├── .github └── workflows │ └── crunchtope-ci.yml ├── .gitignore ├── Containers ├── Containerfile-arm64 └── Containerfile-intel ├── Exercises ├── .gitignore ├── CrunchCourseExerciseDescriptions.pdf ├── Ex10Flow2D │ ├── .gitignore │ ├── COMG-S-14-00112.pdf │ ├── Graph_Exercise10_calcite_gypsum.gle │ ├── Graph_Exercise10_permeability.gle │ ├── Graph_Exercise10_porosity.gle │ ├── Perm.dat │ ├── Perm.z │ ├── PestControl.ant │ ├── Shortcourse10.in │ ├── calcite.dat │ ├── calcite.z │ ├── datacom_mingliangBdot.dbs │ ├── fort.123 │ ├── gypsum.dat │ ├── gypsum.z │ ├── perm5_2D.hyc │ ├── poro.dat │ └── poro.z ├── Ex11CrunchClay │ ├── Diffusion-no-DL-charge │ │ ├── Diffusion-no-charge.in │ │ ├── Graph_Exercise11_no_charge.gle │ │ ├── PestControl.ant │ │ ├── datacom_bench_no_surf_complexes.dbs │ │ └── datacom_bench_with_surf_complexes.dbs │ ├── Diffusion-with-DL-charge-no-surface-complexation │ │ ├── Diffusion-with-charge.in │ │ ├── Graph_Exercise11_with_charge.gle │ │ ├── PestControl.ant │ │ ├── datacom_bench_no_surf_complexes.dbs │ │ └── datacom_bench_with_surf_complexes.dbs │ ├── Diffusion-with-DL-charge-with-surface-complexation │ │ ├── Diffusion-with-charge-with-SC.in │ │ ├── Graph_Exercise11_with_charge_with_SC.gle │ │ ├── PestControl.ant │ │ ├── datacom_bench_no_surf_complexes.dbs │ │ └── datacom_bench_with_surf_complexes.dbs │ └── Graph_diffusion_all.gle ├── Ex12PESTExercises │ ├── .gitignore │ ├── BatchNoGmin.in │ ├── BatchNoGmin.pst │ ├── PestControl.ant │ ├── PestExchange.ins │ ├── batchnogmin.cnd │ ├── batchnogmin.drf │ ├── batchnogmin.jac │ ├── batchnogmin.jco │ ├── batchnogmin.jst │ ├── batchnogmin.mtt │ ├── batchnogmin.par │ ├── batchnogmin.rec │ ├── batchnogmin.rei │ ├── batchnogmin.res │ ├── batchnogmin.rst │ ├── batchnogmin.sen │ ├── batchnogmin.seo │ ├── datacom-SrExchange.dbs │ ├── datacom-SrExchange.tpl │ ├── i64pest.exe │ └── newpestman1.pdf ├── Ex13UnsaturatedFlow │ ├── .gitignore │ ├── PestControl.ant │ ├── ShortCourse13.in │ ├── datacom.dbs │ ├── initial_condition.csv │ ├── tracer.pdf │ ├── tracer_profile.pdf │ ├── tracer_profile_steady.pdf │ ├── tracer_steady.pdf │ ├── water_content.pdf │ └── water_content_steady.pdf ├── Ex14UnsaturatedFlow_evaporation │ ├── .gitignore │ ├── PestControl.ant │ ├── ShortCourse14.in │ ├── datacom.dbs │ ├── tracer_profile.pdf │ └── water_content.pdf ├── Ex15UnsaturatedFlow_transient │ ├── .gitignore │ ├── PestControl.ant │ ├── ShortCourse15.in │ ├── datacom.dbs │ ├── initial_condition.csv │ ├── tracer.pdf │ ├── tracer_profile.pdf │ ├── water_content.pdf │ └── water_upper_BC.dat ├── Ex16UnsaturatedFlow2D │ ├── PestControl.ant │ ├── ShortCourse16-ShorterVersion.in │ ├── ShortCourse16.in │ └── datacom.dbs ├── Ex1Speciation │ ├── .gitignore │ ├── PestControl.ant │ ├── ShortCourse1.in │ └── datacom_13C.dbs ├── Ex2Advection-Pest │ ├── .gitignore │ ├── Graph_Exercise2.gle │ ├── PestControl.ant │ ├── ShortCourse2.tpl │ ├── ShortCourse2react.in │ ├── Shortcourse2.in │ ├── Shortcourse2.pst │ ├── datacom.dbs │ ├── i64pest.exe │ ├── shortcourse2.cnd │ ├── shortcourse2.drf │ ├── shortcourse2.jac │ ├── shortcourse2.jco │ ├── shortcourse2.jst │ ├── shortcourse2.mtt │ ├── shortcourse2.par │ ├── shortcourse2.rec │ ├── shortcourse2.rei │ ├── shortcourse2.res │ ├── shortcourse2.rst │ ├── shortcourse2.sen │ ├── shortcourse2.seo │ └── totcon1.ins ├── Ex2Advection │ ├── .ShortCourse2.in.swp │ ├── .gitignore │ ├── Graph_Exercise2.gle │ ├── PestControl.ant │ ├── ShortCourse2.in │ ├── ShortCourse2react.in │ └── datacom.dbs ├── Ex3FickianDiffusion │ ├── .gitignore │ ├── Graph_Exercise3.gle │ ├── PestControl.ant │ ├── ShortCourse3.in │ ├── datacom.dbs │ └── fort.123 ├── Ex4MulticomponentDiffusion │ ├── .gitignore │ ├── Graph_Exercise4Clisotopes.gle │ ├── Graph_Exercise4Na+Cl.gle │ ├── PestControl.ant │ ├── ProblemSet3.in │ ├── ShortCourse4.in │ ├── ShortCourse4_ClTopes.in │ └── datacom.dbs ├── Ex5RolleTransverseDiffusion │ ├── .gitignore │ ├── Experiment3-Rolle.pdf │ ├── Graph_Exercise5.gle │ ├── PestControl.ant │ ├── Rolle2013.session │ ├── Rolle2013.session.gui │ ├── Rolle2D.in │ ├── Rolle2D_Shorter.in │ └── datacom.dbs ├── Ex6Sorption │ ├── Ex6A-CesiumIonExchange │ │ ├── .gitignore │ │ ├── Graph_Exercise6a.gle │ │ ├── HanfordExpt3RawData.dat │ │ ├── HanfordTank-A.in │ │ ├── HanfordTank-B.in │ │ ├── HanfordTank-C.in │ │ ├── HanfordTank.plt │ │ ├── HanfordTanksColumnFit3Site-GT.dbs │ │ └── PestControl.ant │ └── Ex6B-SurfaceComplexation │ │ ├── .gitignore │ │ ├── PestControl.ant │ │ ├── ShortCourse6b.in │ │ ├── TestSurfaceComplexation-MultipleMineralEDLs.in │ │ └── datacom.dbs ├── Ex7CO2Attack │ ├── .gitignore │ ├── CO2_GCS │ ├── Graph_Exercise7.gle │ ├── LiSteefelJun-2017.pdf │ ├── PestControl.ant │ ├── QL-datacom02.dbs │ ├── QL-saturation.dat │ └── ShortCourse7.in ├── Ex8Precipitation │ ├── .gitignore │ ├── Graph_Exercise8.gle │ ├── OldRifleDatabaseLiLi.dbs │ ├── PestControl.ant │ ├── ShortCourse8.in │ └── SteefelDruhanMaher-GES-10-FinalFinal.pdf ├── Ex9MicrobialSulfur │ ├── .gitignore │ ├── AqueousControl.ant │ ├── CatabolicControl.ant │ ├── CatabolicPathways_RifleColumn.dbs │ ├── Druhan_etal_2014(sulfur).pdf │ ├── Graph_Exercise9.gle │ ├── OldRifleDatabaseLiLi.dbs │ ├── PestControl.ant │ ├── ShortCourse9.in │ └── aqueousRifleColumn.dbs ├── Exercice11-diffusion.pptx └── Plot_files_with_GLE.zip ├── README.md ├── Source ├── .gitattributes ├── .gitignore ├── AllocateALL.F90 ├── AllocateGIMRT.F90 ├── AllocateGasesGimrt.F90 ├── AllocateGasesOS3D.F90 ├── AllocateOS3D.F90 ├── AqueousFluxInitialize.F90 ├── AqueousFluxWrite.F90 ├── AqueousToBulkConvert.F90 ├── AssembleGlobal.F90 ├── AssembleLocal.F90 ├── AverageRo.F90 ├── BreakFindPlusCount.F90 ├── BreakthroughInitialize.F90 ├── BreakthroughWrite.F90 ├── CPUdefinition.F90 ├── CalciteBulkStoichiometry.F90 ├── CalciteStoichiometry.F90 ├── CalciteStoichiometryBoundary.F90 ├── CalculateD.F90 ├── CalculateDHAD.F90 ├── CalculateTortuosity.F90 ├── CourantStep.F90 ├── CourantStepAlt.F90 ├── CrunchFlowNew.F90 ├── CrunchFunctions.F90 ├── CrunchModules.F90 ├── CrunchPETScFinalizeSolver.F90 ├── CrunchPETScInitializeChemistry.F90 ├── CrunchPETScInitializeDiffusion.F90 ├── CrunchPETScInitializePressure.F90 ├── CrunchPETScTolerances.F90 ├── CrunchTope.F90 ├── CrunchTopeDriver.F90 ├── EQ36-Read │ ├── ifnobl.f │ ├── ilnobl.f │ ├── ldbar2.f │ ├── ldbar3.f │ ├── lejust.f │ ├── locase.f │ ├── rdgrid.f │ └── rdpar.f ├── EasyRead │ ├── Easy_Read_and_Store.F90 │ ├── OpenInputFile.F90 │ └── Types_and_parameters.F90 ├── ExchangeConcentration.F90 ├── FRACTUREAPERTURE.F90 ├── FindMaxFlow.F90 ├── FirstAllocation.F90 ├── Flash.F90 ├── FluxWeightedConcentrationInitialize.F90 ├── FluxWeightedConcentrationWrite.F90 ├── FormatForNameList.F90 ├── FxTopeGlobal.F90 ├── FxTopeLocal.F90 ├── GIMRTCrunchPETScTolerances.F90 ├── GammaResidual.F90 ├── GasInjection.F90 ├── GasPartialPressure.F90 ├── GasPartialPressure_Init.F90 ├── GetMineralNumber.F90 ├── GetPrimarySpeciesNumber.F90 ├── GhostCells.F90 ├── GlobalArrayAllocation.F90 ├── GlobalDensity.F90 ├── GraphicsKaleidagraph.F90 ├── GraphicsTecplot.F90 ├── GraphicsVisit.F90 ├── GraphicsXmgr.F90 ├── InitializeCalciteStoichiometry.F90 ├── IsotopeBreakthroughInitialize.F90 ├── IsotopeBreakthroughWrite.F90 ├── JacPotentialLocal.F90 ├── JacobianCT.F90 ├── JacobianNumerical2.F90 ├── Makefile ├── Makefile.mak ├── MineralBreakthroughInitialize.F90 ├── MineralBreakthroughWrite.F90 ├── ModScan.F90 ├── NanoCrystal.F90 ├── NviewInit.F90 ├── NviewOutput.F90 ├── PHREEQc-Gamma.txt ├── ParseKineticMineralDatabase-TryNew.F90 ├── ParseKineticMineralDatabase.F90 ├── PauseFor.F90 ├── PestExchange.F90 ├── PestScaleOutput.F90 ├── PestSurface.F90 ├── PointByPointSolver.F90 ├── Pressure.F90 ├── PressureNS.F90 ├── PrimarySpeciesCheck.F90 ├── ReactionNumerical.F90 ├── ReadFileNameOnly.F90 ├── ReadFlow.F90 ├── ReadFlowField.F90 ├── ReadPressureCondition.F90 ├── ReadRestart.txt ├── ReadSaturation.F90 ├── RunTime.F90 ├── SolveDiffuse.F90 ├── SolveDiffuseSpherical.F90 ├── SolveGasDiffuse.F90 ├── SpeciesLocal.F90 ├── StartTope.F90 ├── SteadyState.F90 ├── SurfLocal.F90 ├── SurfaceCharge.F90 ├── SurfaceCharge_init.F90 ├── SurfaceComplex.F90 ├── SurfaceConcentration.F90 ├── TestIsotopeRead.F90 ├── UpdateExchanger.F90 ├── WaterReacted.F90 ├── WaterReactedNodeByNode.F90 ├── WriteRestart.txt ├── bd_diffuse.F90 ├── bd_diffuse_by_grid.F90 ├── bdcalc.F90 ├── bdexchange.F90 ├── bdgas.F90 ├── bdgas_by_grid.F90 ├── bdrecalc.F90 ├── bdrecalc_by_grid.F90 ├── bdsurf.F90 ├── breakfind.F90 ├── coeff.F90 ├── coeffCylinder.F90 ├── coeffCylinderDiffuse.F90 ├── coeffCylinderNUFT.F90 ├── coeffCylinder_D.F90 ├── coeffDiffuse.F90 ├── coeffNuft.F90 ├── coeffSphericalNew.F90 ├── coeffSphericalNew_d.F90 ├── coeff_D.F90 ├── concentration.F90 ├── convan.F90 ├── crunch_interface.F90 ├── crunchtype.F90 ├── database.F90 ├── databaseNEW.F90 ├── decay.F90 ├── decbt90.F90 ├── density.F90 ├── dispersivity.F90 ├── duan.F90 ├── equilib_co2.F90 ├── erosion.F90 ├── ex_activity.F90 ├── exactivity_init.F90 ├── exchange.F90 ├── exchange_init.F90 ├── find_condition.F90 ├── find_firststring.F90 ├── find_string.F90 ├── fit.F90 ├── fitgamma.F90 ├── flow.F90 ├── gamma.F90 ├── gammaUpdated.F90 ├── gamma_co2.F90 ├── gamma_init.F90 ├── gamma_init_co2.F90 ├── gamma_local.F90 ├── gascoeffCylinder.F90 ├── gasdiff.F90 ├── gases.F90 ├── gases_init.F90 ├── gases_init_co2.F90 ├── graphics3d.F90 ├── harmonic.F90 ├── hydraulic_function.F90 ├── interp.F90 ├── interp3.F90 ├── io.F90 ├── isotope-read_series.F90 ├── isotope.F90 ├── jac_exchange.F90 ├── jac_exchange_local.F90 ├── jac_local.F90 ├── jacexchange.F90 ├── jacexchange_init.F90 ├── jacgas.F90 ├── jacgas_local.F90 ├── jacminTope.F90 ├── jacobian.F90 ├── jacobian_init.F90 ├── jacobian_numerical.F90 ├── jacobian_plus.F90 ├── jacpotential.F90 ├── jacrkin.F90 ├── jacsurf.F90 ├── jacsurf_init.F90 ├── jacsurf_local.F90 ├── keqcalc2.F90 ├── keqcalc2_init.F90 ├── keqcalc2_init_co2.F90 ├── keqcalcGasOnly.F90 ├── lubksb90.F90 ├── ludcmp90.F90 ├── majuscules.F90 ├── medium.F90 ├── mindecay.F90 ├── mineral.F90 ├── mineral_update.F90 ├── mineralfind.F90 ├── modflowModule.F90 ├── modified_vanGenuchten_model.F90 ├── modified_vanGenuchten_model_kr.F90 ├── modread.F90 ├── movie.F90 ├── newfile.F90 ├── nrerror.F90 ├── oldcon.F90 ├── oldcongas.F90 ├── oldkd.F90 ├── oldsurf.F90 ├── oldsurface.F90 ├── os3d_newton.F90 ├── parameters.F90 ├── params.F90 ├── porcalc.F90 ├── porperm.F90 ├── ratecheck.F90 ├── reactionNEW.F90 ├── reactionTope.F90 ├── reactkin.F90 ├── read98.F90 ├── readCaseSensitive.F90 ├── readCaseSensitivePar.F90 ├── readFileName.F90 ├── readModFlowParameters.F90 ├── readModFlowStress.F90 ├── readRecharge.F90 ├── readSingleString.F90 ├── read_AqueousFluxSeries.F90 ├── read_BoundaryConditionsByZone.F90 ├── read_CatabolicPath.F90 ├── read_ConstantTortuosity.F90 ├── read_FluxSeries.F90 ├── read_FluxWeightedConcentration.F90 ├── read_Isotopes.F90 ├── read_Kd.F90 ├── read_MODFLOWfile.F90 ├── read_SolidDensity.F90 ├── read_TortuosityByZone.F90 ├── read_bound.F90 ├── read_burialfile.F90 ├── read_concentration.F90 ├── read_condition.F90 ├── read_constantflow.F90 ├── read_constantgasflow.F90 ├── read_coordinates.F90 ├── read_dbs.F90 ├── read_decay.F90 ├── read_diffusion.F90 ├── read_dispersion.F90 ├── read_eastriver.F90 ├── read_equil.F90 ├── read_erosion.F90 ├── read_evaporation.F90 ├── read_exchange.F90 ├── read_flowfile.F90 ├── read_gasdiffusion.F90 ├── read_gasflowfile.F90 ├── read_gaspump.F90 ├── read_graphics.F90 ├── read_gravity.F90 ├── read_het.F90 ├── read_infiltration.F90 ├── read_infiltration_2.f90 ├── read_integer.F90 ├── read_ionexchangeBS.F90 ├── read_ionexchangeMIN.F90 ├── read_kinetics_Bio.F90 ├── read_logical.F90 ├── read_master.F90 ├── read_mineral.F90 ├── read_mineralfile.F90 ├── read_minkin.F90 ├── read_minkin_TryNew.F90 ├── read_minseries.F90 ├── read_multpar.F90 ├── read_multstring.F90 ├── read_nuft.F90 ├── read_pH.F90 ├── read_par.F90 ├── read_permfile.F90 ├── read_permx.F90 ├── read_permxfile.F90 ├── read_permy.F90 ├── read_permyfile.F90 ├── read_permz.F90 ├── read_porosity.F90 ├── read_pressureAlternative.F90 ├── read_pump.F90 ├── read_pumpfile.F90 ├── read_pumplocations.F90 ├── read_pumplocationsfile.F90 ├── read_pumptimeseries.F90 ├── read_pumptimeseriesfile.F90 ├── read_restart.F90 ├── read_richards.F90 ├── read_series.F90 ├── read_snapshot.F90 ├── read_speciesdiffusion.F90 ├── read_steady.F90 ├── read_string.F90 ├── read_surface.F90 ├── read_surfacecomplex.F90 ├── read_temp.F90 ├── read_temperature.F90 ├── read_tempreg.F90 ├── read_tempregion.F90 ├── read_tempts.F90 ├── read_timeseries.F90 ├── read_title.F90 ├── read_toperatio.F90 ├── read_tortuosityfile.F90 ├── read_transpiration.F90 ├── read_vanGenuchten_parameters.F90 ├── read_walltime.F90 ├── readblock.F90 ├── readbreak.F90 ├── readtype1.F90 ├── readtype2.F90 ├── readtype3.F90 ├── readtypescan1.F90 ├── reallocate.F90 ├── restart.F90 ├── richards.F90 ├── rocalc.F90 ├── satcalc.F90 ├── solbt90.F90 ├── solver.F90 ├── speciation.F90 ├── species.F90 ├── species_init.F90 ├── squeeze.F90 ├── sschaine.F90 ├── sschaine_hyph.F90 ├── stringlen.F90 ├── strings.F90 ├── stringtype.F90 ├── surf_init.F90 ├── swap.F90 ├── temperature.F90 ├── timestep.F90 ├── tot_ex.F90 ├── totconc.F90 ├── totconc_init.F90 ├── totconc_plus.F90 ├── totexchange.F90 ├── totexchange_init.F90 ├── totexchange_local.F90 ├── totgas.F90 ├── totgas_init.F90 ├── totsurf.F90 ├── totsurf_init.F90 ├── totsurf_local.F90 ├── transport.F90 ├── tridag_ser.F90 ├── tvd.F90 ├── tvdNuft.F90 ├── units_concentration.F90 ├── units_distance.F90 ├── units_time.F90 ├── units_timeOutput.F90 ├── velocalc.F90 ├── velocalcNS.F90 ├── xmass.F90 ├── xmassNodeByNode.F90 ├── xtoolInit.F90 └── xtoolOutput.F90 ├── Windows ├── .gitignore ├── CrunchFlow.exe ├── CrunchTope.vfproj ├── MineralRead-OldVersion.txt └── ReadMe.txt ├── docs ├── CrunchCourseExerciseDescriptions.pdf ├── CrunchFlowManual.pdf ├── 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