dataset dataset name data rarray hotilke close print done with everything Example NONUNIFORM _VELOCITY velocity h5 Return to List of Keywords lt 111 gt PFLOTRAN User Manual 84 39 0 August 14 2015 4 39 Keyword NUMERICAL_JACOBIAN_FLOW Return to List of Keywords NUMERICAL_JACOBIAN_FLOW Uses numerically evaluated Jacobian for flow Return to List of Keywords lt 112 gt PFLOTRAN User Manual 84 40 0 August 14 2015 4 40 Keyword NUMERICAL_JACOBIAN_RXN Return to List of Keyword
142. le you can use something like HOME parallellO scorpio Depending on the shell you are using you may use export SCORPIO_DIR lt your iolib install dir gt bash shell or setenv SCORPIO_DIR lt your iolib install dir gt tcsh csh shell To compile the library check to make sure that the Makefile has the right settings for your machine Typically the current configuration suffices So you can just follow the instructions below For advanced users please edit the section for pflotran machine in the Makefile as desired This assumes that you have let PETSc build MPI and mpicc and mpif 90 are located in S PETSC DIR S PETSC ARCH bin If not you may need to alter the Makefile to provide the correct path to the location of the MPI compilers cd DIRNAME src make MACHINE pflotran_machine make install compile with mpicc This will build the library 1ibscorpio a and copy corresponding files to SCORPIO DIR 1ib and SCORPIO_DIR include directories On machines with MPI installed modify the makefile to use the native mpi compilers ifeq MACHINE pflotran machine CC mpicc FC mpi f90 INKER S FC CFLAGS IS PETSC_DIR S PETSC_ARCH include 03 FFLAGS IS PETSC_DIR PETSC_ARCH include 03 LDFLAGS W1 LS PETSC_DIR S PETSC_ARCH lib lhdf5 lz endif 3 Compile PFLOTRAN Please ensure that environmental variable SCORPIO DIR Is pointed
143. lel tests will be skipped Running pflotran regression tests Regression test summary Total time 179259 si Total tests 44 Skipped 8 Tests run 36 Failed 3 1 The progress bar records a period for each successful test an S if a test was skipped an F for failed tests a W for a test that generated a warning and an E for a test that generated an internal error Each time the test suite is run a log file is generated in the regression test directory The log file contains a detailed record of every test run including the directory containing the test the command line call to PFLOTRAN used to run the test a diff command to compare the regression lt 144 gt PFLOTRAN User Manual 85 3 0 August 14 2015 files and a list of failures The log file can quickly be searched for skip fail error to identify the tests that generated the message The test directories contain any files generated by PFLOTRAN during the run Screen output for each test is contained in the file S TEST NAME stdout 5 3 Configuration Files The regression test manager reads tests specified in a series of configuration files in standard cfg or windows ini file format They consist of a series of sections with key value pairs section name key value Section names should be all lower case and spaces must be replaced by a hyphen or underscore Comments
144. ll need to load the following HDF5 module beforehand module load hdf5 parallel 3 3 Building PFLOTRAN PFLOTRAN is compiled with the command make options pflotran where several possible options are Compile Option Description scorpio 1 enable parallel IO coll 1 enable colloid facilitated transport option mfd 1 enable MFD full permeability tensor capability not operational Thus for compiling with the supercritical CO option use make ssco2 1 pflotran See the PFLOTRAN makefile for additional options 3 4 Updating PFLOTRAN To update the PFLOTRAN source code type hg pull u lt 19 gt PFLOTRAN User Manual 83 5 0 August 14 2015 from within the PFLOTRAN source repository Recompile PFLOTRAN using make clean make options pflotran 3 5 Parallel VO using Sarat Sreepathi s SCORPIO library with PFLOTRAN The SCORPIO parallel I O library enables a scalable general purpose parallel I O capability for HPC by taking advantage of existing parallel I O libraries such as HDF5 which are being widely used by scientific applications and modifying these algorithms to better scale to larger number of processors The library has been tested with MPICH 3 0 2 and OpenMPI 1 6 It is recommended that values for the variables HDF5 READ GROUP SIZE and HDF5 WRITE GROUP SIZE be set in the input file If they are unset HDF5_READ_GROUP_SIZE S set to total MPI ranks and HDF5 WRITE GROUP SIZE is set to 1 by default
145. llary pressure or relative permeability and imposing zero slope at the fully saturated end point and matching the derivative at a chosen variably saturated point that is close to fully saturated The resulting equations for coefficients a 1 0 3 are given by ao 0121 age asz fi A 17a ao axa 4923 A323 fa A 17b QL 200971 3a3x fi A 17c ato 209X 3a3x5 fo A 17d for chosen points x and x2 In matrix form these equations become la sf ti fi rn ga f A 18 0 1 2 3a2 E Ii 0 1 De as Je The conditions imposed on the smoothing equations for capillary pressure f s p are x 2p ao p 2 fi se fo 1 fi sL f4 0 For relative permeability f k se 1 1 xa 0 99 f f fo k 2 fi 0 fo ky 2 A 3 Mode MPHASE The mode MPHASE solves the two phase system of water and supercritical CO It may also be coupled to chemistry using the CHEMISTRY keyword and its various associated optional and required keywords for selecting the primary and secondary aqueous species and setting up initial and boundary conditions and source sinks MPHASE requires that the species CO2 aq be used as primary species In addition for pure aqueous and supercritical CO phases the input to MPHASE requires specifying the mole fraction of CO When coupled to chemistry the CO mole fraction is calculated internally directly from the aqueous concentrations specified in the CON
146. lt your iolib install dir gt cd PFLOTRAN_DIR src pflotran make scorpio 1 pflotran SCORPIO Scalable Parallel I O module for Environmental Management Applications This library provides software that read write data sets from to parallel file systems in an efficient and scalable manner In this context scalable means that the simulators read write performance does not degrade significantly as the number of cores grows SCORPIO is distrubuted under the terms of the GNU Lesser General Public lt 21 gt to PFLOTRAN User Manual 3 5 0 August 14 2015 License LGPL The copyright is held jointly by North Carolina State University and Pacific Northwest National Laboratory The copyright and license information is specified in the included file COPYRIGHT Please request write access by contacting Kumar Mahinthakumar gmkumar ncsu edu Use the following command to access repository svn co http ascem io secure water org ascem io MPI C compiler HDF5 libraries preferably with parallel MP1 support Optional Fortran for Fortran example After downloading SCORPIO and gathering details of HDF5 installation the following commands can be used to build and install SCORPIO cd lt SCORPIO check out directory gt src make CC lt C compiler gt HDF5_INCLUDE_DIR lt location of the HDF5 include directory gt make SCORPIO_INSTALL_DIR lt user defined install location gt install In this case CC refers to C compiler wit
147. lution corresponds to a brine with NaCl concentration of 0 5 m Mineral reactions are not considered The initial fluid composition taken from pflotran out is listed in Table 7 10 The defining equations for the saturation and relative permeability functions for the aqueous solution and supercritical CO are given by the van Genuchten Corey relations For the aqueous solution van Genuchten curves are used for capillary pressure P Pals 2 8 PD 7 34 and relative permeability k 2 kn vali h SN 7 35 lt 174 gt PFLOTRAN User Manual 87 4 1 August 14 2015 Table 7 10 Initial concentration of primary and secondary species Mineral reactions are not considered Transport Condition Initial iterations 20 pH 5 0273 ionic strength 4 7915E 01 mol L charge balance 1 1102E 16 pressure 1 6450E 07 Pa temperature 54 50 C density H20 ln activity H20 992 99 kg m 3 0 0000E 00 1 0000E 00 mole fraction H20 9 8093E 01 mass fraction H20 9 7160E 01 primary free total species molal molal act coef constraint H 1 1727E 05 2 5844E 17 8 0079E 01 chrg Na 4 7913E 01 5 0000E 01 6 8288E 01 total aq Cl 4 7913E 01 5 0000E 01 6 4459E 01 total aq co2 ag 1 1380E 04 1 2551E 04 1 1053E 00 CO2 g complex molality act coef logK NaCl aq 2 0866E 02 1 0000E 00 6 8511E 01 HCO3 1 1713E 05 6 8288E 01 6 2239E 00 OH 1 2056E 08 6 6467E 01 1 3123E 01 NaOH aq 1 6487E 09 1 0000E 00 1 3325E 01 CO3
148. ly Visualization support is avail able via XDMF Unstructured grid velocity outputted for internal and boundary faces Data is outputted in HDF5 format only with no visualization support via XDMF VELOCITY AT CENTER Output cell centered velocities supported for structured and unstructured grids applies to TecPlot and HDF5 output formats Note that this is com patible only with TecPlot BLOCK format MASS BALANCE DETAILED Output the mass balance of the system if this card is activated It includes global mass balance as well as fluxes at all boundaries for water and chemical species specified for output in the CHEMISTRY card For the MPHASE mode only global mass balances are provided including supercritical CO2 Output times are controlled by PERIODIC_OBSERVATION TIMESTEP and TIME and printout times Option DETAILED provides total moles of minerals END Explanation lt 119 gt PFLOTRAN User Manual 84 44 0 August 14 2015 OUTPUT keyword to control output TIMES list of output times SCREEN OFF turns off screen output SCREEN PERIODIC controls screen output frequency PERIODIC TIME controls frequency of output times PERIODIC TIMESTEP controls frequency of output time steps PERIODIC_OBSERVATION TIME PERIODIC_OBSERVATION TIMESTEP NO_FINAL NO_PRINT_FINAL FORMAT TECPLOT POINT FORMAT TECPLOT BLOCK FORMAT HDEFS FORMAT MAD FORMAT VTK UNIT PERMEABILITY POROSITY
149. names in multisimulation Note that all simulations run at once The same logic used to allow a processor group to run mul tiple simulations with multirealization is not implemented Choose the number of cores to be a multiple of the number of input filenames listed in the input file i e filenames in All output files have Gn appended to the file name e g sim10G10 001 tec lt 24 gt PFLOTRAN User Manual 84 2 0 August 14 2015 4 Creating the Input File PFLOTRAN Keywords The PFLOTRAN input file construction is based on keywords Lines beginning with are treated as comments Each entry to the input file must begin in the first column Keywords SKIP and NOSKIP are used to skip over sections of the input file Blank lines may occur in input file Al ternate keyword spelling is indicated in round brackets Input options are indicated in square brackets as well as default values Curly brackets indicate the result of invoking the corre sponding keyword Always refer to source code when in doubt Initial and boundary conditions and material properties are assigned to spatial regions using a novel coupler approach In this approach initial and boundary conditions keyword CONDI TION are assigned to regions keyword REGION using keywords INITIAL_CONDITION and BOUNDARY_CONDITION Material properties keyword MATERIAL are assigned to regions using the keyword STRATIGRAPHY 4 1 Conventions and Notation
150. nded derived type character len MAXWORDLENGTH species_name PetscInt species_id PetscReal rate_constant 4 Add the necessary functionality within the following subroutines lt 225 gt PFLOTRAN User Manual 83 2 0 August 14 2015 a ExampleCreate Allocate the reaction object initializing all variables to zero and nul lifying arrays Be sure to nullify ExampleCreate next which comes from the base class E g allocate ExampleCreate rr ExampleCreate species name ExampleCreate species id 0 ExampleCreategrate constant 0 d0 nullify ExampleCreate next b ExampleRead Read parameters in from the input file block EXAMPLE E g case SPECIES NAME call InputReadWord input option this species_name PETSC_TRUE call InputErrorMsg input option species_name CHEMISTRY REACTION_SANDBOX EXAMPLE c ExampleSetup Construct the reaction network e g array allocation establishing link ages etc E g this species id amp GetPrimarySpeciesIDFromName this species name reaction option d ExampleReact Calculate contribution of reaction to the residual units moles sec and Jacobian units kg water sec E g Residual this gspecies id Residual thisgspecies id thissrate_constant porosityx global_auxvar sat iphase volumex 1 d3x amp rt_auxvarStotal thi
151. neous min eral precipitation and dissolution sorption including ion exchange and surface complexation ra dioactive decay microbial reactions are provided Homogeneous complexing reactions may be described through local equilibrium by specifying secondary species or through a kinetic formula tion using the GENERAL REACTION keyword Mineral precipitation and dissolution reactions are described through a kinetic rate law based on transition state theory Surface complexation reactions may involve equilibrium kinetic reversible or irreversible or a multirate formulation Colloid facilitated transport taking into account sorption on colloids is included Input CHEMISTRY PRIMARY_SPECIES Species Name END SECONDARY SPECIES Species Name END REDOX_SPECIES Species Name END GAS_SPECIES Species Name END MINERALS Mineral Name END IMMOBILE_SPECIES lt 44 gt PFLOTRAN User Manual 84 9 0 August 14 2015 Species Name END IMMOBILE_DECAY_REACTION SPECIES_NAME lt string gt RATE_CONSTANT lt float gt END COLLOIDS Colloid Name Mobile_Fraction END Example Specification of primary species secondary species gases and minerals chemistry CHEMISTRY PRIMARY_SPECIES Nat w e 02 aq 2 ag QNQTZ SOR I l ON un ECONDARY_SPECIES OHS COS cos CaCO3 ag CaHCO3
152. notes a mass rate in units of kg s p denotes the fluid density in kg m and r refers to the location of the nth source sink The quantity S represents the sorbed concentration of the jth primary species considered in more detail in the next section Molality m and molarity C are related by the density of water p according to Ci Pumi A 112 The activity of water is calculated from the approximate relation amo 10 017 mi A 113 2 A 9 1 Mineral Precipitation and Dissolution The reaction rate Im is based on transition state theory taken as positive for precipitation and negative for dissolution with the form Im Gm kun 1 CA Rn A 114 i where the sum over represents contributions from parallel reaction mechanisms such as pH de pendence etc and where Km denotes the equilibrium constant om refers to Temkin s constant which is defined as the average stoichiometric coefficient of the overall reaction Lichtner 1996b see also Section A 11 8m denotes the affinity power am refers to the specific mineral surface area and the ion activity product Q is defined as Qn sm AS j with molality m of the jth primary species The rate constant km is a function of temperature given by the Arrhenius relation kmi T KO exp Be 7 A 116 where kl refers to the rate constant at the reference temperature Ty taken as 25 C with T in units of Kelvin Em denotes the activation energy kJ mol and the
153. nother mineral blocking that mineral from reacting Thus suppose mineral Mm is being replaced by the secondary mineral Mm Blocking may be described phenomenologically by the surface area relation f y a n 1 n c la n am t 0 2 2 A A 136 Pm 1 Po Pin for Ym lt Pi and m A 137 if pm t gt 9 where y represents the critical volume fraction necessary for complete blocking of the reaction of mineral M m lt 207 gt PFLOTRAN User Manual 1 9 2 August 14 2015 A 9 2 Sorption Sorption reactions incorporated into PFLOTRAN consist of ion exchange and surface complexa tion reactions for both equilibrium and multirate formulations A 9 2 1 Ion Exchange Ion exchange reactions may be represented either in terms of bulk or mineral specific rock properties Changes in bulk sorption properties can be expected as a result of mineral reactions However only the mineral based formulation enables these effects to be captured in the model The bulk rock sorption site concentration wa in units of moles of sites per bulk sediment volume mol dm is related to the bulk cation exchange capacity Qa mol kg by the expression Nate Noite Ms V Wa V M V V a Qafs 1 A 138 The cation exchange capacity associated with the mth mineral is defined on a molar basis as N Nin Ma Vin im Fp ym In Pmbm A 139 In PFLOTRAN ion exchange reactions are expressed in the form ZA 23 X2A
154. o primary minerals 9 0 The quantity Yc refers to a critical porosity below which the permeability is assumed to be constant with scale factor fmin lt 206 gt PFLOTRAN User Manual 81 9 2 August 14 2015 In PFLOTRAN the solid is represented as an aggregate of minerals described quantitatively by specifying its porosity y and the volume fraction Ym of each primary mineral It is not necessary that Eqn A 123 relating porosity and mineral volume fractions holds Typically however the solid composition is specified by giving the mass fraction y of each of the primary minerals making up the solid phase The volume fraction is related to mole m and mass Ym fractions by the expressions LEmV m Pm 1 AI aV A 129a 1 1 a pal A 129b with inverse relation m s p and similarly for the mass fraction where Pm Walai A 131 and the solid molar density 7 is given by 1 In these relations Wm refers to the formula weight and V m the molar volume of the mth mineral The solid molar density is related to the mass density p by Ps Wins A 133 with the mean molecular weight W of the solid phase equal to 1 Mass and mole fractions are related by the expression Wrtn Wa A 135 A 9 1 3 Affinity Threshold An affinity threshold f for precipitation may be introduced which only allows precipitation to occur if KmQm gt f gt 1 A 9 1 4 Surface Armoring Surface armoring occurs when one mineral precipitates on top of a
155. ometry is fixed at 1 0 The forward rate is applied to that one species as a first order rate constant 1 sec Multiple species are supported as daughter products on the right hand side and stoichiometries can be specified RATE CONSTANT or HALF LIFE but not both RATE CONSTANT lt float gt rate constant for 1st order decay reaction 1 sec The rate constant may be calculated from In 2 half life HALF_LIFE lt float gt half life of species sec Note that rate constant or half life units other than sec or 1 sec may be specified END Examples RADIOACTIVE DECAY REACTION REACTION Tracer lt gt Tracer2 RATE CONSTANT 1 7584d 7 half life at 0 125 y I CHEMISTRY PRIMARY_SPECIES A ag B aq C aa RADIOACTIVE DECAY REACTION REACTION A aq lt gt B aq Calculating forward rate from half life l rate 1n 0 5 half life 1 sec RATE_CONSTANT 1 75836d 9 1 s half life 12 5 yrs RADIOACTIVE DECAY REACTION REACTION B aq lt gt C aq RATE CONSTANT 8 7918d 10 1 s half life 25 yrs RADIOACTIVE DECAY REACTION Note that C aq decays with no daughter products REACTION C aq lt gt HALF_LIFE 5 y lt 52 gt PFLOTRAN User Manual 84 9 3 August 14 2015 Return to List of Keywords lt 53 gt PFLOTRAN User Manual 84 9 4 August 14 2015 4 9 4 Keyword GENERAL_REACTIO
156. omponent system with retardation described by a constant Kz According to this model the sorbed concentration S is related to the aqueous concentration by the linear equation S Kal B 39 The governing equation is given by o OS V DVC B 40 Ave qC q a B 40 If C x t q D is the solution to the case with no retardation i e Ka 0 then C x t q R D R is the solution with retardation K4 gt 0 with 1 R 1 Ka B 41 p Thus propagation of a front is retarded by the retardation factor R lt 223 gt PFLOTRAN User Manual 82 3 1 August 14 2015 In operator splitting form this equation becomes p0 V gC DYC 0 B 42 and a as 2 zu 4 ae di Ba The solution to the latter equation is given by pares N strat S B 44 where C is the solution to the nonreactive transport equation Using Eqn B 39 this result can be written as qu no Je 1 z Ce B 45 Thus for R 1 C 4 C and the solution advances unretarded As R gt x C 4 Ct and the front is fully retarded lt 224 gt PFLOTRAN User Manual 83 2 0 August 14 2015 Appendix C Reaction Sandbox C 1 Background Researchers often have a suite of reactions tailored to a unique problem scenario but these reac tion networks only exist in their respective research codes The reaction sandbox provides these researchers with a venue for implementing user defined reactions within
157. on H20 X GOs SCCO X CO2 2 q PFLOTRAN User Manual 4 17 0 August 14 2015 Keyword Description FLOW TRANSPORT_CONDITION Initiates a condition entry and defines its name CYCLIC INTERPOLATION Instructs PFLOTRAN to cycle the transient data set should the simulation time exceed the last time in the data set Defines the method for interpolating between data set times SYNC_TIMESTEP_WITH_UPDATE Synchronizes time step with waypoints DATUM Location is space where prescribed scalar e g pres sure temperature concentration etc is defined TYPE Specifies condition type PRESSURE Specifies pressure condition type TEMPERATURE Specifies temperature condition type CONCENTRATION Specifies the type of concentration condition SATURATION Specifies saturation condition type ENTHALPY Specifies enthalpy condition type END Terminates type entry GRADIENT Gradient of the scalar field in 3D space PRESSURE Pressure gradient in x y and z directions TEMPERATURE Temperature gradient in x y and z directions CONCENTRATION Concentration gradient in x y and z directions ENTHALPY Enthalpy gradient in x y and z directions END Terminates gradient entry PRESSURE Absolute fluid pressure at the datum FLUX Darcy velocity of fluid defining flux across specified boundary TEMPERATURE Temperature in C at datum CONCENTRATION Solute concentration at datum SATURATION Solute saturation at
158. on coefficient D is assumed to dependend on temperature and pressure as follows Pres TATS D D A aog P 77 aoe where dD is the reference diffusion coefficient at some reference temperature Ter and pressure Feet A 8 Thermal Conduction Multiple Continuum Model A thermal conduction model employing a multiple continuum model has been added to modes MPHASE and TH The formulation is based on Pruess and Narasimhan 1985 using a inte grated finite volume approach to develop equations for fracture primary continuum and matrix secondary continua temperatures 7 and T s respectively with fracture volume fraction denoted by co The DCDM dual continuum discrete matrix model following the classification given in Lichtner 2000 is implemented In what follows the matrix porosity is assumed to be zero lt 199 gt PFLOTRAN User Manual 1 8 0 August 14 2015 In terms of partial differential equations the heat conservation equations may be written as o ge papal F 1 Pa PrCrTa vV dapaHa kaVTa T Agra E A 86a and a a Ta _ en Orla gelo kg a 0 A 86b for fracture and matrix temperatures T and Tz respectively where represents the matrix coor dinate assumed to be an effective 1D domain The boundary condition Ta u t r Talr t A 86c is imposed at the fracture matrix interface where y denotes the outer boundary of the matrix Using the control volume configurat
159. on point is tied e g to monitor fluxes across a boundary face Keyword VELOCITY optional toggles on the printing of Darcy velocities at the observation point Keyword SECONDARY_TEMPERATURE optional toggles on the printing of the secondary continuum matrix nodes temperatures Keyword SECONDARY_CONCENTRATION optional toggles on the printing of the sec ondary continuum matrix nodes concentration Keyword SECONDARY_MINERAL_VOLFRAC optional toggles on the printing of the sec ondary continuum matrix nodes mineral volume fraction lt 115 gt PFLOTRAN User Manual 84 42 0 August 14 2015 Examples OBS ERVATION EGION welll VELOCITY ERVATION BOUNDARY_CONDITION river END lt 116 gt Return to List of Keywords PFLOTRAN User Manual 84 43 0 August 14 2015 4 43 Keyword ORIGIN ORIG Return to List of Keywords ORIGIN ORIG X_DIRECTION Y_DIRECTION Z_DIRECTION Return to List of Keywords lt 117 gt PFLOTRAN User Manual 84 44 0 August 14 2015 4 44 Keyword OUTPUT Return to List of Keywords Description Specifies output options for biogeochemical transport Input OUTPUT TIMES Unit s min h hr d w mo y yr lt float gt SCREEN OFF suppress screen output SCREEN PERIODIC lt int gt print to screen every lt integer gt time steps PERIODIC TIME lt float gt Unit PERIODIC TIMESTEP lt float gt Unit PERIODIC_OBSERVATION TI
160. optional parameters gt END Examples EOS WATER DENSITY EXPONENTIAL 997 16d0 101325 d0 1 d 8 EOS WATER DENSITY CONSTANT 997 16d0 ENTHALPY CONSTANT 1 8890d0 VISCOSITY CONSTANT 8 904156d 4 END Return to List of Keywords lt 72 gt PFLOTRAN User Manual 84 17 0 August 14 2015 4 17 Keyword FLOW_CONDITION Return to List of Keywords Description The FLOW_CONDITION keyword specifies scalar or vector data sets to be asso ciated with a given boundary or initial condition For instance to specify a hydrostatic boundary condition the use would specify a condition with a pressure associated with a point in space 1 e datum in space and a gradient both vector quantities Note that in the case of a hydrostatic boundary condition the vertical gradient specified in the input deck must be zero in order to en able the hydrostatic pressure calculation Otherwise the specified vertical gradient overrides the hydrostatic pressure Transient pressures temperatures concentrations datums gradients etc are specified using the FILE filename combination for the name of the data set Input FLOW CONDITION flow condition name UNITS lt char gt not currently supported lt char gt is one of the following entries s min h hr d day w week mo month y yr time mm cm m dm km length kg s kg yr rate Pa KPa pressure m s m yr velocity C
161. or first order decay of an immobile species Input IMMOBILE_DECAY_REACTION Name SPECIES_NAME lt string gt Name of immobile species to undergo first order decay RATE CONSTANT lt float gt First order rate constant 1 sec HALF_LIFE lt float gt Species half life sec END Explanation Note that units for rate constant or half life other than 1 sec or sec respectively may be specified Only specify one of rate constant or half life but not both Example CHEMISTRY PRIMARY_SPECIES IMMOBILE_SPECIES D im IMMOBILE_DECAY_REACTION SPECIES_NAME D im RATE_CONSTANT 1 d 9 Return to List of Keywords lt 95 gt PFLOTRAN User Manual 84 29 0 August 14 2015 4 29 Keyword INITIAL_CONDITION Return to List of Keywords Description Condition coupler between regions and flow and transport conditions Input INITIAL_CONDITION Nane REGION region_name FLOW_CONDITION condition_name TRANSPORT CONDITION condition name END Explanation Example condition couplers nitial condition INITIAL CONDITION FLOW CONDITION gradient north TRANSPORT CONDITION Initial REGION all END jas Return to List of Keywords lt 96 gt PFLOTRAN User Manual 84 31 0 August 14 2015 4 30 Keyword INITIALIZE_FLOW_FROM_FILE Return to List of Keywords INITIALIZE FLOW FROM FILE
162. ow into and negative for flow out of the domain V Integrating the flux over time gives the cumulative flux F i t F F dt 4 7 0 and time integrated source sink Q t Q 1 Qi dt 4 8 0 Global conservation of mass implies the equality Nit Ni 0 Fi Q 4 9 The header for the MPHASE mass balance file reads for time in years l aqueous liquid phase sc supercritical CO t At y Nio Noto Neo N o Neo Neo kmol l l SC SC F 110 oe Fio Foo kmol Fino Foo mo Fco kmol y Cubo cos kmol Quo co kmol y 4 10 The quantity Ne denotes the trapped component in phase a defined by Nes SANT AV 4 11 V sa lt s0 where s denotes the residual saturation There are as many rows of cumulative and instantaneous fluxes as there are boundaries and source sinks lt 121 gt PFLOTRAN User Manual 84 44 0 August 14 2015 Examples OUTPUT SCREEN PERIODIC 10 IPERIODIC TIME 10 h PERIODIC_OBSERVATION TIMESTEP 1 times h 1 PERIODIC OBSERVATION TIME 50 h FORMAT TECPLOT POINT or BLOCK FORMAT HDF5 VELOCITIES MASS_BALANC END cal E lt 122 gt Return to List of Keywords PFLOTRAN User Manual 84 47 0 August 14 2015 4 45 Keyword OVERWRITE_RESTART_FLOW_PARAMS Return to List of Keywords OVERWRITE RESTART FLOW PARAMS overwrite_restart_flow_params true Overwrites
163. oyed DBASE VALUE lt stringl gt lt string2 gt The names of the parameters to be read from the database file This card combination may be entered anywhere a double precision value is read from the input file The second string lt string2 gt must be preceded by a double colon without spaces and is optional See example below Examples DBASE_FILENAME 543_dbase h5 MATERIAL_PROPERTY soill POROSITY DBASE_VALUE POROSITY SOIL1 END MATERIAL_PROPERTY soil4 PERM_X DBASE_VALUE PERMEABILITY X SOIL4 END CHARACTERISTIC CURVES sf3 ALPHA DBASE VALUE ALPHA sf3 END EGION north FACE NORTH COORDINATES Quan Acao dado 60 d0 46 d0 DBASE VALUE NORTH MAX Z poked END CONSTRAINT river_water CONCENTRATIONS Tracer 1 e 3 F Tracer2 DBASE_VALUE RIVER_TRACER2 F END Values are assigned based on the database stored in 543_dbase h5 and the command line argument realization_id 5 note the zero based index of 4 in the HDFS file is ac lt 69 gt PFLOTRAN User Manual 4 14 0 August 14 2015 PFLOTRAN_DIR src python dbase_creator py tually the 5th realization An example script for creating the database file may be found in 5 543_dbase h5 Ermo m EMI Eev neron P anena H EB NORTH_MAX_Z De BEE e d Eh POROSITY SOIL1 po oo po po po po
164. paper SPE 10528 presented at the Sixth SPE Symposium on Reservoir Simulation of the Society of Petroleum Engineers New Orleans LA January 1982 Pruess K S Yabusaki C Steefel and P Lichtner 2002 Fluid flow heat transfer and so lute transport at nuclear waste storage tanks in the Hanford vadose zone Available at www vadosezonejournal org Vadose Zone J 1 68 88 Pruess K and Narasimhan 1985 A practical method for modeling fluid and heat flow in frac tured porous media SPE 10509 14 26 Somerton W H A H El Shaarani and S M Mobarak 1974 High temperature behavior of rocks associated with geothermal type reservoirs Paper SPE 4897 Proceedings of the 44th An nual California Regional Meeting of the Society of Petroleum Engineers Richardson TX Society of Petroleum Engineers Andreas Voegelin Vijay M Vulava Florian Kuhnen Ruben Kretzschmar 2000 Multicompo nent transport of major cations predicted from binary adsorption experiments Journal of Contaminant Hydrology 46 319 338 lt 186 gt PFLOTRAN User Manual 1 2 1 August 14 2015 Appendix A Governing Equations A 1 Mode RICHARDS RICHARDS Mode applies to single phase variably saturated isothermal systems The governing mass conservation equation is given by o 7 SP V gt pq Qu A 1 with Darcy flux q defined as kk s q ly P W pgz A 2 Here y denotes porosity s saturation m m p water density
165. quantity Pm denotes the prefactor for the Ith parallel reaction with the form m Qil BE Il yam A 117 i 1 Kmi yim where the product index 7 generally runs over both primary and secondary species the quantities air and 57 refer to prefactor coefficients and K is an attenuation factor The quantity R denotes the gas constant 8 317 x 107 kJ mol K lt 205 gt PFLOTRAN User Manual 1 9 1 August 14 2015 A 9 1 1 Rate Limiter A rate limited form of the mineral kinetic rate law can be devised ac cording to the expression 1 om l 1 pin EQ 0 with rate limiter rm In the limit K Q 00 the rate becomes lim y p fim Im kira 2 Pi A 119 Defining the affinity factor O 1 K 0 N A 120 or KnQm 1 0 gt A 121 the rate may be expressed alternatively as K On Im Om Y Poli A 122 Let ho 1 9 m A 9 1 2 Changes in Material Properties Porosity permeability tortuosity and mineral sur face area may be updated optionally due to mineral precipitation and dissolution reactions accord ing to the relations p 1 5 0m A 123 k kof y Po Pes a A 124 with de l A 125 Po Pe fmin if p lt Pe A 126 b T To 2 A 127 Po and n 1 n ANA 2 i A 128 Pm t Po where the super subscript O denotes initial values with a typical value for n of 2 3 reflecting the surface to volume ratio Note that this relation only applies t
166. r species valence z Debye parameter a min eral molar volume V and formula weight w used in PFLOTRAN The database is divided into 5 blocks as listed in Table A 5 consisting of database primary species aqueous complex reactions gaseous reactions mineral reactions and surface complexation reactions Each block is termi nated by a line beginning with null The quantity Niemp refers to the number of temperatures at which log K values are stored in the database In the hanford dat database Niemp 8 with equilibrium constants stored at the temperatures 0 25 60 100 150 200 250 and 300 C The pressure is assumed to lie along the saturation curve of pure water for temperatures above 25 C and is equal to 1 bar at lower temperatures Reactions in the database are assumed to be written in the canonical form nspec A bo Vir As A 200 i l for species A where nspec refers to the number of aqueous or gaseous species A on the right hand side of the reaction Redox reactions in the standard database hanford dat are usually written in terms of O y Complexation reactions involving redox sensitive species are written in such a manner as to preserve the redox state Table A 5 Format of thermodynamic database Primary Species name do 2 W Secondary Species name nspec v n name n n 1 nspec log K 1 Niemp do 2 w Gaseous Species name V nspec v n name n n 1 nspec log K 1 Niemp w Minerals
167. r queries The final challenge is setting up an input file Various modes available are listed in Table 2 3 and example input decks are stored in the pflotran example_problems and pflotran shortcourse directories Table 2 3 Available modes in PFLOTRAN MODE Description Required Databases RICHARDS Solves Richards equation MPHASE Supercritcal CO2 co2data0 dat TH Thermal Hydrology mode CHEMISTRY Reactive Transport hanford dat Provided with the PFLOTRAN distribution in directory pflotran database An equivalent user supplied thermodynamic database for chemi cal reactions may also be used see A 11 for a description of the database format An example input file is listed in 4 4 for a coupled problem using Richards and Chemistry modes lt 14 gt PFLOTRAN User Manual 82 2 0 August 14 2015 2 2 Running on Big Iron Parallel Architectures Generally these machines use module to load the computing environment Make sure the correct compilers are loaded that are compatible with Fortran 2003 The following instructions apply to Yellowstone running Red Hat linux using the Intel compiler As MPI is already installed it is not necessary to reinstall it through PETSc Use a recent version of CMAKE module load cmake 2 8 10 2 Set the environmental variable for the BLAS LAPACK libraries to use MKL e g setenv BLAS_LAPACK_LIB_DIR ncar opt intel 12 1 0 233 composer_xe_2013 1 117 mkl Configure PETSc
168. rce code use Mercurial Mercurial hg is the version control system used by both PETSc and PFLO TRAN Often one can find executables for particular platforms and there is no need to com pile the application from scratch On a UNIX system you can check to see if Mercurial is already installed by issuing the command which hg PFLOTRAN can be downloaded from bitbucket org by issuing the command line hg clone https bitbucket org pflotran pflotran dev Step 3 Compiling PFLOTRAN Once PETSc and associated third party software has been in stalled it is easy to install PFLOTRAN To compile PFLOTRAN first decide on the options needed to run your problem The most common of these are listed in Table 2 2 lt 13 gt PFLOTRAN User Manual 82 2 0 August 14 2015 Table 2 2 Compile options for PFLOTRAN Option Description scco2 1 MPHASE mode for supercritical CO scorpio 1 SCORPIO parallel IO See 3 5 for installing SCORPIO cd PLOTRAN_DIR src pflotran make options pflotran For example make scco2 1 ppflotran Step 4 Running PFLOTRAN PFLOTRAN is run in parallel on N cores using the command mpirun np N pflotran pflotranin input_file_name in with input file input_file_name in The default input file name is simply pflotran in To get the most out of PFLOTRAN subscribe to the PFLOTRAN User Group pflotran users googlegroups com PFLOTRAN developers monitor this site and will as quickly as possible respond to you
169. riable MP1_HOME and add to the PATH variable setenv MPI_HOME PETSC_DIR PETSC_ARCH setenv PATH SMPI HOME bin SPATH Decide which options are needed for running PFLOTRAN structured grids are the simplest if unstructured grids are needed then install METIS and ParMETIS See Table 2 1 for several of the different configure options possible For example to configure PETSC to run in production mode and install openmpi HDFS METIS and ParMETIS use lt 12 gt PFLOTRAN User Manual 82 1 0 August 14 2015 cd petsc dev config configure py with debugging 0 with shared libraries 0 with x 0 download openmpi 1 download hdf5 1 download metis 1 download parmetis 1 Check to make sure mpi cc and mpi f90 are working and are recent versions that are compat ible with Fortran 2003 e g GNU gfortran version 4 7 x Intel version 12 x or PGI Table 2 1 Options for configuring petsc dev Option Package MPI Parallel OpenMPI download openmpi 1 MPICH download mpich 1 Grid Structured Unstructured METIS and ParMETIS download metis 1 download parmetis 1 Output TecPlot VTK HDF5 Parallel HDF5 download hdf5 1 Solvers Iterative GMRES Direct Parallel Direct MUMPS download mumps 1 Multigrid ML download ml 1 Preconditioners Hypre download hypre 1 Need CMAKE Step 2 Downloading PFLOTRAN To obtain the latest version of the PFLOTRAN sou
170. rom where it left off when the file pflotran chk3000 was printed ps ESTART pflotran chk3000 Return to List of Keywords lt 127 gt PFLOTRAN User Manual 84 51 0 August 14 2015 4 51 Keyword SATURATION_FUNCTION Return to List of Keywords Description Currently being revised to use a common set of saturation and relative permeability functions across all modes Check source code for up to date implementation Note for GENERAL and RICHARDS modes use keyword CHARACTERISTIC_CURVES SATURATION_FUNCTION should be used in all other flow modes Input SATURATION_FUNCTION Name SATURATION_FUNCTION_TYPE VAN_GENUCHTEN BROOKS_COREY THOMEER_COREY NMT_EXP PRUESS_1 VAN_GENUCHTEN_PARKER PERMEABILITY_FUNCTION_TYPE MUALEM BURDINE RESIDUAL_SATURATION lt Value gt MODES RICHARDS TH RESIDUAL_SATURATION_LIQUID lt Value gt MODES MPHASE RESIDUAL_SATURATION_GAS lt Value gt MODES MPHASE VAN_GENUCHTEN_PARKER LAMBDA lt Value gt ALPHA lt Value gt Pa7 MAX CAPILLARY PRESSURE lt Value gt Pa BETAC lt Value gt Only used in NMT EXP POWER lt Value gt Only used in NMT_EXP END Explanation Example lt 128 gt PFLOTRAN User Manual 84 51 0 August 14 2015 SATURATION FUNCTION sf1 SATURATION FUNCTION TYPE VAN GENUCHTEN RESIDUAL SATURATION 0 1d0 LAMBDA 2 6700 ALPHA 2 042d 4 MAX_CAPILLARY_PRESSURE 1d8 END
171. ry species Ar in the ath fluid phase defined by Nsec DO 6 01 vee A 100 i 1 In this equation the subscript represents the aqueous electrolyte phase from which the primary species are chosen The secondary species concentrations C are obtained from mass action equa tions corresponding to equilibrium conditions of the reactions U A Af A 101 j yielding the mass action equations K Vii n a A 102 i y with equilibrium constant K and activity coefficients y For the molality of the kth aqueous species the Debye Hiickel activity coefficient algorithm is given by 2AV T 3 k dE Hol A 103 1 Ba vI log lt 203 gt PFLOTRAN User Manual 1 9 0 August 14 2015 and the Davies algorithm by the expression 2 Zk 2 log Yr VI 0 31 A 104 1 vV1 with valence z Debye Hiickel parameters A B and ionic radius Ops and ionic strength J defined as 1 Ne 1 Nsec a 2 2 I IES A 105 for molality m and m of primary and secondary species respectively note C pyy m PMi py fluid density y mass fraction of H O For high ionic strength solutions approxi mately above 0 1 M the Pitzer model should be used Currently however only the Debye H ckel algorithm is implemented in PFLOTRAN The total flux 92 for species independent diffusion is given by O ga PSaDaV Un A 106 The diffusion dispersion coefficient Ds may be different for differ
172. s NUMERICAL_JACOBIAN_RXN Uses numerically evaluated Jacobian for reactions Return to List of Keywords lt 113 gt PFLOTRAN User Manual 84 41 0 August 14 2015 4 41 Keyword NUMERICAL_JACOBIAN_MULTI_COUPLE Return to List of Keywords NUMERICAL JACOBIAN MULTI COUPLE The contribution to the primary continuum Ja cobian due to primary secondary continua coupling term is numerically evaluated Return to List of Keywords lt 114 gt PFLOTRAN User Manual 84 42 0 August 14 2015 4 42 Keyword OBSERVATION Return to List of Keywords Description The OBSERVATION card specifies a location REGION at which flow and transport results e g pressure saturation flow velocities solute concentrations etc will be monitored in the output The user must specify either a region or boundary condition to which the observation object is linked The velocity keyword toggles on the printing of velocities at a point in space Input OBSERVATION BOUNDARY_CONDITION boundary condition name REGION region name VELOCITY AT_CELL_CENTER SECONDARY_TEMPERATURE SECONDARY_CONCENTRATION SECONDARY_MINERAL_VOLFRAC END Explanation Keyword OBSERVATION initiates an observation point entry Keyword REGION optional defines the name of the region usually a point in space to which the observation point is linked Keyword BOUNDARY_CONDITION optional specifies the name of a boundary condition to which the observati
173. s and solute concentrations are identical as obtained from solving the reactive transport equations For this relation to hold it is necessary that the kinetic rate constant transform as ka fa km A 209 From the above relations it is found that the reaction rate transforms according to In KiyAm 1 Knn r A 210a 1 l om Am 1 Kim Qm 1 0 A 210b 1 Im A 210c Fra where the last result is obtained by scaling Temkin s constant according to e A 211 It should be noted that the mineral concentration C Va Y bm fm Cm differs in the two formulations however mass density pm WmV is an invariant unlike molar density nm Vee A 12 Eh pe Output for Eh and pe is calculated from the half cell reaction 2H 0 4H 4e O A 212 with the corresponding equilibrium constant fit to the Maier Kelly expansion Eqn A 199 The fit coefficients are listed in Table A 6 lt 218 gt PFLOTRAN User Manual 82 0 0 August 14 2015 Table A 6 Fit coefficients for log K of reaction A 212 ca 6 745529048 Co 48 205936593 0 000557816 ca 27780 749538022 C3 4027 337694858 A 13 Geomechanics In PFLOTRAN linear elasticity model is assumed as the constitutive model for deformation of the rock Biot s model is used to incorporate the effect of flow on the geomechanics In addition the effect of temperature on geomechanics is considered via coefficient of thermal
174. s species id iphase Jacobian this species_id this species_id Jacobian this species_id this species_id thissrate_constantx porosityx global_auxvar sat iphase volumex 1 d3x rt_auxvar Saqueous dtotal thissspecies_id amp this species id iphase lt 226 gt PFLOTRAN User Manual 83 2 0 August 14 2015 e ExampleDestroy Deallocate any dynamic memory within the class without deallocat ing the object itself 5 Ensure that the methods within the extended derived type point to the proper procedures in the module procedure public ReadInput gt ExampleRead procedure public Setup gt ExampleSetup procedure public Evaluate gt ExampleReact procedure public Destroy gt ExampleDestroy 6 Within reaction_sandbox F90 a Add Reaction_Sandbox_Example_class to the list of modules to be used at the top of the file b Add a case statement in RSandboxRead2 for the keyword defining the new reaction and create the reaction within Le Case EXAMPLE new sandbox gt ExampleCreate lt 227 gt
175. scription This keyword is required for output of geomechanics data The geomechanics data is saved in separate set of files unlike flow and transport The filenames of these files have the word geomech included in them Uses the same keywords as OUTPUT lt 85 gt PFLOTRAN User Manual 84 25 0 August 14 2015 4 25 Keyword GEOMECHANICS_REGION Return to List of Keywords Description The GEOMECHANICS_REGION keyword defines a set of geomechanics finite ele ment grid vertices The GEOMECHANICS_REGION name can then be used to link this set of ver tices to geomechanics material properties strata and boundary conditions The list of vertices can be read from an ASCH file by using the keyword FILE under the GEOMECHANICS_REGION card Examples GEOMECHANICS_REGION top ETLE Op vset Return to List of Keywords lt 86 gt PFLOTRAN User Manual 84 26 0 August 14 2015 4 26 Keyword GEOMECHANICS_STRATA Return to List of Keywords Description Couples geomechanics material IDs and or properties with a geomechanics region in the problem domain GEOMECHANICS_STRATA GEOMECHANICS_MATERIAL lt string gt name of the geomechanics material property to be associated with a geomechanics region GEOMECHANICS_REGION lt string gt name of geomechanics region associated with a ge omechanics material property END Example GEOMECHANICS_STRATA GEOMECHANICS_MATERIAL granite GEO
176. ser Manual 84 7 0 August 14 2015 Parameter Description Required cards within block e SATURATION_FUNCTION Opens a saturation function block with the string indicating the type of function options include VAN_GENUCHTEN BROOKS_COREY e PERMEABILITY_FUNCTION Opens a relative permeability function block with the string indicating the type of function options include MUALEM BURDINE MUALEM_VG_GAS BURDINE_BC_GAS e ALPHA lt float gt Inverse of the air entry pressure for the saturation function Pa e GAS RESIDUAL SATURATION lt float gt Residual saturation for gas phase e LAMBDA lt float gt Brooks Corey lambda e LIQUID RESIDUAL SATURATION lt float gt Residual saturation for liquid phase e M lt float gt van Genuchten m m 1 1 n e SMOOTH Applies polynomial smoothing to relative permeability or saturation function Strongly recommended for the Brooks Corey saturation function if cells in the domain tran sition from saturated to variably saturated conditions Optional Cards e PHASE lt string gt Phase to which the permeability function applies LIQUID GAS e MAX_CAPILLARY_PRESSURE lt float gt Cut off for maximum capillary pressure default 10 Pa e POWER lt float gt Placeholder Currently not used Examples CHARACTERISTIC_CURV M 0 5d0 ALPHA 1 d 4 SATURATION_FUNCTION VAN_GI LIQUID RESIDUAL SATURATION 0 d0 Es ecel
177. t 14 2015 OUTPUT ALL FREE_ION TOTAL Example Output total and free ion primary species concentrations Keyword Primary_Species Return to List of Keywords Description List of primary species that fully describe the chemical composition of the fluid terminated by END or The set of primary species must form an independent set of species in terms of which all homogeneous aqueous equilibrium reactions can be expressed Secondary_Species Gas_Species Minerals List of aqueous species in equilibrium with primary species terminated by END or List of gas species terminated by END or List of minerals both passive and active terminated by END or Active minerals must be associated with a kinetic rate law under MIN ERAL_KINETICS and listed under CONSTRAINTS For passive min eral only the mineral saturation index is calculated for initial and bound ary conditions Sorption Surface complexation ion exchange and specified isotherm Output To print secondary aqueous complex concentrations either add the individual names of the secondary species of interest or add the keyword SECONDARY_SPECIES for all secondary species to the CHEMISTRY OUTPUT card Example CHEMISTRY OUTPUT lt 61 gt PFLOTRAN User Manual 84 9 7 August 14 2015 co2 ag where co2 aq is a secondary species SECONDARY_SPECIES END
178. t must be solved simultaneously with the primary species equations A typical expression for 1 might be IE Kal S S A 194 with rate constant ky and where 9 1 is a known function of the solute concentrations In this case Eqn A 190 must be added to the primary species transport equations Further reduction of the transport equations for the case where a flux term is present in the kinetic equation is not possible in general for complex flux terms A 9 5 Microbial Reactions Kinetic rate law Ca Ca i kX I A 195 i Ka Ca Ka Ca i l C _ Ce C Oe Rah x d a I A 196 ee lies Biomass creation and degradation X y Ri Ka A 197 lt 214 gt PFLOTRAN User Manual 1 10 0 August 14 2015 Table A 4 Definition of symbols used in modeling microbial reactions Symbol Definition Ri reaction rate for ith biomass reaction ki rate constant Xi biomass concentration I inhibition factor Ca electron acceptor concentration Ca electron donor concentration Coe electron acceptor threshold concentration oe electron donor threshold concentration where V denotes the yield and Kgecay refers to the biomass decay rate constant Other parameters are listed in Table A 4 e Monod inhibition below a concentration K 1 C K C e Inverse monod inhibition above a concentration K J K K C e Kinzelbach inhibition 7 1 2 arctan C C f 7 where f 1
179. t why you updated gold standard files in your revision control commit mes sage lt 147 gt PFLOTRAN User Manual 6 2 0 August 14 2015 6 Visualization Visualization of the results produced by PFLOTRAN can be achieved using several different util ities including commercial and open source software Plotting 2D or 3D output files can be done using the commercial package Tecplot or the opensource packages Vislt and ParaView Paraview 1s similar to VisIt and both are capable of remote visualization on parallel architectures Several potentially useful hints on using these packages are provided below 6 1 Tecplot e In order to change the default file format in TecPlot so that it recognizes tec files place the following in the tecplot cfg file FileConfig FNameFilter InputDataFile x tec 6 2 Visit e Inactive cells can be omitted by going to Controls gt Subset and unchecking Mate rial ID 0 e In 3D to scale the size of one of the coordinate axes go to Controls gt View and check box Scale 3D Axes and set desired scaling factor in box to right e To make 2D plots use Operators gt Slicing gt Slice e For 3D plots Operators gt Slicing gt ThreeSlice is useful e Instructions to set up geomechanical and flow data simultaneously in Vislt Open Vislt Select the 1 x 2 layout button on Window 1 to open a new window Window 2 Now make Window 1 active by checking the first button on Window 1
180. teral grid spacing lt 178 gt PFLOTRAN User Manual 87 4 2 August 14 2015 DB pflotran 026 h5 pflotran 026 h5 Time 250 Ime 250 or Figure 7 11 Left pressure right supercritical CO saturation for an elapsed time of 250 days 0 1 T T T 0 09 0 08 0 07 0 06 E 0 05 0 04 E Leakage Flux Ratio 0 03 E 0 02 F 0 01 0 1 1 1 L J 0 200 400 600 800 1000 Time a Figure 7 12 Leakage rate relative to injection rate lt 179 gt PFLOTRAN User Manual 87 4 2 August 14 2015 Table 7 12 Input file for 3D CO sequestration example problem with a leaky well SIMULATION SIMULATION_TYPE SUBSURFACE PROCESS_MODELS SUBSURFACE_FLOW flow MODE MPHASE CO2_DATABASE Users lichtner pflotran pflotran dev database co2data0 dat CO2_DATABASE co2data0 dat TYPE structured ORIGIN 0 d0 0 d0 0 d0 NXYZ 200 200 32 BOUNDS 0 d0 0 d0 0 d0 1000 d0 1000 d0 160 d0 TIMESTEPPER FLOW TS_ACCELERATION 8 MAX_PRESSURE_CHANGE 5 e6 MAX_TEMPERATURE_CHANGE 2 MAX_CONCENTRATION_CHANGE 1 e 3 MAX_SATURATION_CHANGE 0 1 MAX_STEPS 1 NEWTON_SOLVER FLOW ATOL 1D 8 RTOL 1D 8 STOL 1D 30 DTOL 1D15 ITOL 1D 8 MAXIT 25 MAXF 100 MAX_NORM 1d6 END times TIME FINAL_TIME 1000 d0 d INITIAL_TIMESTEP_SIZE 1 d 6 MAXIMUM TIMESTEP SIZE 1 0 d MAXIMUM TIMESTEP SIZE 10 0 d at 100 d d output options OUTPUT TIMES d 0 15 10 25 0 5 0 75 120 255 5 0 10 0
181. the formula weight W is a function of composition according to the relation es Wer A 23 The quantities p Cr and x refer to the mass density heat capacity and thermal conductivity of the porous rock A 3 1 Source Sink Terms The source sink terms Q and Qe describe injection and extraction of mass and heat respectively for various well models Several different well models are available The simplest is a volume or mass rate injection production well given by Qi 2 2 Nat Olr ra A 24a y gt ada O r Pn A 24b uw gh a n ra A 24c where q qM refer to volume and mass rates with units m s kg s respectively related by the density de Palos A 25 lt 190 gt PFLOTRAN User Manual 1 3 2 August 14 2015 Table A 1 Choice of primary variables State Xi Xo X3 Liquid mo aie 2 Gas Dy T Eo Two Phase p T sg The position vector r refers to the location of the nth source sink A less simplistic approach is to specify the bottom well pressure to regulate the flow rate in the well In this approach the mass flow rate is determined from the expression ka da Poor Pa Pe A 26 with bottom well pressure p gt and where I denotes the well factor production index given by onkA i oe A 27 In re Tw 0 1 2 In this expression k denotes the permeability of the porous medium Az refers to the layer thick ness re denotes the grid block radius r denotes
182. um node For better convergence uniform logarithmic spacing is used for the matrix nodes Alm p AEm 1 A 90a specifying A y and ly for the outer most matrix node and matrix block size respectively The factor p is determined from the constraint M Im 2 Abn A 90b m 1 which requires that p satisfy the equation l M 1 ee A 90c 2A 1 pl with the inner and outer grid spacing related by A m pM Ag A 90d Matrix Block Figure A 2 Control volumes in DCDM multiple continuum model with fracture aperture 20 and matrix block size d According to the geometry in Figure A 2 assuming a 3D orthogonal set of fractures Va d 26 A 91 lt 201 gt PFLOTRAN User Manual 1 9 0 August 14 2015 Table A 2 DCDM geometric parameters Geometry Area AR Volume V Slab A Al Nested Cubes 6d d Nested Spheres 4rR TR and vo d 26 d A 92 giving 3 d 1 Ea 1 a4 253 1 95 E A 93a I d x A 93b The fracture aperture 20 is found to be in terms of ca and d 1 28 d 1 A 94 a a A list of different sub continua geometries and parameters implemented in PFLOTRAN is given in Table A 2 Different independent and dependent parameters for the nested cube geometry are listed in Table A 3 The interfacial area A between fracture control volumes is equal to AyAz AzAz AxAy for x y and z directions respectively In the case of nested cubes there are four possible param
183. vapor phases at a known temperature and liquid pressure the following two relations are used see Painter 2011 S Pag A 80a l g E di HA A 80b S 8 Oil lt 198 gt PFLOTRAN User Manual 1 8 0 August 14 2015 S is the retention curve for unfrozen liquid gas phases P is the gas liquid capillary pressure Pe is the ice liquid capillary pressure o and dy are the ice liquid and gas liquid interfacial tensions Also Pe Pih w 0 where h is the heat of fusion of ice at 273 15 K p is the mass density of ice Y re with To 273 15 K For S the van Genuchten model is used ee eS S le A 81 il e 0 with the Mualem model implemented for the relative permeability of liquid water 1 1 A a kri 81 E 1 803 A 82 where A a are parameters with y The thermal conductivity for the frozen soil is chosen to be k Keira Rea 1 Keu Refis A 83 Where Kwet f Kwetu are the liquid and ice saturated thermal conductivities Kar is the dry ther mal conducitivity Key Ke are the Kersten numbers in frozen and unfrozen conditions and are assumed to be related to the ice and liquid saturations by power law relations as follows Kep 5 A 84a Kes s A 84b with ay a being the power law coefficients Care is also taken to ensure that the derivatives of the Kersten numbers do not blow up when s s go to zero when a a are less than one The gas diffusi
184. where N is the number of the timestep when the checkpoint file was printed A file named restart chk will also be written when PFLOTRAN properly terminates execution One use this file to pick up from where the simulation stopped by increasing the final time Checkpointing can be used to start from an initial steady state solution but note that poros ity and permeability are checkpointed as there are scenarios where they can change over time To override this behavior add OVERWRITE_RESTART_FLOW_PARAMS to the input file to set porosity permeability to their read in values Input CHECKPOINT lt checkpoint_frequency gt Explanation Keyword Description CHECKPOINT toggles on checkpointing checkpoint_frequency frequency at which checkpoint files are printed lt integer gt Examples CHECKPOINT 1000 CHECKPOINT 5 Return to List of Keywords lt 43 gt PFLOTRAN User Manual 84 9 0 August 14 2015 4 9 Keyword CHEMISTRY Return to List of Keywords Description Specifies geochemisty for multicomponent transport The CHEMISTRY keyword invokes the reactive transport mode coupling a reaction network consisting of aqueous species minerals and gases to advection diffusion and dispersion This keyword provides input for pri mary species secondary species implemented through local equilibrium mass action relations minerals gases colloids Homogeneous aqueous complexing reactions and heteroge
185. xen sw Ye he ee ek eea eG ee Ber Br Be ee A 8 Thermal Conduction Multiple Continuum Model A 9 Mode Reactive Transport Keyword CHEMISTRY o A 9 1 Mineral Precipitation and Dissolution 2 sus 222 u 20 casa AIR Rate Linter 2 sos s 84 3 200 2 den ae we aoe ee ee ae A 9 12 Changes in Material Properties 2x 624585 se ganas A 9 1 3 Affinity Threshold eS sos s sos wie sea RA weh A 9 1 4 Surface Armoring xs si ar RA A O 2 Sortie fs che bee Er RSE era a A921 Ion Exchange eee eee a A 9 2 2 Surface Complexation o A923 Multirate Sorption ss a AD A 9 3 Sorption Isotherm lt Under Revision gt 222020000 A 9 4 Colloid Facilitated Transport 2 22 2m none A 9 5 Microbial Reactions s ssc a eee wu va u na nur SS AE MA A l0 Tracer Mean Age sion ae holed a S O eee wee oe amp 4 A 11 Thermodynamic Database u a au a na nn a ee AAA A AA AAA A 13 Geomechanics lt e 2 0 0 m uw m ee nu ne er nenne Appendix B Method of Solution B Integrated Finite Volume Discretization mossos B 2 Fully Implicit Newton Raphson Iteration with Linear and Logarithm Update B 21 Example ssa rm sd ee eRe HRS e EEE One BES B 22 Multirate Sorption 2 2 2 2 2 u ARA ee ROA O gs B 3 Operator Splitting pos ss e za a we Eu na aa de ae ee ee Bel 2Constant Ay use ia ee Sie Geo ede o Eee ee lt 7 gt PFLOTRAN User Manual 0 0 0 August
186. y to define the solute concentration and referencing the sorbed concentration to the bulk volume V pa o 3 NH My Mj A 178 A sorption isotherm S may be specified for any primary species A resulting in the transport equation o OS y3 iC V F gt a Mee at for a partially saturated medium Substituting S ys 7 C from Eqn A 175 and introducing the retardation R gives A 179 I Ryo V F 0 A 180 lt 212 gt PFLOTRAN User Manual 1 9 4 August 14 2015 with the retardation given by the alternative forms Rie Lo Ro dimensionless A 181a een 4 conventional A 181b Psi 1 a 1 K molality based A 181c PSIPw Three distinct models are available for the sorption isotherm S in PFLOTRAN e linear Kp model A Sj ys KPC Kms A 182 with distribution coefficient K A e Langmuir isotherm K O pu Ktm ds JOP a as A A 183 1 K5C5 Pw 1 Kym with Langmuir coefficients E and br and e Freundlich isotherm ONG ni See Km A 184 with coefficients K A and n A 9 4 Colloid Facilitated Transport Colloid facilitated transport is implemented into PFLOTRAN based on surface complexation re actions Competition between mobile and immobile colloids and stationary mineral surfaces is taken into account Colloid filtration processes are not currently implemented into PFLOTRAN A colloid is treated as a solid particle suspended in solution or att

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