diff --git a/.vscode/settings.json b/.vscode/settings.json index e29c489..88b76e8 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -2,6 +2,13 @@ "files.associations": { "MonodGrowth.C": "cpp", "phreeqcRM.C": "cpp", - "simpleFirstOrderKineticMole.C": "cpp" + "simpleFirstOrderKineticMole.C": "cpp", + "darcyFoam.C": "cpp", + "constantVelocityFoam.C": "cpp", + "impesFoam.C": "cpp", + "dbsFoam.C": "cpp", + "PDRFoam.C": "cpp", + "ostream": "cpp", + "KozenyCarman.C": "cpp" } } \ No newline at end of file diff --git a/Allwmake b/Allwmake index 63b9239..fa90b37 100755 --- a/Allwmake +++ b/Allwmake @@ -18,7 +18,7 @@ wmake libraries/porousBoundaryConditions # Compiling solvers wmake solvers/darcyFoam wmake solvers/impesFoam -wmake solvers/dbsSimpleFoam +#wmake solvers/dbsSimpleFoam wmake solvers/dbsFoam wmake solvers/constantVelocityFoam #wmake solvers/anisoImpesFoam diff --git a/libraries/porousModels/Make/files b/libraries/porousModels/Make/files index 82d5c27..1f57fe6 100644 --- a/libraries/porousModels/Make/files +++ b/libraries/porousModels/Make/files @@ -22,14 +22,6 @@ porousModels/absolutePermeabilityModels/heterogeneousScalarConstant/heterogeneou porousModels/absolutePermeabilityModels/ColebrookWhite/ColebrookWhite.C porousModels/absolutePermeabilityModels/none/none.C -porousModels/dispersionModels/dispersionModel/dispersionModel.C -porousModels/dispersionModels/dispersionModel/dispersionModelNew.C -porousModels/dispersionModels/linearDispersion/linearDispersion.C -porousModels/dispersionModels/archiesLaw/archiesLaw.C -porousModels/dispersionModels/taylorAris/taylorAris.C -porousModels/dispersionModels/diffusionOnly/diffusionOnly.C -porousModels/dispersionModels/dispersionNone/dispersionNone.C - porousModels/dispersionTensorModels/dispersionTensorModel/dispersionTensorModel.C porousModels/dispersionTensorModels/dispersionTensorModel/dispersionTensorModelNew.C diff --git a/libraries/porousModels/geochemicalModels/phreeqcRM/phreeqcRM.C b/libraries/porousModels/geochemicalModels/phreeqcRM/phreeqcRM.C index befe14f..fb857be 100644 --- a/libraries/porousModels/geochemicalModels/phreeqcRM/phreeqcRM.C +++ b/libraries/porousModels/geochemicalModels/phreeqcRM/phreeqcRM.C @@ -949,7 +949,7 @@ void Foam::geochemicalModels::phreeqcRM::updateMineralDistribution() { forAll(mineralList_,s) { - Ys_[s].storeOldTime(); + Ys_[s].storeOldTimes(); if(activatePhaseEquilibrium_[s] == true) { Ys_[s][i] = so[2*s*nxyz_ + i]*Vm_[s].value()*1e3; diff --git a/solvers/constantVelocityFoam/constantVelocityFoam.C b/solvers/constantVelocityFoam/constantVelocityFoam.C index d36e08a..64aa7a9 100644 --- a/solvers/constantVelocityFoam/constantVelocityFoam.C +++ b/solvers/constantVelocityFoam/constantVelocityFoam.C @@ -31,10 +31,16 @@ Developers - Cyprien Soulaine \*---------------------------------------------------------------------------*/ -#include "fvCFD.H" +#include "argList.H" #include "incompressiblePhase.H" #include "geochemicalModel.H" +#include "fvcFlux.H" +#include "fvcSurfaceIntegrate.H" + + +using namespace Foam; + // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // int main(int argc, char *argv[]) @@ -42,7 +48,7 @@ int main(int argc, char *argv[]) // argList::addOption("phase","a","specify the phase name"); // Foam::argList args(argc,argv); - #include "setRootCaseLists.H" + #include "setRootCase.H" #include "createTime.H" #include "createMesh.H" #include "createFields.H" diff --git a/solvers/constantVelocityFoam/createFields.H b/solvers/constantVelocityFoam/createFields.H index 95a7b52..cfa84d4 100644 --- a/solvers/constantVelocityFoam/createFields.H +++ b/solvers/constantVelocityFoam/createFields.H @@ -1,6 +1,22 @@ //word phaseName(""); //if (args.optionFound("phase")) phaseName = args.option("phase"); +Info << nl << "Reading field p\n" << endl; +volScalarField p +( + IOobject + ( + "p", + runTime.timeName(), + mesh, + IOobject::READ_IF_PRESENT, + IOobject::NO_WRITE + ), + mesh, + dimensionedScalar("p",dimPressure,1e5) +); + + Info << nl << "Reading field U\n" << endl; volVectorField U ( diff --git a/solvers/darcyFoam/darcyFoam.C b/solvers/darcyFoam/darcyFoam.C index 16e7f21..8d0ee9d 100644 --- a/solvers/darcyFoam/darcyFoam.C +++ b/solvers/darcyFoam/darcyFoam.C @@ -30,11 +30,26 @@ Description Developers - Pierre Horgue - 10/02/2020 - CS : modified with the porousModel class + - 17/11/2023 - CS : upgrade to v11 + \*---------------------------------------------------------------------------*/ -#include "fvCFD.H" + +#include "argList.H" #include "incompressiblePhase.H" #include "geochemicalModel.H" + +#include "uniformDimensionedFields.H" +//#include "fvcDdt.H" +//#include "fvcGrad.H" +#include "fvcFlux.H" +#include "fvcReconstruct.H" + +#include "fvmDdt.H" +//#include "fvmDiv.H" +#include "fvmLaplacian.H" + +using namespace Foam; //#include "porousModel.H" //#include "sourceEventFile.H" @@ -45,7 +60,7 @@ int main(int argc, char *argv[]) // argList::addOption("phase","a","specify the phase name"); // Foam::argList args(argc,argv); - #include "setRootCaseLists.H" + #include "setRootCase.H" #include "createTime.H" #include "createMesh.H" #include "readGravitationalAcceleration.H" @@ -88,7 +103,7 @@ Info<< "init OK " << nl << endl; // U.correctBoundaryConditions(); runTime.write(); - if(runTime.outputTime()) + if(runTime.writeTime()) { sourceTerm.write(); } diff --git a/solvers/dbsFoam/Make/options b/solvers/dbsFoam/Make/options index 0158a35..f6242d3 100644 --- a/solvers/dbsFoam/Make/options +++ b/solvers/dbsFoam/Make/options @@ -1,20 +1,29 @@ EXE_INC = \ + -I$(LIB_SRC)/physicalProperties/lnInclude \ + -I$(LIB_SRC)/thermophysicalModels/specie/lnInclude \ + -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \ + -I$(LIB_SRC)/MomentumTransportModels/momentumTransportModels/lnInclude \ + -I$(LIB_SRC)/MomentumTransportModels/compressible/lnInclude \ + -I$(LIB_SRC)/ThermophysicalTransportModels/thermophysicalTransportModel/lnInclude \ + -I$(LIB_SRC)/ThermophysicalTransportModels/fluid/lnInclude \ + -I$(LIB_SRC)/ThermophysicalTransportModels/fluidThermo/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ - -I$(LIB_SRC)/sampling/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude \ - -I$(LIB_SRC)/thermophysicalModels/specie/lnInclude \ + -I$(LIB_SRC)/triSurface/lnInclude \ -I../../libraries/porousModels/lnInclude \ -I../../libraries/otherModels/lnInclude \ -I../../ThirdParty/phreeqcrm/include \ EXE_LIBS = \ + -lmeshTools \ + -lspecie \ + -lmomentumTransportModels \ + -lcompressibleMomentumTransportModels \ -lfiniteVolume \ -lfvModels \ -lfvConstraints \ - -lsampling \ - -lmeshTools \ -lspecie \ -L$(FOAM_USER_LIBBIN) \ -lporousModels \ -lotherModels \ - -L../../ThirdParty/phreeqcrm/lib/ -lphreeqcrm-3.6.2 + -L../../ThirdParty/phreeqcrm/lib/ -lphreeqcrm-3.6.2 \ No newline at end of file diff --git a/solvers/dbsFoam/StCourantNo.H b/solvers/dbsFoam/StCourantNo.H new file mode 100644 index 0000000..378451d --- /dev/null +++ b/solvers/dbsFoam/StCourantNo.H @@ -0,0 +1,48 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Global + CourantNo + +Description + Calculates and outputs the mean and maximum Courant Numbers. + +\*---------------------------------------------------------------------------*/ + +{ + const scalarField sumPhi + ( + fvc::surfaceSum(mag(phiSt))().primitiveField() + /rho.primitiveField() + ); + + StCoNum = 0.5*gMax(sumPhi/mesh.V().field())*runTime.deltaTValue(); + + const scalar meanStCoNum = + 0.5*(gSum(sumPhi)/gSum(mesh.V().field()))*runTime.deltaTValue(); + + Info<< "St courant Number mean: " << meanStCoNum + << " max: " << StCoNum << endl; +} + +// ************************************************************************* // diff --git a/solvers/dbsFoam/UEqn.H b/solvers/dbsFoam/UEqn.H index 0b6c2ab..b0eb612 100644 --- a/solvers/dbsFoam/UEqn.H +++ b/solvers/dbsFoam/UEqn.H @@ -1,26 +1,21 @@ -// Solve the Momentum equation + fvVectorMatrix UEqn + ( + 1./(eps+SMALL)*(fvm::ddt(U) + fvm::div(phi, U)) + // - fvm::laplacian(turbulence->nu()/(eps+SMALL),U, "laplacian(nu,U)") + // + fvm::Sp(turbulence->nu()*invK,U) + - fvm::laplacian(nu/(eps+SMALL),U, "laplacian(nu,U)") + + fvm::Sp(nu*invK,U) + == + fvModels.source(U) + ); -MRF.correctBoundaryVelocity(U); + UEqn.relax(); -tmp tUEqn -( - 1./(eps+SMALL)*(fvm::ddt(U) + fvm::div(phi, U)) -// - fvm::laplacian(turbulence->nu()/(eps+SMALL),U, "laplacian(nu,U)") -// + fvm::Sp(turbulence->nu()*invK,U) - - fvm::laplacian(nu/(eps+SMALL),U, "laplacian(nu,U)") - + fvm::Sp(nu*invK,U) - == - fvModels.source(U) -); -fvVectorMatrix& UEqn = tUEqn.ref(); + fvConstraints.constrain(UEqn); -UEqn.relax(); + if (pimple.momentumPredictor()) + { + solve(UEqn == -fvc::grad(p)); -fvConstraints.constrain(UEqn); - -if (pimple.momentumPredictor()) -{ - solve(UEqn == -fvc::grad(p)); - - fvConstraints.constrain(U); -} + fvConstraints.constrain(U); + } \ No newline at end of file diff --git a/solvers/dbsFoam/createFieldRefs.H b/solvers/dbsFoam/createFieldRefs.H new file mode 100644 index 0000000..502b3b4 --- /dev/null +++ b/solvers/dbsFoam/createFieldRefs.H @@ -0,0 +1 @@ +const volScalarField& psi = thermo.psi(); diff --git a/solvers/dbsFoam/createFields.H b/solvers/dbsFoam/createFields.H index 593e8b4..3d5eaf0 100644 --- a/solvers/dbsFoam/createFields.H +++ b/solvers/dbsFoam/createFields.H @@ -1,4 +1,3 @@ -#include "createRDeltaT.H" Info<< "Reading field p\n" << endl; volScalarField p @@ -14,13 +13,13 @@ volScalarField p mesh ); -Info<< "Reading field U\n" << endl; +Info<< "\nReading field U\n" << endl; volVectorField U ( IOobject ( "U", - runTime.timeName(), + runTime.name(), mesh, IOobject::MUST_READ, IOobject::AUTO_WRITE @@ -30,8 +29,6 @@ volVectorField U #include "createPhi.H" -pressureReference pressureReference(p, pimple.dict()); - mesh.schemes().setFluxRequired(p.name()); @@ -51,7 +48,27 @@ volScalarField sourceTerm ); -IOdictionary transportProperties + +/* +Info<< "Creating field dpdt\n" << endl; +volScalarField dpdt +( + IOobject + ( + "dpdt", + runTime.name(), + mesh + ), + mesh, + dimensionedScalar(p.dimensions()/dimTime, 0) +); + +Info<< "Creating field kinetic energy K\n" << endl; +volScalarField K("K", 0.5*magSqr(U)); +*/ + + +IOdictionary physicalProperties ( IOobject ( @@ -63,10 +80,7 @@ IOdictionary transportProperties ) ); -//autoPtr geochemistry -// = geochemicalModel::New(mesh,transportProperties); - -geochemicalModel geochemistry(mesh,transportProperties); +geochemicalModel geochemistry(mesh,physicalProperties); Info << nl << "Reading/generating porosity field eps" << endl; @@ -78,7 +92,7 @@ const volScalarField & invK = geochemistry.inversePermeability(); Switch activateHeleShaw ( - transportProperties.lookupOrDefault("activateHeleShaw",false) + physicalProperties.lookupOrDefault("activateHeleShaw",false) ); @@ -86,7 +100,7 @@ volScalarField HeleShawCorrection ("HeleShawCorrection", 0.0*invK); if (activateHeleShaw) { - Foam::absolutePermeabilityModels::HeleShaw HeleShaw(mesh,transportProperties); + Foam::absolutePermeabilityModels::HeleShaw HeleShaw(mesh,physicalProperties); HeleShawCorrection = HeleShaw.inversePermeability(); Info << "HeleShaw correction is activated" << nl << endl; } @@ -94,19 +108,6 @@ if (activateHeleShaw) const volScalarField & nu = geochemistry.nu(); -/* -Info << nl << "Reading/generating momentumTransportModel"; -//autoPtr viscosity(viscosityModel::New(mesh)); - - -autoPtr turbulence -( - incompressible::momentumTransportModel::New(U, phi, geochemistry.viscosity()) -); -Info << " ... OK" << endl; -*/ - - #include "createMRF.H" #include "createFvModels.H" #include "createFvConstraints.H" diff --git a/solvers/dbsFoam/dbsFoam.C b/solvers/dbsFoam/dbsFoam.C index 7aa843b..16c3731 100644 --- a/solvers/dbsFoam/dbsFoam.C +++ b/solvers/dbsFoam/dbsFoam.C @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation + \\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation \\/ M anipulation | ------------------------------------------------------------------------------- License @@ -22,29 +22,43 @@ License along with OpenFOAM. If not, see . Application - pimpleFoam + PDRFoam Description - Transient solver for incompressible, turbulent flow of Newtonian fluids, - with optional mesh motion and mesh topology changes. - Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected. \*---------------------------------------------------------------------------*/ -#include "fvCFD.H" -//#include "viscosityModel.H" -//#include "incompressibleMomentumTransportModels.H" +#include "argList.H" +#include "timeSelector.H" + + #include "pimpleControl.H" #include "pressureReference.H" -#include "CorrectPhi.H" +#include "findRefCell.H" +#include "constrainPressure.H" +#include "constrainHbyA.H" +#include "adjustPhi.H" +#include "uniformDimensionedFields.H" #include "fvModels.H" #include "fvConstraints.H" -#include "localEulerDdtScheme.H" + +#include "fvcDdt.H" +#include "fvcGrad.H" +#include "fvcFlux.H" +#include "fvcReconstruct.H" +#include "fvcMeshPhi.H" + +#include "fvmDdt.H" +#include "fvmDiv.H" +#include "fvmLaplacian.H" + + #include "fvcSmooth.H" #include "geochemicalModel.H" #include "HeleShaw.H" +using namespace Foam; // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // @@ -52,21 +66,20 @@ int main(int argc, char *argv[]) { #include "postProcess.H" - #include "setRootCaseLists.H" + #include "setRootCase.H" #include "createTime.H" #include "createMesh.H" - #include "initContinuityErrs.H" - #include "createDyMControls.H" + #include "createControl.H" + #include "readGravitationalAcceleration.H" #include "createFields.H" - #include "createUfIfPresent.H" - -// turbulence->validate(); + // #include "createFieldRefs.H" + #include "initContinuityErrs.H" + #include "createTimeControls.H" + #include "CourantNo.H" + #include "setInitialDeltaT.H" - if (!LTS) - { - #include "CourantNo.H" - #include "setInitialDeltaT.H" - } + //turbulence->validate(); + scalar StCoNum = 0.0; // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // @@ -74,53 +87,26 @@ int main(int argc, char *argv[]) while (pimple.run(runTime)) { - #include "readDyMControls.H" - - if (LTS) - { - #include "setRDeltaT.H" - } - else - { - #include "CourantNo.H" - #include "setDeltaT.H" - } - - fvModels.preUpdateMesh(); - - // Update the mesh for topology change, mesh to mesh mapping - mesh.update(); + #include "readTimeControls.H" + #include "CourantNo.H" + #include "setDeltaT.H" runTime++; + Info<< "\n\nTime = " << runTime.name() << endl; - Info<< "Time = " << runTime.userTimeName() << nl << endl; +// #include "rhoEqn.H" // --- Pressure-velocity PIMPLE corrector loop while (pimple.loop()) { - if (pimple.firstPimpleIter() || moveMeshOuterCorrectors) + fvModels.correct(); + + if (pimple.predictTransport()) { - // Move the mesh - mesh.move(); - - if (mesh.changing()) - { - MRF.update(); - - if (correctPhi) - { - #include "correctPhi.H" - } - - if (checkMeshCourantNo) - { - #include "meshCourantNo.H" - } - } + // turbulence->predict(); + // thermophysicalTransport.predict(); } - fvModels.correct(); - #include "UEqn.H" // --- Pressure corrector loop @@ -129,22 +115,22 @@ int main(int argc, char *argv[]) #include "pEqn.H" } - if (pimple.turbCorr()) + if (pimple.correctTransport()) { - // viscosity->correct(); - // turbulence->correct(); - geochemistry.update(); + // turbulence->correct(); + // thermophysicalTransport.correct(); + geochemistry.update(); } } runTime.write(); - Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s" - << " ClockTime = " << runTime.elapsedClockTime() << " s" - << nl << endl; + Info<< "\nExecutionTime = " + << runTime.elapsedCpuTime() + << " s\n" << endl; } - Info<< "End\n" << endl; + Info<< "\n end\n"; return 0; } diff --git a/solvers/dbsFoam/pEqn.H b/solvers/dbsFoam/pEqn.H index f820869..1ad24e6 100644 --- a/solvers/dbsFoam/pEqn.H +++ b/solvers/dbsFoam/pEqn.H @@ -1,73 +1,54 @@ +//rho = thermo.rho(); + volScalarField rAU(1.0/UEqn.A()); volVectorField HbyA(constrainHbyA(rAU*UEqn.H(), U, p)); -surfaceScalarField phiHbyA -( - "phiHbyA", - fvc::flux(HbyA) - + MRF.zeroFilter(fvc::interpolate(rAU)*fvc::ddtCorr(U, phi, Uf)) -); - -MRF.makeRelative(phiHbyA); - -if (p.needReference()) -{ - fvc::makeRelative(phiHbyA, U); - adjustPhi(phiHbyA, U, p); - fvc::makeAbsolute(phiHbyA, U); -} tmp rAtU(rAU); -if (pimple.consistent()) { - rAtU = 1.0/max(1.0/rAU - UEqn.H1(), 0.1/rAU); - phiHbyA += - fvc::interpolate(rAtU() - rAU)*fvc::snGrad(p)*mesh.magSf(); - HbyA -= (rAU - rAtU())*fvc::grad(p); -} - -if (pimple.nCorrPiso() <= 1) -{ - tUEqn.clear(); -} - -// Update the pressure BCs to ensure flux consistency -constrainPressure(p, U, phiHbyA, rAtU(), MRF); - -// Non-orthogonal pressure corrector loop -while (pimple.correctNonOrthogonal()) -{ - fvScalarMatrix pEqn - ( - fvm::laplacian(rAtU(), p) == fvc::div(phiHbyA) - sourceTerm - ); - - pEqn.setReference + surfaceScalarField phiHbyA ( - pressureReference.refCell(), - pressureReference.refValue() + "phiHbyA", + ( + fvc::flux(HbyA) +// + fvc::interpolate(rAU)*fvc::ddtCorr(rho, U, phi) + + fvc::interpolate(rAU)*fvc::ddtCorr(U, phi) + ) ); - pEqn.solve(); - - if (pimple.finalNonOrthogonalIter()) + while (pimple.correctNonOrthogonal()) { - phi = phiHbyA - pEqn.flux(); + fvScalarMatrix pEqn + ( + fvc::div(phiHbyA) + - fvm::laplacian(rAtU(), p) + - sourceTerm +// == +// betav*fvModels.source(psi, p, rho.name()) + ); + + pEqn.solve(); + + if (pimple.finalNonOrthogonalIter()) + { + phi = phiHbyA + pEqn.flux(); + } } } +//#include "rhoEqn.H" #include "continuityErrs.H" // Explicitly relax pressure for momentum corrector p.relax(); +//U = HbyA - (invA & (betav*fvc::grad(p))); U = fvc::reconstruct(phi); -//U = HbyA - rAtU*fvc::grad(p); U.correctBoundaryConditions(); fvConstraints.constrain(U); +//K = 0.5*magSqr(U); -// Correct Uf if the mesh is moving -fvc::correctUf(Uf, U, phi, MRF); - -// Make the fluxes relative to the mesh motion -fvc::makeRelative(phi, U); +//if (thermo.dpdt()) +//{ +// dpdt = fvc::ddt(p); +//} diff --git a/solvers/dbsFoam/rhoEqn.H b/solvers/dbsFoam/rhoEqn.H new file mode 100644 index 0000000..2bd54bf --- /dev/null +++ b/solvers/dbsFoam/rhoEqn.H @@ -0,0 +1,36 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Global + rhoEqn + +Description + Solve the continuity for density. + +\*---------------------------------------------------------------------------*/ + +{ + solve(betav*fvm::ddt(rho) + fvc::div(phi)); +} + +// ************************************************************************* // diff --git a/solvers/dbsFoam/setDeltaT.H b/solvers/dbsFoam/setDeltaT.H new file mode 100644 index 0000000..958210c --- /dev/null +++ b/solvers/dbsFoam/setDeltaT.H @@ -0,0 +1,48 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Global + setDeltaT + +Description + Reset the timestep to maintain a constant maximum courant Number. + Reduction of time-step is immediate but increase is damped to avoid + unstable oscillations. + +\*---------------------------------------------------------------------------*/ + +if (adjustTimeStep) +{ + scalar deltaT = maxCo*runTime.deltaTValue()/(CoNum + StCoNum + small); + deltaT = min(deltaT, fvModels.maxDeltaT()); + deltaT = min + ( + min(deltaT, runTime.deltaTValue() + 0.1*deltaT), + 1.2*runTime.deltaTValue() + ); + runTime.setDeltaT(min(deltaT, maxDeltaT)); + + Info<< "deltaT = " << runTime.deltaTValue() << endl; +} + +// ************************************************************************* // diff --git a/solvers/dbsFoamOld/Make/files b/solvers/dbsFoamOld/Make/files new file mode 100644 index 0000000..aaa1f69 --- /dev/null +++ b/solvers/dbsFoamOld/Make/files @@ -0,0 +1,3 @@ +dbsFoam.C + +EXE = $(FOAM_USER_APPBIN)/dbsFoam diff --git a/solvers/dbsFoamOld/Make/options b/solvers/dbsFoamOld/Make/options new file mode 100644 index 0000000..0158a35 --- /dev/null +++ b/solvers/dbsFoamOld/Make/options @@ -0,0 +1,20 @@ +EXE_INC = \ + -I$(LIB_SRC)/finiteVolume/lnInclude \ + -I$(LIB_SRC)/sampling/lnInclude \ + -I$(LIB_SRC)/meshTools/lnInclude \ + -I$(LIB_SRC)/thermophysicalModels/specie/lnInclude \ + -I../../libraries/porousModels/lnInclude \ + -I../../libraries/otherModels/lnInclude \ + -I../../ThirdParty/phreeqcrm/include \ + +EXE_LIBS = \ + -lfiniteVolume \ + -lfvModels \ + -lfvConstraints \ + -lsampling \ + -lmeshTools \ + -lspecie \ + -L$(FOAM_USER_LIBBIN) \ + -lporousModels \ + -lotherModels \ + -L../../ThirdParty/phreeqcrm/lib/ -lphreeqcrm-3.6.2 diff --git a/solvers/dbsFoamOld/UEqn.H b/solvers/dbsFoamOld/UEqn.H new file mode 100644 index 0000000..0b6c2ab --- /dev/null +++ b/solvers/dbsFoamOld/UEqn.H @@ -0,0 +1,26 @@ +// Solve the Momentum equation + +MRF.correctBoundaryVelocity(U); + +tmp tUEqn +( + 1./(eps+SMALL)*(fvm::ddt(U) + fvm::div(phi, U)) +// - fvm::laplacian(turbulence->nu()/(eps+SMALL),U, "laplacian(nu,U)") +// + fvm::Sp(turbulence->nu()*invK,U) + - fvm::laplacian(nu/(eps+SMALL),U, "laplacian(nu,U)") + + fvm::Sp(nu*invK,U) + == + fvModels.source(U) +); +fvVectorMatrix& UEqn = tUEqn.ref(); + +UEqn.relax(); + +fvConstraints.constrain(UEqn); + +if (pimple.momentumPredictor()) +{ + solve(UEqn == -fvc::grad(p)); + + fvConstraints.constrain(U); +} diff --git a/solvers/dbsFoam/correctPhi.H b/solvers/dbsFoamOld/correctPhi.H similarity index 100% rename from solvers/dbsFoam/correctPhi.H rename to solvers/dbsFoamOld/correctPhi.H diff --git a/solvers/dbsFoamOld/createFields.H b/solvers/dbsFoamOld/createFields.H new file mode 100644 index 0000000..593e8b4 --- /dev/null +++ b/solvers/dbsFoamOld/createFields.H @@ -0,0 +1,112 @@ +#include "createRDeltaT.H" + +Info<< "Reading field p\n" << endl; +volScalarField p +( + IOobject + ( + "p", + runTime.timeName(), + mesh, + IOobject::MUST_READ, + IOobject::AUTO_WRITE + ), + mesh +); + +Info<< "Reading field U\n" << endl; +volVectorField U +( + IOobject + ( + "U", + runTime.timeName(), + mesh, + IOobject::MUST_READ, + IOobject::AUTO_WRITE + ), + mesh +); + +#include "createPhi.H" + +pressureReference pressureReference(p, pimple.dict()); + +mesh.schemes().setFluxRequired(p.name()); + + +Info<< "Reading field sourceTerm\n" << endl; +volScalarField sourceTerm +( + IOobject + ( + "sourceTerm", + runTime.timeName(), + mesh, + IOobject::READ_IF_PRESENT, + IOobject::AUTO_WRITE + ), + mesh, + dimensionedScalar("sourceTerm",dimensionSet(0,0,-1,0,0,0,0),0.0) +); + + +IOdictionary transportProperties +( + IOobject + ( + "physicalProperties", + runTime.constant(), + mesh, + IOobject::MUST_READ_IF_MODIFIED, + IOobject::NO_WRITE + ) +); + +//autoPtr geochemistry +// = geochemicalModel::New(mesh,transportProperties); + +geochemicalModel geochemistry(mesh,transportProperties); + + +Info << nl << "Reading/generating porosity field eps" << endl; +const volScalarField & eps = geochemistry.porosity(); + +Info << nl << "Reading/generating permeability field invK" << endl; +const volScalarField & invK = geochemistry.inversePermeability(); + + +Switch activateHeleShaw +( + transportProperties.lookupOrDefault("activateHeleShaw",false) +); + + +volScalarField HeleShawCorrection ("HeleShawCorrection", 0.0*invK); + +if (activateHeleShaw) +{ + Foam::absolutePermeabilityModels::HeleShaw HeleShaw(mesh,transportProperties); + HeleShawCorrection = HeleShaw.inversePermeability(); + Info << "HeleShaw correction is activated" << nl << endl; +} + +const volScalarField & nu = geochemistry.nu(); + + +/* +Info << nl << "Reading/generating momentumTransportModel"; +//autoPtr viscosity(viscosityModel::New(mesh)); + + +autoPtr turbulence +( + incompressible::momentumTransportModel::New(U, phi, geochemistry.viscosity()) +); +Info << " ... OK" << endl; +*/ + + +#include "createMRF.H" +#include "createFvModels.H" +#include "createFvConstraints.H" diff --git a/solvers/dbsFoamOld/createRDeltaT.H b/solvers/dbsFoamOld/createRDeltaT.H new file mode 100644 index 0000000..8482866 --- /dev/null +++ b/solvers/dbsFoamOld/createRDeltaT.H @@ -0,0 +1,26 @@ +bool LTS = fv::localEulerDdt::enabled(mesh); + +tmp trDeltaT; + +if (LTS) +{ + Info<< "Using LTS" << endl; + + trDeltaT = tmp + ( + new volScalarField + ( + IOobject + ( + fv::localEulerDdt::rDeltaTName, + runTime.timeName(), + mesh, + IOobject::READ_IF_PRESENT, + IOobject::AUTO_WRITE + ), + mesh, + dimensionedScalar(dimless/dimTime, 1), + extrapolatedCalculatedFvPatchScalarField::typeName + ) + ); +} diff --git a/solvers/dbsFoamOld/createUfIfPresent.H b/solvers/dbsFoamOld/createUfIfPresent.H new file mode 100644 index 0000000..715c5d2 --- /dev/null +++ b/solvers/dbsFoamOld/createUfIfPresent.H @@ -0,0 +1,54 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2017-2018 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Global + createUfIfPresent + +Description + Creates and initialises the velocity field Uf if required. + +\*---------------------------------------------------------------------------*/ + +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + +autoPtr Uf; + +if (mesh.dynamic()) +{ + Info<< "Constructing face velocity Uf\n" << endl; + + Uf = new surfaceVectorField + ( + IOobject + ( + "Uf", + runTime.timeName(), + mesh, + IOobject::READ_IF_PRESENT, + IOobject::AUTO_WRITE + ), + fvc::interpolate(U) + ); +} + +// ************************************************************************* // diff --git a/solvers/dbsFoamOld/dbsFoam.C b/solvers/dbsFoamOld/dbsFoam.C new file mode 100644 index 0000000..62c0d78 --- /dev/null +++ b/solvers/dbsFoamOld/dbsFoam.C @@ -0,0 +1,175 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Application + pimpleFoam + +Description + Transient solver for incompressible, turbulent flow of Newtonian fluids, + with optional mesh motion and mesh topology changes. + + Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected. + +\*---------------------------------------------------------------------------*/ + +//#include "fvCFD.H" +//#include "viscosityModel.H" +//#include "incompressibleMomentumTransportModels.H" + +#include "argList.H" +#include "timeSelector.H" +#include "pimpleControl.H" + +#include "pressureReference.H" +#include "CorrectPhi.H" +#include "fvModels.H" +#include "fvConstraints.H" +#include "localEulerDdtScheme.H" + +#include "constrainPressure.H" +#include "constrainHbyA.H" +#include "adjustPhi.H" + +#include "fvCorrectPhi.H" + +#include "fvcFlux.H" +#include "fvcReconstruct.H" +#include "fvcDdt.H" +#include "fvcSnGrad.H" + +#include "fvmDdt.H" +#include "fvmDiv.H" +#include "fvmLaplacian.H" + + +#include "fvcSmooth.H" +#include "geochemicalModel.H" +#include "HeleShaw.H" + +using namespace Foam; + +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + +int main(int argc, char *argv[]) +{ + #include "postProcess.H" + + #include "setRootCase.H" + #include "createTime.H" + #include "createMesh.H" + #include "initContinuityErrs.H" + #include "createDyMControls.H" + #include "createFields.H" + #include "createUfIfPresent.H" + +// turbulence->validate(); + + if (!LTS) + { + #include "CourantNo.H" + #include "setInitialDeltaT.H" + } + + // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + + Info<< "\nStarting time loop\n" << endl; + + while (pimple.run(runTime)) + { + #include "readDyMControls.H" + + if (LTS) + { + #include "setRDeltaT.H" + } + else + { + #include "CourantNo.H" + #include "setDeltaT.H" + } + + fvModels.preUpdateMesh(); + + // Update the mesh for topology change, mesh to mesh mapping + mesh.update(); + + runTime++; + + Info<< "Time = " << runTime.userTimeName() << nl << endl; + + // --- Pressure-velocity PIMPLE corrector loop + while (pimple.loop()) + { + if (pimple.firstPimpleIter() || moveMeshOuterCorrectors) + { + // Move the mesh + mesh.move(); + + if (mesh.changing()) + { + MRF.update(); + + if (correctPhi) + { + #include "correctPhi.H" + } + + if (checkMeshCourantNo) + { + #include "meshCourantNo.H" + } + } + } + + fvModels.correct(); + + #include "UEqn.H" + + // --- Pressure corrector loop + while (pimple.correct()) + { + #include "pEqn.H" + } + + if (pimple.correctTransport()) + { + // viscosity->correct(); + // turbulence->correct(); + geochemistry.update(); + } + } + + runTime.write(); + + Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s" + << " ClockTime = " << runTime.elapsedClockTime() << " s" + << nl << endl; + } + + Info<< "End\n" << endl; + + return 0; +} + + +// ************************************************************************* // diff --git a/solvers/dbsFoamOld/meshCourantNo.H b/solvers/dbsFoamOld/meshCourantNo.H new file mode 100644 index 0000000..f8eea4c --- /dev/null +++ b/solvers/dbsFoamOld/meshCourantNo.H @@ -0,0 +1,50 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Copyright (C) 2011-2021 OpenFOAM Foundation + \\/ M anipulation | +------------------------------------------------------------------------------- +License + This file is part of OpenFOAM. + + OpenFOAM is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OpenFOAM is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License + along with OpenFOAM. If not, see . + +Global + meshCourantNo + +Description + Calculates and outputs the mean and maximum Courant Numbers. + +\*---------------------------------------------------------------------------*/ + +scalar meshCoNum = 0.0; +scalar meanMeshCoNum = 0.0; + +{ + scalarField sumPhi + ( + fvc::surfaceSum(mag(mesh.phi()))().primitiveField() + ); + + meshCoNum = 0.5*gMax(sumPhi/mesh.V().field())*runTime.deltaTValue(); + + meanMeshCoNum = + 0.5*(gSum(sumPhi)/gSum(mesh.V().field()))*runTime.deltaTValue(); +} + +Info<< "Mesh Courant Number mean: " << meanMeshCoNum + << " max: " << meshCoNum << endl; + +// ************************************************************************* // diff --git a/solvers/dbsFoamOld/pEqn.H b/solvers/dbsFoamOld/pEqn.H new file mode 100644 index 0000000..f820869 --- /dev/null +++ b/solvers/dbsFoamOld/pEqn.H @@ -0,0 +1,73 @@ +volScalarField rAU(1.0/UEqn.A()); +volVectorField HbyA(constrainHbyA(rAU*UEqn.H(), U, p)); +surfaceScalarField phiHbyA +( + "phiHbyA", + fvc::flux(HbyA) + + MRF.zeroFilter(fvc::interpolate(rAU)*fvc::ddtCorr(U, phi, Uf)) +); + +MRF.makeRelative(phiHbyA); + +if (p.needReference()) +{ + fvc::makeRelative(phiHbyA, U); + adjustPhi(phiHbyA, U, p); + fvc::makeAbsolute(phiHbyA, U); +} + +tmp rAtU(rAU); + +if (pimple.consistent()) +{ + rAtU = 1.0/max(1.0/rAU - UEqn.H1(), 0.1/rAU); + phiHbyA += + fvc::interpolate(rAtU() - rAU)*fvc::snGrad(p)*mesh.magSf(); + HbyA -= (rAU - rAtU())*fvc::grad(p); +} + +if (pimple.nCorrPiso() <= 1) +{ + tUEqn.clear(); +} + +// Update the pressure BCs to ensure flux consistency +constrainPressure(p, U, phiHbyA, rAtU(), MRF); + +// Non-orthogonal pressure corrector loop +while (pimple.correctNonOrthogonal()) +{ + fvScalarMatrix pEqn + ( + fvm::laplacian(rAtU(), p) == fvc::div(phiHbyA) - sourceTerm + ); + + pEqn.setReference + ( + pressureReference.refCell(), + pressureReference.refValue() + ); + + pEqn.solve(); + + if (pimple.finalNonOrthogonalIter()) + { + phi = phiHbyA - pEqn.flux(); + } +} + +#include "continuityErrs.H" + +// Explicitly relax pressure for momentum corrector +p.relax(); + +U = fvc::reconstruct(phi); +//U = HbyA - rAtU*fvc::grad(p); +U.correctBoundaryConditions(); +fvConstraints.constrain(U); + +// Correct Uf if the mesh is moving +fvc::correctUf(Uf, U, phi, MRF); + +// Make the fluxes relative to the mesh motion +fvc::makeRelative(phi, U); diff --git a/solvers/dbsFoam/setRDeltaT.H b/solvers/dbsFoamOld/setRDeltaT.H similarity index 100% rename from solvers/dbsFoam/setRDeltaT.H rename to solvers/dbsFoamOld/setRDeltaT.H diff --git a/solvers/impesFoam/impesFoam.C b/solvers/impesFoam/impesFoam.C index 3140955..2f6003d 100644 --- a/solvers/impesFoam/impesFoam.C +++ b/solvers/impesFoam/impesFoam.C @@ -40,7 +40,7 @@ Developers \*---------------------------------------------------------------------------*/ -#include "fvCFD.H" +#include "argList.H" #include "harmonic.H" #include "incompressiblePhase.H" #include "unsaturatedPorousModel.H" @@ -51,9 +51,23 @@ Developers //#include "patchEventFile.H" //#include "eventInfiltration.H" -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // +#include "uniformDimensionedFields.H" + +#include "fvcSnGrad.H" +#include "fvcFlux.H" +#include "fvcSurfaceIntegrate.H" +#include "fvcReconstruct.H" + +#include "fvmDdt.H" +//#include "fvmDiv.H" +#include "fvmLaplacian.H" + +#include "fixedValueFvPatchField.H" + using namespace Foam; +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + int main(int argc, char *argv[]) { #include "setRootCase.H" @@ -92,7 +106,7 @@ int main(int argc, char *argv[]) // #include "eventWrite.H" - if(runTime.outputTime()) + if(runTime.writeTime()) { runTime.write(); } diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/U b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/U similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/U rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/U diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite similarity index 95% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite index 70d5587..c670a04 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite similarity index 95% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite index 882d92b..980b5c8 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/Ys.Dolomite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/inertMineral b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/inertMineral similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/inertMineral rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/inertMineral diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/p b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/p similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/p rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/0/p diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allclean b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allrun b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allrun new file mode 100755 index 0000000..e99eda6 --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/Allrun @@ -0,0 +1,21 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -time 1200,2400,3600 -func graphCell + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/README.txt b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/README.txt similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/README.txt rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/README.txt diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/g b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/g similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/g rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/g diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqc.dat b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqc.dat similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqc.dat rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqc.dat diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqcInput b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqcInput similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqcInput rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/phreeqcInput diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/transportProperties b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/physicalProperties similarity index 94% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/transportProperties rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/physicalProperties index 99ff951..cce3bc1 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/transportProperties +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/physicalProperties @@ -25,6 +25,13 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plot.gp b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plot.gp similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plot.gp rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plot.gp diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip0600.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip0600.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip0600.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip0600.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1200.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1200.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1200.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1200.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1800.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1800.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1800.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip1800.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip2400.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip2400.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip2400.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip2400.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3000.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3000.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3000.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3000.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3600.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3600.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3600.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/CalciteDissDoloPrecip3600.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.log b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.log similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.log rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.log diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.phr b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.phr similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.phr rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/plots/phreeqcRun.phr diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/blockMeshDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/blockMeshDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/blockMeshDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/blockMeshDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict similarity index 93% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict index 9130d72..47fd7aa 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application dbsPhreeqcFoam; +application constantVelocityFoam; startFrom latestTime; @@ -25,7 +25,7 @@ stopAt endTime; endTime 3600; -deltaT 0.75; +deltaT 0.5; //75; writeControl runTime; @@ -47,7 +47,7 @@ runTimeModifiable true; maxCo 10; // Or other Courant number you wish -adjustTimeStep yes; // Or no +adjustTimeStep no; // Or no maxDeltaT 0.75; //Maximum deltaT in seconds diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/decomposeParDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/decomposeParDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/decomposeParDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/decomposeParDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSchemes b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSchemes similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSchemes rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSchemes diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSolution b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSolution similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSolution rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/fvSolution diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/graphCell b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/graphCell similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/graphCell rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/graphCell diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/mapFieldsDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/mapFieldsDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/mapFieldsDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/mapFieldsDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sG b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sG similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sG rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sG diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sampleDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sampleDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sampleDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/sampleDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/setFieldsDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/setFieldsDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/setFieldsDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/setFieldsDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/snappyHexMeshDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/snappyHexMeshDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/snappyHexMeshDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/system/snappyHexMeshDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/U b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/U similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/U rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/U diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite similarity index 95% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite index 70d5587..c670a04 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/inertMineral b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/inertMineral similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/inertMineral rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/inertMineral diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/p b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/p similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/p rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/p diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allclean b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allrun b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allrun new file mode 100755 index 0000000..d9086ee --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/Allrun @@ -0,0 +1,21 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -func graphCell + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/README.txt b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/README.txt similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/README.txt rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/README.txt diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/CalciteDiss_KinEq.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/CalciteDiss_KinEq.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/CalciteDiss_KinEq.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/CalciteDiss_KinEq.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.dat b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.dat similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.dat rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.dat diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.log b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.log similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.log rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqc.log diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcInput b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcInput similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcInput rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcInput diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.log b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.log similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.log rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.log diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.phr b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.phr similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.phr rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/phreeqcRun.phr diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/transportProperties b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/physicalProperties similarity index 91% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/transportProperties rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/physicalProperties index 706f522..b4db3a4 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/transportProperties +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/constant/physicalProperties @@ -28,6 +28,14 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + + } geochemicalModel phreeqcRM; @@ -60,10 +68,10 @@ geochemicalProperties rhos rhos [1 -3 0 0 0 0 0] 2707; Vm Vm [0 3 0 0 -1 0 0] 36.93336e-6; surfaceAreaModel constantSurfaceArea; - constantSurfaceAreaCoeffs - { - A0 A0 [0 -1 0 0 0 0 0] 1; - } + constantSurfaceAreaCoeffs + { + A0 A0 [0 -1 0 0 0 0 0] 1; + } } phreeqcRM diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T20 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T20 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T20 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T20 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T40 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T40 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T40 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T40 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T60 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T60 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T60 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/T60 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/runFile b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/runFile similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/runFile rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/phreeqcDataExtraction/runFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/plot.gp b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/plot.gp similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/plot.gp rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/plot.gp diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/blockMeshDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/blockMeshDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/blockMeshDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/blockMeshDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict similarity index 93% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict index 9130d72..e363117 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application dbsPhreeqcFoam; +application constantVelocityFoam; startFrom latestTime; @@ -25,7 +25,7 @@ stopAt endTime; endTime 3600; -deltaT 0.75; +deltaT 0.5; //0.75; writeControl runTime; @@ -47,7 +47,7 @@ runTimeModifiable true; maxCo 10; // Or other Courant number you wish -adjustTimeStep yes; // Or no +adjustTimeStep no; // Or no maxDeltaT 0.75; //Maximum deltaT in seconds diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSchemes b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSchemes similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSchemes rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSchemes diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSolution b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSolution similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSolution rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/fvSolution diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/graphCell b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/graphCell similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/graphCell rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/system/graphCell diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/U b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/U similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/U rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/U diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite similarity index 95% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite index 70d5587..c670a04 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/inertMineral b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/inertMineral similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/inertMineral rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/inertMineral diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/p b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/p similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/p rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/p diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allclean b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allrun b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allrun new file mode 100755 index 0000000..d9086ee --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/Allrun @@ -0,0 +1,21 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -func graphCell + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/README.txt b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/README.txt similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/README.txt rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/README.txt diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/CalciteDiss_ThermoEq.op b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/CalciteDiss_ThermoEq.op similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/CalciteDiss_ThermoEq.op rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/CalciteDiss_ThermoEq.op diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.dat b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.dat similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.dat rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.dat diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.log b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.log similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.log rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqc.log diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcInput b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcInput similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcInput rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcInput diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.log b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.log similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.log rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.log diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.phr b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.phr similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.phr rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/phreeqcRun.phr diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/transportProperties b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/physicalProperties similarity index 92% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/transportProperties rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/physicalProperties index 1cb3623..37654b5 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/transportProperties +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/constant/physicalProperties @@ -11,7 +11,7 @@ FoamFile format ascii; class dictionary; location "constant"; - object transportProperties; + object physicalProperties; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // @@ -27,6 +27,13 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } geochemicalModel phreeqcRM; diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T20 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T20 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T20 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T20 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T40 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T40 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T40 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T40 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T60 b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T60 similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T60 rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/T60 diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/runFile b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/runFile similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/runFile rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/phreeqcDataExtraction/runFile diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/plot.gp b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/plot.gp similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/plot.gp rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/plot.gp diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/blockMeshDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/blockMeshDict similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/blockMeshDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/blockMeshDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict similarity index 97% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict index 526ac8e..3138b94 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application dbsPhreeqcFoam; +application constantVelocityFoam; startFrom latestTime; diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes similarity index 98% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes index 00251b7..3abe328 100755 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes +++ b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSchemes @@ -62,7 +62,6 @@ snGradSchemes fluxRequired { default no; - p ; } diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSolution b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSolution similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSolution rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/fvSolution diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/graphCell b/tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/graphCell similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/graphCell rename to tutorials-pM4F/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/system/graphCell diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/Ci b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/Ci similarity index 100% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/Ci rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/Ci diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/U b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/U similarity index 100% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/U rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/U diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite similarity index 95% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite index 2b20c90..d4a24b0 100755 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allclean b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allclean new file mode 100755 index 0000000..b6150bb --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allrun b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allrun new file mode 100755 index 0000000..25e059b --- /dev/null +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/Allrun @@ -0,0 +1,23 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -func "probes(points=((10 0 0)), fields=(Ci))" + +## postProcess -func "boundaryProbes(points=((10 0 0)),maxDistance=1e-3 fields=(Ci))" + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/constant/transportProperties b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/constant/physicalProperties similarity index 93% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/constant/transportProperties rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/constant/physicalProperties index f90306d..c1bc49f 100755 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/constant/transportProperties +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/constant/physicalProperties @@ -25,6 +25,13 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/plot.gp b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/plot.gp similarity index 78% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/plot.gp rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/plot.gp index 09a898d..147f6eb 100644 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/plot.gp +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/plot.gp @@ -1,5 +1,6 @@ reset -set terminal postscript enhanced +##set terminal postscript enhanced +set terminal postscript eps enhanced color font 'Verdana,16' set size square 0.65,0.65 set output "breakthroughCurve.eps" ##set xrange [0 : 1] @@ -39,6 +40,6 @@ C(x,t)=0.5*C0*(erfc((L-U1*t)*0.5/(sqrt(Deff*t))) + exp((U*L)/(Deff))*erfc((L+U1 ##plot [x=-100:100] erfc(x) with lines lw 5 title "Analytical" -plot [t=0:100] C(L,t) with lines lw 5 title "Analytical", \ - "postProcessing/probes(points=((1000)),fields=(Ci))/0/Ci" using 1:2 title "Numerical" +plot [t=0:100] C(L,t) with lines lc 1 lw 5 title "Analytical", \ + "postProcessing/probes(points=((1000)),fields=(Ci))/0/Ci" using 1:2 every 3 with points pt 82 lc 1 title "Numerical" diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/blockMeshDict b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/blockMeshDict similarity index 100% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/blockMeshDict rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/blockMeshDict diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict similarity index 97% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict index 4cf3b99..dd8f112 100755 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict +++ b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application icoFoam; +application constantVelocityFoam; startFrom latestTime; diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/fvSchemes b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/fvSchemes similarity index 100% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/fvSchemes rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/fvSchemes diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/fvSolution b/tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/fvSolution similarity index 100% rename from tutorials/constantVelocityFoam/transportOnly/linearDispersion/system/fvSolution rename to tutorials-pM4F/constantVelocityFoam/transportOnly/linearDispersion/system/fvSolution diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/K b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/K.orig similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/K rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/K.orig diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/U b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/U similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/U rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/U diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite old mode 100755 new mode 100644 similarity index 95% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite index 2af1aeb..1eed8a6 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/inertMineral b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/inertMineral similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/inertMineral rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/inertMineral diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/p b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/p similarity index 98% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/p rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/p index 999bbe7..0fe9782 100644 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/p +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/0/p @@ -29,7 +29,7 @@ boundaryField inlet { type fixedValue; - value uniform 1e5; + value uniform 1e5; } frontAndBack diff --git a/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allclean b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allclean new file mode 100755 index 0000000..b6150bb --- /dev/null +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allrun b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allrun new file mode 100755 index 0000000..1282d47 --- /dev/null +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/Allrun @@ -0,0 +1,21 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh +runApplication setFields +runApplication $application + +runApplication postProcess -func graphCell + +runApplication gnuplot plot.gp + +runApplication evince Pressure.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/constant/g b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/constant/g similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/constant/g rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/constant/g diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties old mode 100755 new mode 100644 similarity index 79% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties index 7400756..cfa39ae --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties @@ -15,24 +15,43 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // +fluidProperties +{ + densityModel constantDensity; + + constantDensityCoeffs + { + rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; + } + + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + + + +} + + transportModel Newtonian; mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -rho rho [ 1 -3 0 0 0 0 0 ] 1000; -nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; +//nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; +geochemicalModel flowOnly; + geochemicalProperties { - geochemicalModel flowOnly; - rhol rhol [ 1 -3 0 0 0 0 0 ] 1000; - mineral (Calcite); absolutePermeabilityModel heterogeneousScalarConstant; heterogeneousScalarConstantCoeffs { K0 K0 [0 2 0 0 0 0 0] 1e-11; - updateFromInitialValue off; + // updateFromInitialValue on; } dispersionModel none; @@ -47,7 +66,4 @@ geochemicalProperties } - // ************************************************************************* // - - diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp similarity index 72% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp index a85cb49..195bb88 100644 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp +++ b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/plot.gp @@ -38,7 +38,8 @@ f(x) = x < l ? P0-(P0-P1)/l*x : x<2*l ? (2*P1-P2)-(P1-P2)/l*x : x<3*l ? (P2+(P2- -set terminal postscript enhanced +##set terminal postscript enhanced +set terminal postscript eps enhanced color font 'Verdana,16' set size square 0.65,0.65 set output "Permeability.eps" ##set yrange [1e-12 : 5e-11] @@ -65,13 +66,14 @@ set ylabel "Velocity (m/s)" -plot "postProcessing/graphCell/100/line.xy" using 1:3 with lines lw 5 title "darcyFoam",\ - V(x) with linespoints pointinterval 3 ps 2 title "analytical" +plot "postProcessing/graphCell/100/line.xy" using 1:3 every 50 with points pt 82 lc 1 title "darcyFoam",\ + V(x) with lines lw 5 lc 1 title "analytical" -set terminal postscript enhanced +##set terminal postscript enhanced +set terminal postscript eps enhanced color font 'Verdana,16' set size square 0.65,0.65 set output "Pressure.eps" ##set xrange [0 : 1] @@ -82,8 +84,8 @@ set ylabel "Pressure (Pa)" -plot "postProcessing/graphCell/100/line.xy" using 1:2 with lines lw 5 title "darcyFoam",\ - f(x) with linespoints pointinterval 3 ps 2 title "analytical" +plot "postProcessing/graphCell/100/line.xy" using 1:2 every 50 with points pt 82 lc 1 title "darcyFoam",\ + f(x) with lines lw 5 lc 1 title "analytical" diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/controlDict b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/controlDict similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/controlDict rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/controlDict diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSchemes b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSchemes similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSchemes rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSchemes diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSolution b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSolution similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSolution rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/fvSolution diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/graphCell b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/graphCell similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/graphCell rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/graphCell diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict b/tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict rename to tutorials-pM4F/darcyFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/U b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/U similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/U rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/U diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite old mode 100644 new mode 100755 similarity index 95% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite index 2af1aeb..1eed8a6 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum similarity index 95% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum index 1e29511..a8a1a47 100755 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/Ys.Gypsum @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/inertMineral b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/inertMineral similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/inertMineral rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/inertMineral diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/p b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/p similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/p rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/0/p diff --git a/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allclean b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allrun b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allrun new file mode 100755 index 0000000..980e6ff --- /dev/null +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/Allrun @@ -0,0 +1,23 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -time 3.149928e+08,3.1499928e+09 -func graphCell + +postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/g b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/g similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/g rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/g diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqc.dat b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqc.dat similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqc.dat rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqc.dat diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqcInput b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqcInput similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqcInput rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/phreeqcInput diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/transportProperties b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/physicalProperties similarity index 91% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/transportProperties rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/physicalProperties index b092d1f..f2a08b7 100755 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/transportProperties +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/physicalProperties @@ -11,7 +11,7 @@ FoamFile format ascii; class dictionary; location "constant"; - object transportProperties; + object physicalProperties; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // @@ -24,6 +24,13 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } @@ -41,6 +48,7 @@ geochemicalProperties absolutePermeabilityModel KozenyCarman; KozenyCarmanCoeffs { + updateFromInitialValue true; K0 K0 [0 2 0 0 0 0 0] 1.18602e-11; } diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/turbulenceProperties b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/turbulenceProperties similarity index 100% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/constant/turbulenceProperties rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/turbulenceProperties diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plot.gp b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plot.gp similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plot.gp rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plot.gp diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_100y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_100y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_100y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_100y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_10y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_10y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_10y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_10y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_Flux_150y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_Flux_150y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_Flux_150y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/MIN3P_Data_Paper/B2_Flux_150y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Flux.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Flux.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Flux.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Flux.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_1000y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_1000y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_1000y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_1000y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_100y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_100y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_100y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_100y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_10y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_10y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_10y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/Porosity/B2_10y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_1000y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_1000y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_1000y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_1000y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_100y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_100y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_100y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_100y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_10y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_10y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_10y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/calc_VF/calc_VF_10y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_1000y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_1000y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_1000y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_1000y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_100y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_100y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_100y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_100y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_10y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_10y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_10y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/gyp_VF/gyp_VF_10y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_1000y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_1000y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_1000y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_1000y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_100y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_100y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_100y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_100y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_10y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_10y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_10y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyCond/hyCond_10y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_1000Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_1000Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_1000Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_1000Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_100Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_100Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_100Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_100Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_10Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_10Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_10Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/plots/Tough_WebExtraction/hyHead/hh_10Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/blockMeshDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/blockMeshDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/blockMeshDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/blockMeshDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/controlDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/controlDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/controlDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/controlDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/decomposeParDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/decomposeParDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/decomposeParDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/decomposeParDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSchemes b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSchemes similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSchemes rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSchemes diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSolution b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSolution similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSolution rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/fvSolution diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/graphCell b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/graphCell similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/graphCell rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/graphCell diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/mapFieldsDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/mapFieldsDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/mapFieldsDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/mapFieldsDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/sampleDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/sampleDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/sampleDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/sampleDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/setFieldsDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/setFieldsDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/setFieldsDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/setFieldsDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/singleGraph b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/singleGraph similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/singleGraph rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/singleGraph diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/snappyHexMeshDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/snappyHexMeshDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/snappyHexMeshDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/system/snappyHexMeshDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite similarity index 95% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite index 2af1aeb..1eed8a6 100644 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p diff --git a/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun new file mode 100755 index 0000000..b87ad45 --- /dev/null +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun @@ -0,0 +1,23 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -time 3.149928e+08,3.1499928e+09,3.78e+09 -func graphCell + +postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties similarity index 78% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties index 7594c82..5014a6e 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties @@ -11,19 +11,38 @@ FoamFile format ascii; class dictionary; location "constant"; - object transportProperties; + object physicalProperties; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + +fluidProperties +{ + densityModel constantDensity; + + constantDensityCoeffs + { + rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; + } + + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + +} + transportModel Newtonian; -mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -rho rho [ 1 -3 0 0 0 0 0 ] 1000; +mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; + +geochemicalModel phreeqcRM; + -nu nu [0 2 -1 0 0 0 0] 1e-6; geochemicalProperties { - rhol rhol [1 -3 0 0 0 0 0] 1000; - geochemicalModel phreeqcRM; + mineral (Calcite); @@ -31,6 +50,7 @@ geochemicalProperties KozenyCarmanCoeffs { K0 K0 [0 2 0 0 0 0 0] 1.18602e-11; + updateFromInitialValue true; } dispersionModel none; diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Flux.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Flux.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Flux.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Flux.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/100Y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/100Y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/100Y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/100Y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/10Y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/10Y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/10Y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/10Y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/120Y_poro.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/120Y_poro.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/120Y_poro.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/Porosity/120Y_poro.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/100Y_cvf.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/100Y_cvf.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/100Y_cvf.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/100Y_cvf.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/10Y_cvf.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/10Y_cvf.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/10Y_cvf.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/10Y_cvf.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/120Y_cvf.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/120Y_cvf.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/120Y_cvf.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/calcVF/120Y_cvf.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/100Y_hh.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/100Y_hh.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/100Y_hh.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/100Y_hh.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/10Y_hh.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/10Y_hh.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/10Y_hh.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/10Y_hh.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/120Y_hh.txt b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/120Y_hh.txt similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/120Y_hh.txt rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/Tough_Data_WebExtract/hyHead/120Y_hh.txt diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev2.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev2.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev2.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calc_VFRev2.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calcite_VF.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calcite_VF.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calcite_VF.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/calcite_VF.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/legend.eps b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/legend.eps similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/legend.eps rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/calcite_VF/legend.eps diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/flux.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/flux.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/flux.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/flux.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev2.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev2.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev2.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/fluxRev2.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/legend.eps b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/legend.eps similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/legend.eps rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/flux/legend.eps diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHead.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHead.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHead.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHead.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev2.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev2.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev2.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/hydHeadRev2.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/legend.eps b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/legend.eps similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/legend.eps rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/hydHead/legend.eps diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/legend.eps b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/legend.eps similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/legend.eps rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/legend.eps diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev2.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev2.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev2.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porRev2.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porosity.py b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porosity.py similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porosity.py rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/porosity/porosity.py diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/.fvSchemes.swp b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/.fvSchemes.swp similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/.fvSchemes.swp rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/.fvSchemes.swp diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict similarity index 96% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict index 86e305f..0440eaa 100644 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict +++ b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict @@ -25,7 +25,7 @@ stopAt endTime; endTime 4.75e9; -deltaT 21600; +deltaT 21600; //21600; writeControl runTime; diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell b/tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell rename to tutorials-pM4F/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell diff --git a/tutorials/dbsSimpleFoam/constrictedTube/.~lock.tttt0.csv# b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/.~lock.tttt0.csv# similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/.~lock.tttt0.csv# rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/.~lock.tttt0.csv# diff --git a/tutorials/dbsSimpleFoam/constrictedTube/0/K.org b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/K.orig similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/0/K.org rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/K.orig diff --git a/tutorials/dbsSimpleFoam/constrictedTube/0/U b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/U similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/0/U rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/U diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/0/p b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/Ys.Calcite.orig similarity index 73% rename from tutorials/dbsSimpleFoam/planarPoiseuille/0/p rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/Ys.Calcite.orig index 1a4b248..86d58f6 100755 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/0/p +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/Ys.Calcite.orig @@ -1,8 +1,8 @@ /*--------------------------------*- C++ -*----------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | +| \\ / O peration | Version: 5.x | +| \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile @@ -10,41 +10,38 @@ FoamFile version 2.0; format ascii; class volScalarField; - object p; + location "0"; + object Ys.Calcite; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -dimensions [0 2 -2 0 0 0 0]; +dimensions [0 0 0 0 0 0 0]; internalField uniform 0; boundaryField { - left - { - type fixedFluxPressure; - } - right { - type fixedValue; - value uniform 0; + type zeroGradient; } - - top + left { - type symmetryPlane; + type zeroGradient; } - bottom { type zeroGradient; } - + top + { + type zeroGradient; + } frontAndBack { type empty; } } + // ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/constrictedTube/0/eps.org b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/eps.orig similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/0/eps.org rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/eps.orig diff --git a/tutorials/dbsSimpleFoam/constrictedTube/0/p b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/p similarity index 97% rename from tutorials/dbsSimpleFoam/constrictedTube/0/p rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/p index 2fb89a8..d697e10 100755 --- a/tutorials/dbsSimpleFoam/constrictedTube/0/p +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/0/p @@ -29,7 +29,7 @@ boundaryField left { type fixedValue; - value uniform 10; + value uniform 1; } bottom { diff --git a/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allclean b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allclean new file mode 100755 index 0000000..fee34fe --- /dev/null +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allclean @@ -0,0 +1,8 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allrun b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allrun new file mode 100755 index 0000000..f777ba0 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/Allrun @@ -0,0 +1,18 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh +runApplication setFields + +runApplication transformPoints scale='(1e-3 1e-3 1e-3)' + +runApplication $application + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/g b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/g similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/g rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/g diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/transportProperties b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/physicalProperties old mode 100644 new mode 100755 similarity index 92% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/transportProperties rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/physicalProperties index 564559d..2a6aa68 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/physicalProperties @@ -24,12 +24,20 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + + } transportModel Newtonian; mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; + geochemicalModel flowOnly; @@ -44,7 +52,6 @@ geochemicalProperties heterogeneousScalarConstantCoeffs { K0 K0 [0 2 0 0 0 0 0] 1e-11; - updateFromInitialValue off; } dispersionModel none; @@ -60,3 +67,5 @@ geochemicalProperties } // ************************************************************************* // + + diff --git a/tutorials/dbsSimpleFoam/constrictedTube/constant/turbulenceProperties b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/turbulenceProperties similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/constant/turbulenceProperties rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/constant/turbulenceProperties diff --git a/tutorials/dbsSimpleFoam/constrictedTube/geometry.stl.gz b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/geometry.stl.gz similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/geometry.stl.gz rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/geometry.stl.gz diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/blockMeshDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/blockMeshDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/blockMeshDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/blockMeshDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/controlDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/controlDict similarity index 97% rename from tutorials/dbsSimpleFoam/constrictedTube/system/controlDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/controlDict index b41b14d..c542f81 100755 --- a/tutorials/dbsSimpleFoam/constrictedTube/system/controlDict +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application simpleFoam; +application dbsFoam; startFrom startTime; diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/decomposeParDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/decomposeParDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/decomposeParDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/decomposeParDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/fvSchemes b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/fvSchemes similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/fvSchemes rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/fvSchemes diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSolution b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/fvSolution similarity index 77% rename from tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSolution rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/fvSolution index bbb0127..04fa8f9 100755 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSolution +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/fvSolution @@ -19,33 +19,28 @@ solvers p { solver GAMG; - smoother DIC; - tolerance 1e-6; - relTol 0.05; - } - - U - { - solver smoothSolver; - smoother symGaussSeidel; - tolerance 1e-6; + tolerance 1e-06; relTol 0.1; + smoother GaussSeidel; } - pFinal + pcorr { - $p; + solver GAMG; + tolerance 1e-06; relTol 0; + smoother GaussSeidel; } - UFinal + "(U|k|epsilon|omega|f|v2)" { - $U; - relTol 0; + solver smoothSolver; + smoother symGaussSeidel; + tolerance 1e-05; + relTol 0.1; } } - SIMPLE { nNonOrthogonalCorrectors 0; @@ -53,8 +48,9 @@ SIMPLE residualControl { - p 1e-5; - U 1e-5; + p 1e-2; + U 1e-3; + "(k|epsilon|omega|f|v2)" 1e-3; } } @@ -65,6 +61,11 @@ relaxationFactors U 0.9; // 0.9 is more stable but 0.95 more convergent ".*" 0.9; // 0.9 is more stable but 0.95 more convergent } + + fields + { + p 0.5; // + } } // ************************************************************************* // diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/mapFieldsDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/mapFieldsDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/mapFieldsDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/mapFieldsDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/refineMeshDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/refineMeshDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/refineMeshDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/refineMeshDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/sampleDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/sampleDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/sampleDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/sampleDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/setFieldsDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/setFieldsDict similarity index 91% rename from tutorials/dbsSimpleFoam/constrictedTube/system/setFieldsDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/setFieldsDict index 20c1888..bd9502b 100755 --- a/tutorials/dbsSimpleFoam/constrictedTube/system/setFieldsDict +++ b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/setFieldsDict @@ -19,7 +19,8 @@ valueAlpha 0.99; //0.9999; defaultFieldValues ( - volScalarFieldValue eps 0.001//0.9999 +// volScalarFieldValue eps 0.001//0.9999 + volScalarFieldValue Ys.Calcite 0.999//0.9999 volScalarFieldValue K 1e-20//0.9999 ); @@ -38,7 +39,8 @@ regions curvature 0.9; // cells within nearDistance fieldValues ( - volScalarFieldValue eps 1 + // volScalarFieldValue eps 1 + volScalarFieldValue Ys.Calcite 0.//0.9999 volScalarFieldValue K 1 ); } diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/snappyHexMeshDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/snappyHexMeshDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/snappyHexMeshDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/snappyHexMeshDict diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/topoSetDict b/tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/topoSetDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/topoSetDict rename to tutorials-pM4F/dbsFoam/flowOnly/constrictedTube/system/topoSetDict diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/K.Orig b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/K.orig similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/K.Orig rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/K.orig diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/U b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/U similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/U rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/U diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite similarity index 95% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite index 2af1aeb..1eed8a6 100644 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/Ys.Calcite @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/inertMineral b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/inertMineral similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/inertMineral rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/inertMineral diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/p b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/p similarity index 98% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/p rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/p index ff935d9..d55d66f 100644 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/p +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/0/p @@ -29,7 +29,7 @@ boundaryField inlet { type fixedValue; - value uniform 1e2; + value uniform 1e5; } frontAndBack diff --git a/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allclean b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allclean new file mode 100755 index 0000000..b6150bb --- /dev/null +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allrun b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allrun new file mode 100755 index 0000000..1282d47 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/Allrun @@ -0,0 +1,21 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh +runApplication setFields +runApplication $application + +runApplication postProcess -func graphCell + +runApplication gnuplot plot.gp + +runApplication evince Pressure.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/g similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/g diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/momentumTransport b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/momentumTransport similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/constant/momentumTransport rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/momentumTransport diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/constant/transportProperties b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties old mode 100644 new mode 100755 similarity index 92% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/constant/transportProperties rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties index d29757e..2a6aa68 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/constant/physicalProperties @@ -24,25 +24,34 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + + } transportModel Newtonian; mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; + geochemicalModel flowOnly; + geochemicalProperties { + mineral (Calcite); absolutePermeabilityModel heterogeneousScalarConstant; heterogeneousScalarConstantCoeffs { K0 K0 [0 2 0 0 0 0 0] 1e-11; - updateFromInitialValue off; } dispersionModel none; @@ -58,3 +67,5 @@ geochemicalProperties } // ************************************************************************* // + + diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp similarity index 69% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp index 2a1f639..195bb88 100644 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp +++ b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/plot.gp @@ -6,21 +6,19 @@ k3 = 1e-12 k4 = 5e-11 l = 0.5 -L = 4. +L = 4 S = 0.1*0.1 K = L/(l/k1+l/k2+l/k3+l/k4) -mu = 1.e-3 -rho = 1.e3 +mu = 1e-3 +V(x) = -K/mu*(P4-P0)/L -P0 = 1.e5/rho -P4 = 0 -V(x) = -K/mu*(P4-P0)/L*rho -print "V = ", V(0) +P0 = 1e5 +P4 = 0 P3 = P4 + K/L*l/k4*(P0-P4) P2 = P3 + k4/l*l/k3*(P3-P4) @@ -40,7 +38,8 @@ f(x) = x < l ? P0-(P0-P1)/l*x : x<2*l ? (2*P1-P2)-(P1-P2)/l*x : x<3*l ? (P2+(P2- -set terminal postscript enhanced +##set terminal postscript enhanced +set terminal postscript eps enhanced color font 'Verdana,16' set size square 0.65,0.65 set output "Permeability.eps" ##set yrange [1e-12 : 5e-11] @@ -67,13 +66,14 @@ set ylabel "Velocity (m/s)" -plot "postProcessing/graphCell/100/line.xy" using 1:3 with lines lw 5 title "darcyFoam",\ - V(x) with linespoints pointinterval 3 ps 2 title "analytical" +plot "postProcessing/graphCell/100/line.xy" using 1:3 every 50 with points pt 82 lc 1 title "darcyFoam",\ + V(x) with lines lw 5 lc 1 title "analytical" -set terminal postscript enhanced +##set terminal postscript enhanced +set terminal postscript eps enhanced color font 'Verdana,16' set size square 0.65,0.65 set output "Pressure.eps" ##set xrange [0 : 1] @@ -84,8 +84,8 @@ set ylabel "Pressure (Pa)" -plot "postProcessing/graphCell/100/line.xy" using 1:2 with lines lw 5 title "darcyFoam",\ - f(x) with linespoints pointinterval 3 ps 2 title "analytical" +plot "postProcessing/graphCell/100/line.xy" using 1:2 every 50 with points pt 82 lc 1 title "darcyFoam",\ + f(x) with lines lw 5 lc 1 title "analytical" diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/.fvSchemes.swp diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/blockMeshDict diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/controlDict b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/controlDict similarity index 100% rename from tutorials/darcyFoam/flowOnly/heterogeneousPermeability/system/controlDict rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/controlDict diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSchemes b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSchemes similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSchemes rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSchemes diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSolution b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSolution similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSolution rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/fvSolution diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/graphCell b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/graphCell similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/graphCell rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/graphCell diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict b/tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict similarity index 100% rename from tutorials/dbsFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict rename to tutorials-pM4F/dbsFoam/flowOnly/heterogeneousPermeability/system/setFieldsDict diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/U diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C index 6955195..0b85b18 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.C @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca index 92c1943..e33d0de 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Ca @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge index c8a6cfc..1925db5 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.Charge @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H index 49a169e..bab5dd9 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.H @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O index 9eb1434..7f67224 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.O @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S similarity index 95% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S index 695f3fd..8268425 100644 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Y.S @@ -2,7 +2,7 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite new file mode 100644 index 0000000..1eed8a6 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite @@ -0,0 +1,38 @@ +/*--------------------------------*- C++ -*----------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Version: 11 + \\/ M anipulation | +\*---------------------------------------------------------------------------*/ +FoamFile +{ + format ascii; + class volScalarField; + location "0"; + object Ys.Calcite; +} +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + +dimensions [0 0 0 0 0 0 0]; + +internalField uniform 0.3; + +boundaryField +{ + outlet + { + type zeroGradient; + } + inlet + { + type zeroGradient; + } + frontAndBack + { + type empty; + } +} + + +// ************************************************************************* // diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/inertMineral diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/p diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean new file mode 100755 index 0000000..2bbfae2 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun new file mode 100755 index 0000000..b87ad45 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/Allrun @@ -0,0 +1,23 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh + +runApplication $application + +runApplication postProcess -time 3.149928e+08,3.1499928e+09,3.78e+09 -func graphCell + +postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' + +runApplication gnuplot plot.gp + +runApplication evince *.eps + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/README.txt b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/README.txt similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/README.txt rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/README.txt diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/dbs diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/constant/turbulenceProperties b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g old mode 100755 new mode 100644 similarity index 62% rename from tutorials/dbsSimpleFoam/planarPoiseuille/constant/turbulenceProperties rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g index fd6f708..f6f9725 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/constant/turbulenceProperties +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/g @@ -1,20 +1,22 @@ /*--------------------------------*- C++ -*----------------------------------*\ | ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | +| \\ / F ield | foam-extend: Open Source CFD | +| \\ / O peration | Version: 4.0 | +| \\ / A nd | Web: http://www.foam-extend.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile { version 2.0; format ascii; - class dictionary; + class uniformDimensionedVectorField; location "constant"; - object turbulenceProperties; + object g; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -simulationType laminar; +dimensions [0 1 -2 0 0 0 0]; +value ( 0.0 0.0 0.0 );//( 0 -9.81 0 ); + // ************************************************************************* // diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/phreeqcInput diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties similarity index 92% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties index 882e85e..64491d6 100644 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/physicalProperties @@ -15,7 +15,6 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - fluidProperties { densityModel constantDensity; @@ -25,6 +24,13 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } transportModel Newtonian; @@ -43,7 +49,7 @@ geochemicalProperties KozenyCarmanCoeffs { K0 K0 [0 2 0 0 0 0 0] 1.18602e-11; - updateFromInitialValue off; + updateFromInitialValue true; } dispersionModel none; @@ -72,4 +78,5 @@ geochemicalProperties } + // ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Charge b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/boundary old mode 100755 new mode 100644 similarity index 60% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Charge rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/boundary index c12ee41..81065f9 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Charge +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/boundary @@ -2,38 +2,39 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile { format ascii; - class volScalarField; - location "0"; - object Y.Charge; + class polyBoundaryMesh; + location "constant/polyMesh"; + object boundary; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -dimensions [0 0 0 0 0 0 0]; - -internalField uniform -4.686e-12; - -boundaryField -{ +3 +( outlet { - type zeroGradient; + type patch; + nFaces 1; + startFace 79; } inlet { - type fixedValue; - value uniform -6.397e-11; + type patch; + nFaces 1; + startFace 80; } frontAndBack { type empty; + inGroups List 1(empty); + nFaces 320; + startFace 81; } -} - +) // ************************************************************************* // diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/faces b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/faces new file mode 100644 index 0000000..7d86b6c --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/faces @@ -0,0 +1,424 @@ +/*--------------------------------*- C++ -*----------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Version: 11 + \\/ M anipulation | +\*---------------------------------------------------------------------------*/ +FoamFile +{ + format ascii; + class faceList; + location "constant/polyMesh"; + object faces; +} +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + + +401 +( +4(1 82 244 163) +4(2 83 245 164) +4(3 84 246 165) +4(4 85 247 166) +4(5 86 248 167) +4(6 87 249 168) +4(7 88 250 169) +4(8 89 251 170) +4(9 90 252 171) +4(10 91 253 172) +4(11 92 254 173) +4(12 93 255 174) +4(13 94 256 175) +4(14 95 257 176) +4(15 96 258 177) +4(16 97 259 178) +4(17 98 260 179) +4(18 99 261 180) +4(19 100 262 181) +4(20 101 263 182) +4(21 102 264 183) +4(22 103 265 184) +4(23 104 266 185) +4(24 105 267 186) +4(25 106 268 187) +4(26 107 269 188) +4(27 108 270 189) +4(28 109 271 190) +4(29 110 272 191) +4(30 111 273 192) +4(31 112 274 193) +4(32 113 275 194) +4(33 114 276 195) +4(34 115 277 196) +4(35 116 278 197) +4(36 117 279 198) +4(37 118 280 199) +4(38 119 281 200) +4(39 120 282 201) 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71) +4(71 152 153 72) +4(72 153 154 73) +4(73 154 155 74) +4(74 155 156 75) +4(75 156 157 76) +4(76 157 158 77) +4(77 158 159 78) +4(78 159 160 79) +4(79 160 161 80) +4(162 163 244 243) +4(163 164 245 244) +4(164 165 246 245) +4(165 166 247 246) +4(166 167 248 247) +4(167 168 249 248) +4(168 169 250 249) +4(169 170 251 250) +4(170 171 252 251) +4(171 172 253 252) +4(172 173 254 253) +4(173 174 255 254) +4(174 175 256 255) +4(175 176 257 256) +4(176 177 258 257) +4(177 178 259 258) +4(178 179 260 259) +4(179 180 261 260) +4(180 181 262 261) +4(181 182 263 262) +4(182 183 264 263) +4(183 184 265 264) +4(184 185 266 265) +4(185 186 267 266) +4(186 187 268 267) +4(187 188 269 268) +4(188 189 270 269) +4(189 190 271 270) +4(190 191 272 271) +4(191 192 273 272) +4(192 193 274 273) +4(193 194 275 274) +4(194 195 276 275) +4(195 196 277 276) +4(196 197 278 277) +4(197 198 279 278) +4(198 199 280 279) +4(199 200 281 280) +4(200 201 282 281) +4(201 202 283 282) +4(202 203 284 283) +4(203 204 285 284) +4(204 205 286 285) +4(205 206 287 286) +4(206 207 288 287) +4(207 208 289 288) +4(208 209 290 289) +4(209 210 291 290) +4(210 211 292 291) +4(211 212 293 292) +4(212 213 294 293) +4(213 214 295 294) +4(214 215 296 295) +4(215 216 297 296) +4(216 217 298 297) +4(217 218 299 298) +4(218 219 300 299) +4(219 220 301 300) +4(220 221 302 301) +4(221 222 303 302) +4(222 223 304 303) +4(223 224 305 304) +4(224 225 306 305) +4(225 226 307 306) +4(226 227 308 307) +4(227 228 309 308) +4(228 229 310 309) +4(229 230 311 310) +4(230 231 312 311) +4(231 232 313 312) +4(232 233 314 313) +4(233 234 315 314) +4(234 235 316 315) +4(235 236 317 316) +4(236 237 318 317) +4(237 238 319 318) +4(238 239 320 319) +4(239 240 321 320) +4(240 241 322 321) +4(241 242 323 322) +) + + +// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.C b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/neighbour old mode 100755 new mode 100644 similarity index 55% rename from tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.C rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/neighbour index 0069d20..ad0172d --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.C +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/neighbour @@ -2,38 +2,102 @@ ========= | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 + \\ / A nd | Version: 11 \\/ M anipulation | \*---------------------------------------------------------------------------*/ FoamFile { format ascii; - class volScalarField; - location "0"; - object Y.C; + class labelList; + note "nPoints: 324 nCells: 80 nFaces: 401 nInternalFaces: 79"; + location "constant/polyMesh"; + object neighbour; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -dimensions [0 0 0 0 0 0 0]; -internalField uniform 0.001018; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0; - } - frontAndBack - { - type empty; - } -} +79 +( +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +) // ************************************************************************* // diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/owner b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/owner new file mode 100644 index 0000000..8037ca8 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/polyMesh/owner @@ -0,0 +1,425 @@ +/*--------------------------------*- C++ -*----------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Version: 11 + \\/ M anipulation | +\*---------------------------------------------------------------------------*/ +FoamFile +{ + format ascii; + class labelList; + note "nPoints: 324 nCells: 80 nFaces: 401 nInternalFaces: 79"; + location "constant/polyMesh"; + object owner; +} +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + + +401 +( +0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 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| +\*---------------------------------------------------------------------------*/ +FoamFile +{ + format ascii; + class vectorField; + location "constant/polyMesh"; + object points; +} +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // + + +324 +( +(0 0 0) +(0.025 0 0) +(0.05 0 0) +(0.075 0 0) +(0.1 0 0) +(0.125 0 0) +(0.15 0 0) +(0.175 0 0) +(0.2 0 0) +(0.225 0 0) +(0.25 0 0) +(0.275 0 0) +(0.3 0 0) +(0.325 0 0) +(0.35 0 0) +(0.375 0 0) +(0.4 0 0) +(0.425 0 0) +(0.45 0 0) +(0.475 0 0) +(0.5 0 0) +(0.525 0 0) +(0.55 0 0) +(0.575 0 0) +(0.6 0 0) +(0.625 0 0) +(0.65 0 0) +(0.675 0 0) +(0.7 0 0) +(0.725 0 0) +(0.75 0 0) +(0.775 0 0) +(0.8 0 0) +(0.825 0 0) +(0.85 0 0) +(0.875 0 0) +(0.9 0 0) +(0.925 0 0) +(0.95 0 0) +(0.975 0 0) +(1 0 0) +(1.025 0 0) +(1.05 0 0) +(1.075 0 0) +(1.1 0 0) +(1.125 0 0) +(1.15 0 0) +(1.175 0 0) +(1.2 0 0) +(1.225 0 0) +(1.25 0 0) +(1.275 0 0) +(1.3 0 0) +(1.325 0 0) +(1.35 0 0) +(1.375 0 0) +(1.4 0 0) +(1.425 0 0) +(1.45 0 0) 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+(0.675 0.1 0.1) +(0.7 0.1 0.1) +(0.725 0.1 0.1) +(0.75 0.1 0.1) +(0.775 0.1 0.1) +(0.8 0.1 0.1) +(0.825 0.1 0.1) +(0.85 0.1 0.1) +(0.875 0.1 0.1) +(0.9 0.1 0.1) +(0.925 0.1 0.1) +(0.95 0.1 0.1) +(0.975 0.1 0.1) +(1 0.1 0.1) +(1.025 0.1 0.1) +(1.05 0.1 0.1) +(1.075 0.1 0.1) +(1.1 0.1 0.1) +(1.125 0.1 0.1) +(1.15 0.1 0.1) +(1.175 0.1 0.1) +(1.2 0.1 0.1) +(1.225 0.1 0.1) +(1.25 0.1 0.1) +(1.275 0.1 0.1) +(1.3 0.1 0.1) +(1.325 0.1 0.1) +(1.35 0.1 0.1) +(1.375 0.1 0.1) +(1.4 0.1 0.1) +(1.425 0.1 0.1) +(1.45 0.1 0.1) +(1.475 0.1 0.1) +(1.5 0.1 0.1) +(1.525 0.1 0.1) +(1.55 0.1 0.1) +(1.575 0.1 0.1) +(1.6 0.1 0.1) +(1.625 0.1 0.1) +(1.65 0.1 0.1) +(1.675 0.1 0.1) +(1.7 0.1 0.1) +(1.725 0.1 0.1) +(1.75 0.1 0.1) +(1.775 0.1 0.1) +(1.8 0.1 0.1) +(1.825 0.1 0.1) +(1.85 0.1 0.1) +(1.875 0.1 0.1) +(1.9 0.1 0.1) +(1.925 0.1 0.1) +(1.95 0.1 0.1) +(1.975 0.1 0.1) +(2 0.1 0.1) +) + + +// ************************************************************************* // diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/turbulenceProperties b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/turbulenceProperties old mode 100755 new mode 100644 similarity index 100% rename from tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/constant/turbulenceProperties rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/turbulenceProperties diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.blockMesh b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.blockMesh new file mode 100644 index 0000000..8649a77 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.blockMesh @@ -0,0 +1,73 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Version: 11 + \\/ M anipulation | +\*---------------------------------------------------------------------------*/ +Build : 11 +Exec : blockMesh +Date : Nov 18 2023 +Time : 22:28:10 +Host : "69d9k13" +PID : 26919 +I/O : uncollated +Case : /home/local/ISTO/csoulaine/OpenFOAM/csoulaine-11/run/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange +nProcs : 1 +sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). +fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) +allowSystemOperations : Allowing user-supplied system call operations + +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // +Create time + +Reading "blockMeshDict" + +Creating block mesh from + "system/blockMeshDict" +Creating block edges +No non-planar block faces defined +Creating topology blocks +Creating topology patches + +Creating block mesh topology + +Check topology + + Basic statistics + Number of internal faces : 0 + Number of boundary faces : 6 + Number of defined boundary faces : 6 + Number of undefined boundary faces : 0 + Checking patch -> block consistency + +Creating block offsets +Creating merge list . + +Creating polyMesh from blockMesh +Creating patches +Creating cells +Creating points with scale 1 + Block 0 cell size : + i : 0.025 .. 0.025 + j : 0.1 + k : 0.1 + +Writing polyMesh +---------------- +Mesh Information +---------------- + boundingBox: (0 0 0) (2 0.1 0.1) + nPoints: 324 + nCells: 80 + nFaces: 401 + nInternalFaces: 79 +---------------- +Patches +---------------- + patch 0 (start: 79 size: 1) name: outlet + patch 1 (start: 80 size: 1) name: inlet + patch 2 (start: 81 size: 320) name: frontAndBack + +End + diff --git a/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.dbsFoam b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.dbsFoam new file mode 100644 index 0000000..01c2ab2 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/log.dbsFoam @@ -0,0 +1,890 @@ +/*---------------------------------------------------------------------------*\ + ========= | + \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + \\ / O peration | Website: https://openfoam.org + \\ / A nd | Version: 11 + \\/ M anipulation | +\*---------------------------------------------------------------------------*/ +Build : 11 +Exec : dbsFoam +Date : Nov 18 2023 +Time : 22:28:10 +Host : "69d9k13" +PID : 26920 +I/O : uncollated +Case : /home/local/ISTO/csoulaine/OpenFOAM/csoulaine-11/run/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange +nProcs : 1 +sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). +fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10) +allowSystemOperations : Allowing user-supplied system call operations + +// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // +Create time + +Create mesh for time = 0 + + +PIMPLE: No convergence criteria found + + +PIMPLE: Corrector convergence criteria found + p: tolerance 1e-05, relTol 1e-06 + Calculations will do 100 corrections if the convergence criteria are not met + + +PIMPLE: Operating solver in transient mode with 100 outer correctors + + + +Reading g +Reading field p + + +Reading field U + +Reading/calculating face flux field phi + +Reading field sourceTerm + +Selecting Geochemical package phreeqcRM +Selecting density model constantDensity +Selecting viscosity model constantViscosity +Selecting absolute permeability model KozenyCarman +Selecting dispersion model none + Doing stuff for mineral: Calcite +Selecting surface area model mingliangLaw +------------------------------------------------------------- +-------- Initialization of geochemistry with PhreeqC -------- + +Load database... Set properties... OK + +Set concentration units... OK + +set Temperature ...OK + +set Pressure ...OK + +Set volume, initial porosity and saturation... OK + +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +WARNING: Unknown input, no keyword has been specified. +number of components = 6 + +Database: constant/dbs +Number of threads: 1 +Number of MPI processes: 1 +MPI task number: 0 +File prefix: "myrun" +Number of grid cells in the user's model: 80 +Number of chemistry cells in the reaction module: 80 +Number of components for transport: 6 +Partioning of UZ solids: false +Error handler mode: 1 + +Activate SELECTED_OUTPUT ...OK + + Doing stuff for mineral: Calcite +Calcite is KINETICS +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry +Using RK to solve chemistry + Doing stuff for mineral: Calcite +Species Save On + +nspecies = 17 + +"CO3-2" + Charge: -2 + Dw: 0 +"Ca+2" + Charge: 2 + Dw: 0 +"CaCO3" + Charge: 0 + Dw: 0 +"CaHCO3+" + Charge: 1 + Dw: 0 +"CaHSO4+" + Charge: 1 + Dw: 0 +"CaOH+" + Charge: 1 + Dw: 0 +"CaSO4" + Charge: 0 + Dw: 0 +"H+" + Charge: 1 + Dw: 0 +"H2" + Charge: 0 + Dw: 0 +"H2CO3" + Charge: 0 + Dw: 0 +"H2O" + Charge: 0 + Dw: 0 +"H2SO4" + Charge: 0 + Dw: 0 +"HCO3-" + Charge: -1 + Dw: 0 +"HSO4-" + Charge: -1 + Dw: 0 +"O2" + Charge: 0 + Dw: 0 +"OH-" + Charge: -1 + Dw: 0 +"SO4-2" + Charge: -2 + Dw: 0 + +Get boundary conditions... OK + +Set concentrations fields and transport properties with OpenFOAM... + Doing stuff for components: H + Doing stuff for components: O + Doing stuff for components: Charge + Doing stuff for components: C + Doing stuff for components: Ca + Doing stuff for components: S +OK + + +--------------- End initialization of PhreeqC --------------- +------------------------------------------------------------- + + +Reading/generating porosity field eps + +Reading/generating permeability field invK +No MRF models present + +No fvModels present +No fvConstraints present +Courant Number mean: 0 max: 0 + +Starting time loop + +Courant Number mean: 0 max: 0 + + +Time = 21600 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 1, Final residual = 2.62178e-15, No Iterations 1 +time step continuity errors : sum local = 2.55276e-15, global = 2.54606e-17, cumulative = 2.54606e-17 +DICPCG: Solving for p, Initial residual = 3.04978e-10, Final residual = 8.62573e-25, No Iterations 1 +time step continuity errors : sum local = 2.19676e-15, global = 8.0402e-18, cumulative = 3.35008e-17 +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 3.13066e-13, Final residual = 3.13066e-13, No Iterations 0 +time step continuity errors : sum local = 3.97968e-13, global = 1.97916e-13, cumulative = 1.97949e-13 +DICPCG: Solving for p, Initial residual = 3.08107e-11, Final residual = 9.47633e-26, No Iterations 1 +time step continuity errors : sum local = 2.25661e-15, global = 1.48297e-16, cumulative = 1.98097e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 3 +DICPCG: Solving for p, Initial residual = 2.79774e-13, Final residual = 2.79774e-13, No Iterations 0 +time step continuity errors : sum local = 3.56308e-13, global = -3.54067e-13, cumulative = -1.5597e-13 +DICPCG: Solving for p, Initial residual = 2.77378e-12, Final residual = 9.42037e-27, No Iterations 1 +time step continuity errors : sum local = 2.25929e-15, global = -9.82691e-18, cumulative = -1.55979e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 1, Final residual = 1.81774e-17, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 1, Final residual = 2.49085e-16, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.99999, Final residual = 2.02232e-16, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 1, Final residual = 1.73655e-16, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 1, Final residual = 4.38404e-16, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 1, Final residual = 1.55872e-17, No Iterations 1 +run phreeqc within Strang loop...WARNING: Negative moles in solution 1 for C, -1.798746e-04. Recovering... +WARNING: Negative moles in solution 2 for Ca, -3.287789e-05. Recovering... +WARNING: Negative moles in solution 3 for Ca, -2.271988e-05. Recovering... +WARNING: Negative moles in solution 4 for Ca, -2.269830e-05. Recovering... +WARNING: Negative moles in solution 5 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 6 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 7 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 8 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 9 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 10 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 11 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 12 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 13 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 14 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 15 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 16 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 17 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 18 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 19 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 20 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 21 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 22 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 23 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 24 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 25 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 26 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 27 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 28 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 29 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 30 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 31 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 32 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 33 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 34 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 35 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 36 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 37 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 38 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 39 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 40 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 41 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 42 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 43 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 44 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 45 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 46 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 47 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 48 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 49 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 50 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 51 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 52 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 53 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 54 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 55 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 56 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 57 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 58 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 59 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 60 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 61 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 62 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 63 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 64 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 65 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 66 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 67 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 68 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 69 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 70 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 71 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 72 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 73 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 74 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 75 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 76 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 77 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 78 for Ca, -2.269829e-05. Recovering... +WARNING: Negative moles in solution 79 for Ca, -2.269829e-05. Recovering... + OK +DILUPBiCG: Solving for Y.H, Initial residual = 0.19776, Final residual = 5.65052e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.123446, Final residual = 3.08367e-17, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.189605, Final residual = 4.79816e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.119513, Final residual = 2.6786e-17, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.151694, Final residual = 3.09807e-17, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.19776, Final residual = 7.60159e-18, No Iterations 1 +geochemistry updated + +PIMPLE: Converged in 3 iterations + +ExecutionTime = 0.628678 s + +Courant Number mean: 0.352648 max: 0.352648 + + +Time = 43200 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 1.13992e-06, Final residual = 9.97235e-21, No Iterations 1 +time step continuity errors : sum local = 2.07928e-16, global = -6.09715e-17, cumulative = -1.5604e-13 +DICPCG: Solving for p, Initial residual = 2.73682e-10, Final residual = 6.98065e-25, No Iterations 1 +time step continuity errors : sum local = 1.90061e-16, global = -3.57342e-17, cumulative = -1.56076e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 3.04594e-12, Final residual = 1.44833e-26, No Iterations 1 +time step continuity errors : sum local = 1.85706e-16, global = -4.55611e-17, cumulative = -1.56122e-13 +DICPCG: Solving for p, Initial residual = 2.73692e-11, Final residual = 8.34014e-26, No Iterations 1 +time step continuity errors : sum local = 2.08431e-16, global = -3.56784e-17, cumulative = -1.56157e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 0.0141504, Final residual = 2.20921e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.0103705, Final residual = 4.61252e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.0139622, Final residual = 1.17702e-17, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.0101335, Final residual = 2.33411e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0125573, Final residual = 3.02779e-18, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0141504, Final residual = 3.45792e-18, No Iterations 1 +run phreeqc within Strang loop...WARNING: Negative moles in solution 1 for C, -4.114220e-02. Recovering... +WARNING: Negative moles in solution 2 for C, -4.723829e-03. Recovering... +WARNING: Negative moles in solution 3 for C, -4.450986e-02. Recovering... +WARNING: Negative moles in solution 4 for C, -4.373326e-03. Recovering... +WARNING: Negative moles in solution 5 for C, -4.496365e-03. Recovering... +WARNING: Negative moles in solution 6 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 7 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 8 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 9 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 10 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 11 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 12 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 13 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 14 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 15 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 16 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 17 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 18 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 19 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 20 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 21 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 22 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 23 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 24 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 25 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 26 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 27 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 28 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 29 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 30 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 31 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 32 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 33 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 34 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 35 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 36 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 37 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 38 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 39 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 40 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 41 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 42 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 43 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 44 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 45 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 46 for C, -4.496411e-03. Recovering... +WARNING: Negative moles in solution 47 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 48 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 49 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 50 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 51 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 52 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 53 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 54 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 55 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 56 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 57 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 58 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 59 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 60 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 61 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 62 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 63 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 64 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 65 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 66 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 67 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 68 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 69 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 70 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 71 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 72 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 73 for C, -4.496410e-03. Recovering... +WARNING: Negative moles in solution 74 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 75 for C, -4.496414e-03. Recovering... +WARNING: Negative moles in solution 76 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 77 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 78 for C, -4.496409e-03. Recovering... +WARNING: Negative moles in solution 79 for C, -4.496409e-03. Recovering... + OK +DILUPBiCG: Solving for Y.H, Initial residual = 0.01344, Final residual = 7.66992e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00907797, Final residual = 1.47961e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.0132776, Final residual = 2.27667e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00922992, Final residual = 7.47814e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0157687, Final residual = 2.49913e-18, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0134401, Final residual = 9.48816e-19, No Iterations 1 +geochemistry updated + +PIMPLE: Converged in 2 iterations + +ExecutionTime = 1.19466 s + +Courant Number mean: 0.038991 max: 0.038991 + + +Time = 64800 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 1.0362e-06, Final residual = 8.48526e-21, No Iterations 1 +time step continuity errors : sum local = 2.01563e-16, global = -2.72473e-17, cumulative = -1.56185e-13 +DICPCG: Solving for p, Initial residual = 2.73752e-12, Final residual = 6.74582e-27, No Iterations 1 +time step continuity errors : sum local = 2.15857e-16, global = -5.22613e-17, cumulative = -1.56237e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 4.50926e-15, Final residual = 4.50926e-15, No Iterations 0 +time step continuity errors : sum local = 6.18202e-16, global = 3.56002e-16, cumulative = -1.55881e-13 +DICPCG: Solving for p, Initial residual = 2.72152e-13, Final residual = 2.72152e-13, No Iterations 0 +time step continuity errors : sum local = 3.51052e-14, global = 3.47683e-16, cumulative = -1.55533e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 0.0117819, Final residual = 2.27625e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00807811, Final residual = 3.45017e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.0116634, Final residual = 2.17551e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00820246, Final residual = 2.09119e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0137815, Final residual = 1.0754e-17, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.011782, Final residual = 3.13156e-18, No Iterations 1 +run phreeqc within Strang loop...WARNING: Negative moles in solution 1 for C, -3.054968e-03. Recovering... +WARNING: Negative moles in solution 2 for C, -1.735820e-02. Recovering... +WARNING: Negative moles in solution 3 for Ca, -1.330369e-05. Recovering... +WARNING: Negative moles in solution 3 for Ca, -5.051124e-05. Recovering... +WARNING: Negative moles in solution 4 for C, -1.708688e-04. Recovering... +WARNING: Negative moles in solution 5 for C, -6.124902e-04. Recovering... +WARNING: Negative moles in solution 6 for C, -6.127834e-04. Recovering... +WARNING: Negative moles in solution 7 for C, -6.127840e-04. Recovering... +WARNING: Negative moles in solution 8 for C, -6.127840e-04. Recovering... +WARNING: Negative moles in solution 9 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 10 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 11 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 12 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 13 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 14 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 15 for C, -6.127497e-04. Recovering... +WARNING: Negative moles in solution 16 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 17 for C, -6.127498e-04. Recovering... +WARNING: Negative moles in solution 18 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 19 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 20 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 21 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 22 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 23 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 24 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 25 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 26 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 27 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 28 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 29 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 30 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 31 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 32 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 33 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 34 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 35 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 36 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 37 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 38 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 39 for C, -6.127839e-04. Recovering... +WARNING: Negative moles in solution 40 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 41 for C, -6.127847e-04. Recovering... +WARNING: Negative moles in solution 42 for C, -6.127840e-04. Recovering... +WARNING: Negative moles in solution 43 for C, -6.127840e-04. Recovering... +WARNING: Negative moles in solution 44 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 45 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 46 for C, -6.128239e-04. Recovering... +WARNING: Negative moles in solution 47 for C, -6.127884e-04. Recovering... +WARNING: Negative moles in solution 48 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 49 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 50 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 51 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 52 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 53 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 54 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 55 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 56 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 57 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 58 for C, -6.126999e-04. Recovering... +WARNING: Negative moles in solution 59 for C, -6.127747e-04. Recovering... +WARNING: Negative moles in solution 60 for C, -6.127798e-04. Recovering... +WARNING: Negative moles in solution 61 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 62 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 63 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 64 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 65 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 66 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 67 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 68 for C, -6.127361e-04. Recovering... +WARNING: Negative moles in solution 69 for C, -6.127792e-04. Recovering... +WARNING: Negative moles in solution 70 for C, -6.127474e-04. Recovering... +WARNING: Negative moles in solution 71 for C, -6.127799e-04. Recovering... +WARNING: Negative moles in solution 72 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 73 for C, -6.127441e-04. Recovering... +WARNING: Negative moles in solution 74 for C, -6.127802e-04. Recovering... +WARNING: Negative moles in solution 75 for C, -6.127707e-04. Recovering... +WARNING: Negative moles in solution 76 for C, -6.127699e-04. Recovering... +WARNING: Negative moles in solution 77 for C, -6.127840e-04. Recovering... +WARNING: Negative moles in solution 78 for C, -6.127841e-04. Recovering... +WARNING: Negative moles in solution 79 for C, -6.127445e-04. Recovering... + OK +DILUPBiCG: Solving for Y.H, Initial residual = 0.0112878, Final residual = 8.60129e-19, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.0085855, Final residual = 1.38715e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.0111949, Final residual = 2.2614e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00873023, Final residual = 3.87454e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0144441, Final residual = 3.88422e-18, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0112879, Final residual = 3.26687e-18, No Iterations 1 +geochemistry updated + +PIMPLE: Converged in 2 iterations + +ExecutionTime = 1.75433 s + +Courant Number mean: 0.0358546 max: 0.0358546 + + +Time = 86400 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 4.10427e-07, Final residual = 2.31501e-21, No Iterations 1 +time step continuity errors : sum local = 2.13568e-16, global = 5.68956e-17, cumulative = -1.55476e-13 +DICPCG: Solving for p, Initial residual = 2.89317e-14, Final residual = 2.89317e-14, No Iterations 0 +time step continuity errors : sum local = 3.73093e-15, global = 5.62255e-17, cumulative = -1.5542e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 1.67696e-14, Final residual = 1.67696e-14, No Iterations 0 +time step continuity errors : sum local = 2.17856e-15, global = 2.91457e-17, cumulative = -1.55391e-13 +DICPCG: Solving for p, Initial residual = 1.94812e-14, Final residual = 1.94812e-14, No Iterations 0 +time step continuity errors : sum local = 2.5311e-15, global = 2.9034e-17, cumulative = -1.55362e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 0.0108252, Final residual = 5.26781e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00829501, Final residual = 5.83731e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.0107508, Final residual = 9.04183e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00842604, Final residual = 6.59358e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.013771, Final residual = 6.63674e-18, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0108253, Final residual = 4.48192e-18, No Iterations 1 +run phreeqc within Strang loop...WARNING: Negative moles in solution 3 for C, -5.105448e-02. Recovering... +WARNING: Negative moles in solution 3 for Ca, -6.808546e-05. Recovering... +WARNING: Negative moles in solution 4 for C, -5.506350e-04. Recovering... +WARNING: Negative moles in solution 5 for C, -1.796694e-04. Recovering... +WARNING: Negative moles in solution 6 for C, -1.749289e-04. Recovering... +WARNING: Negative moles in solution 7 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 8 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 9 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 10 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 11 for C, -1.749516e-04. Recovering... +WARNING: Negative moles in solution 12 for C, -1.749389e-04. Recovering... +WARNING: Negative moles in solution 13 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 14 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 15 for C, -1.749325e-04. Recovering... +WARNING: Negative moles in solution 16 for C, -1.749369e-04. Recovering... +WARNING: Negative moles in solution 17 for C, -1.749339e-04. Recovering... +WARNING: Negative moles in solution 18 for C, -1.749371e-04. Recovering... +WARNING: Negative moles in solution 19 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 20 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 21 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 22 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 23 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 24 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 25 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 26 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 27 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 28 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 29 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 30 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 31 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 32 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 33 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 34 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 35 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 36 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 37 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 38 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 39 for C, -1.749373e-04. Recovering... +WARNING: Negative moles in solution 40 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 41 for C, -1.749376e-04. Recovering... +WARNING: Negative moles in solution 42 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 43 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 44 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 45 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 46 for C, -1.749462e-04. Recovering... +WARNING: Negative moles in solution 47 for C, -1.749394e-04. Recovering... +WARNING: Negative moles in solution 48 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 49 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 50 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 51 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 52 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 53 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 54 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 55 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 56 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 57 for C, -1.749375e-04. Recovering... +WARNING: Negative moles in solution 58 for C, -1.749188e-04. Recovering... +WARNING: Negative moles in solution 59 for C, -1.749336e-04. Recovering... +WARNING: Negative moles in solution 60 for C, -1.749367e-04. Recovering... +WARNING: Negative moles in solution 61 for C, -1.749326e-04. Recovering... +WARNING: Negative moles in solution 62 for C, -1.749370e-04. Recovering... +WARNING: Negative moles in solution 63 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 64 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 65 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 66 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 67 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 68 for C, -1.749269e-04. Recovering... +WARNING: Negative moles in solution 69 for C, -1.749353e-04. Recovering... +WARNING: Negative moles in solution 70 for C, -1.749292e-04. Recovering... +WARNING: Negative moles in solution 71 for C, -1.749356e-04. Recovering... +WARNING: Negative moles in solution 72 for C, -1.749374e-04. Recovering... +WARNING: Negative moles in solution 73 for C, -1.749286e-04. Recovering... +WARNING: Negative moles in solution 74 for C, -1.749358e-04. Recovering... +WARNING: Negative moles in solution 75 for C, -1.749342e-04. Recovering... +WARNING: Negative moles in solution 76 for C, -1.749347e-04. Recovering... +WARNING: Negative moles in solution 77 for C, -1.749372e-04. Recovering... +WARNING: Negative moles in solution 78 for C, -1.749230e-04. Recovering... +WARNING: Negative moles in solution 79 for C, -1.749297e-04. Recovering... + OK +DILUPBiCG: Solving for Y.H, Initial residual = 0.0104091, Final residual = 1.77072e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00846394, Final residual = 8.91804e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.010334, Final residual = 3.21936e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.0086017, Final residual = 9.39352e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0139146, Final residual = 7.05704e-18, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0104092, Final residual = 3.26179e-18, No Iterations 1 +geochemistry updated + +PIMPLE: Converged in 2 iterations + +ExecutionTime = 2.32703 s + +Courant Number mean: 0.0358233 max: 0.0358233 + + +Time = 108000 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 2.58484e-07, Final residual = 1.60683e-21, No Iterations 1 +time step continuity errors : sum local = 2.46175e-16, global = -2.07147e-17, cumulative = -1.55383e-13 +DICPCG: Solving for p, Initial residual = 2.09398e-15, Final residual = 2.09398e-15, No Iterations 0 +time step continuity errors : sum local = 2.76828e-16, global = -2.06588e-17, cumulative = -1.55403e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 2.41498e-15, Final residual = 2.41498e-15, No Iterations 0 +time step continuity errors : sum local = 3.12842e-16, global = -2.64098e-17, cumulative = -1.5543e-13 +DICPCG: Solving for p, Initial residual = 2.39686e-15, Final residual = 2.39686e-15, No Iterations 0 +time step continuity errors : sum local = 3.10273e-16, global = -2.64098e-17, cumulative = -1.55456e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 0.010025, Final residual = 6.05843e-20, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00818284, Final residual = 1.45445e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.00993948, Final residual = 2.16899e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00830804, Final residual = 1.60519e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0132764, Final residual = 2.36185e-17, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0100251, Final residual = 3.9775e-18, No Iterations 1 +run phreeqc within Strang loop...WARNING: Negative moles in solution 3 for C, -5.323901e-02. Recovering... +WARNING: Negative moles in solution 3 for C, -2.127582e-05. Recovering... +WARNING: Negative moles in solution 4 for C, -1.884856e-03. Recovering... +WARNING: Negative moles in solution 5 for C, -1.203127e-02. Recovering... +WARNING: Negative moles in solution 6 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 7 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 8 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 9 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 10 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 11 for C, -1.195701e-02. Recovering... +WARNING: Negative moles in solution 12 for C, -1.195697e-02. Recovering... +WARNING: Negative moles in solution 13 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 14 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 15 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 16 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 17 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 18 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 19 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 20 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 21 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 22 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 23 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 24 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 25 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 26 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 27 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 28 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 29 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 30 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 31 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 32 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 33 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 34 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 35 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 36 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 37 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 38 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 39 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 40 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 41 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 42 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 43 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 44 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 45 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 46 for C, -1.195699e-02. Recovering... +WARNING: Negative moles in solution 47 for C, -1.195697e-02. Recovering... +WARNING: Negative moles in solution 48 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 49 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 50 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 51 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 52 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 53 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 54 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 55 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 56 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 57 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 58 for C, -1.195690e-02. Recovering... +WARNING: Negative moles in solution 59 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 60 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 61 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 62 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 63 for C, -1.196076e-02. Recovering... +WARNING: Negative moles in solution 64 for C, -1.195735e-02. Recovering... +WARNING: Negative moles in solution 65 for C, -1.195697e-02. Recovering... +WARNING: Negative moles in solution 66 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 67 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 68 for C, -1.195693e-02. Recovering... +WARNING: Negative moles in solution 69 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 70 for C, -1.195694e-02. Recovering... +WARNING: Negative moles in solution 71 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 72 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 73 for C, -1.195693e-02. Recovering... +WARNING: Negative moles in solution 74 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 75 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 76 for C, -1.195695e-02. Recovering... +WARNING: Negative moles in solution 77 for C, -1.195696e-02. Recovering... +WARNING: Negative moles in solution 78 for C, -1.195692e-02. Recovering... +WARNING: Negative moles in solution 79 for C, -1.195693e-02. Recovering... + OK +DILUPBiCG: Solving for Y.H, Initial residual = 0.00966971, Final residual = 4.70998e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00830414, Final residual = 2.22666e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.00957295, Final residual = 2.99635e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00843456, Final residual = 2.19575e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0133808, Final residual = 1.2748e-17, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.0096698, Final residual = 7.84455e-18, No Iterations 1 +geochemistry updated + +PIMPLE: Converged in 2 iterations + +ExecutionTime = 2.93124 s + +Courant Number mean: 0.035823 max: 0.035823 + + +Time = 129600 +PIMPLE: Iteration 1 +DICPCG: Solving for p, Initial residual = 2.43027e-07, Final residual = 2.00354e-21, No Iterations 1 +time step continuity errors : sum local = 2.04355e-16, global = 1.03853e-17, cumulative = -1.55446e-13 +DICPCG: Solving for p, Initial residual = 1.53068e-15, Final residual = 1.53068e-15, No Iterations 0 +time step continuity errors : sum local = 2.05695e-16, global = 1.03853e-17, cumulative = -1.55435e-13 +PIMPLE: Converged + Doing final iteration +PIMPLE: Iteration 2 +DICPCG: Solving for p, Initial residual = 1.55864e-15, Final residual = 1.55864e-15, No Iterations 0 +time step continuity errors : sum local = 2.10162e-16, global = 1.29536e-17, cumulative = -1.55422e-13 +DICPCG: Solving for p, Initial residual = 1.55805e-15, Final residual = 1.55805e-15, No Iterations 0 +time step continuity errors : sum local = 2.1005e-16, global = 1.29536e-17, cumulative = -1.55409e-13 +DILUPBiCG: Solving for Y.H, Initial residual = 0.00934015, Final residual = 1.5906e-18, No Iterations 1 +DILUPBiCG: Solving for Y.O, Initial residual = 0.00801971, Final residual = 1.27219e-18, No Iterations 1 +DILUPBiCG: Solving for Y.Charge, Initial residual = 0.00923459, Final residual = 5.47549e-18, No Iterations 1 +DILUPBiCG: Solving for Y.C, Initial residual = 0.00813781, Final residual = 1.42958e-19, No Iterations 1 +DILUPBiCG: Solving for Y.Ca, Initial residual = 0.0127374, Final residual = 2.12217e-27, No Iterations 1 +DILUPBiCG: Solving for Y.S, Initial residual = 0.00934023, Final residual = 4.59256e-18, No Iterations 1 diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plot.gp diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/100Y.txt diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/10Y.txt diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/120Y.txt diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/plots/MIN3P_Data_Paper/Flux.txt diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/blockMeshDict diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/controlDict diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSchemes diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/fvSolution diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell b/tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell rename to tutorials-pM4F/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/system/graphCell diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ci b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ci similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ci rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ci diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/U b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/U similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/U rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/U diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite.orig similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite.orig diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/p b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/p similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/p rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/p diff --git a/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allclean b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allclean new file mode 100755 index 0000000..7104cd2 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +##rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allrun b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allrun new file mode 100755 index 0000000..db0c796 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/Allrun @@ -0,0 +1,18 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh +runApplication postProcess -func "randomise(field=Ys.Calcite, magPerturbation=0.04)" + +mv 0/'randomise(Ys.Calcite)' 0/Ys.Calcite + +runApplication $application + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/g b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/g similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/g rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/g diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/transportProperties b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties similarity index 90% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/transportProperties rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties index 72f5231..16225b8 100755 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties @@ -24,12 +24,19 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + } transportModel Newtonian; mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; +//nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; geochemicalModel simpleFirstOrderKineticMole; @@ -65,7 +72,7 @@ geochemicalProperties KozenyCarmanCoeffs { K0 K0 [ 0 2 0 0 0 0 0 ] 1e-12; - updateFromInitialValue off; + updateFromInitialValue true; } dispersionModel archiesLaw; @@ -78,8 +85,6 @@ geochemicalProperties } - - // ************************************************************************* // diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/turbulenceProperties b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/turbulenceProperties old mode 100644 new mode 100755 similarity index 100% rename from tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/constant/turbulenceProperties rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/turbulenceProperties diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/blockMeshDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/blockMeshDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/blockMeshDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/blockMeshDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/controlDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/controlDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/controlDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/controlDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/decomposeParDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/decomposeParDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/decomposeParDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/decomposeParDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSchemes b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSchemes similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSchemes rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSchemes diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSolution b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSolution similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSolution rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/fvSolution diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/mapFieldsDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/mapFieldsDict similarity index 100% rename from tutorials/dbsSimpleFoam/constrictedTube/system/mapFieldsDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/mapFieldsDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/setFieldsDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/setFieldsDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/setFieldsDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/system/setFieldsDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ci b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ci similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ci rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ci diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/U b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/U similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/U rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/U diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite.orig similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite.orig diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/p b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/p similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/p rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/p diff --git a/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allclean b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allclean new file mode 100755 index 0000000..7104cd2 --- /dev/null +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allclean @@ -0,0 +1,10 @@ +#!/bin/sh +cd "${0%/*}" || exit 1 + +. $WM_PROJECT_DIR/bin/tools/CleanFunctions + +cleanCase + +##rm *.eps 0/Y.* 0/pH + +#------------------------------------------------------------------------------ diff --git a/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allrun b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allrun new file mode 100755 index 0000000..05edcdd --- /dev/null +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/Allrun @@ -0,0 +1,15 @@ +#!/bin/sh +cd ${0%/*} || exit 1 # Run from this directory + +# Source tutorial run functions +. $WM_PROJECT_DIR/bin/tools/RunFunctions + +application=$(getApplication) + +runApplication blockMesh +runApplication setFields +runApplication $application + + + +#------------------------------------------------------------------------------ diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/constant/transportProperties b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/g old mode 100755 new mode 100644 similarity index 52% rename from tutorials/dbsSimpleFoam/planarPoiseuille/constant/transportProperties rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/g index 4a9e084..f6f9725 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/g @@ -1,34 +1,22 @@ /*--------------------------------*- C++ -*----------------------------------*\ | ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | +| \\ / F ield | foam-extend: Open Source CFD | +| \\ / O peration | Version: 4.0 | +| \\ / A nd | Web: http://www.foam-extend.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ FoamFile { version 2.0; format ascii; - class dictionary; + class uniformDimensionedVectorField; location "constant"; - object transportProperties; + object g; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -transportModel Newtonian; +dimensions [0 1 -2 0 0 0 0]; +value ( 0.0 0.0 0.0 );//( 0 -9.81 0 ); -nu [0 2 -1 0 0 0 0] 0.1; // kinematic -> 0.002 dynamic - - -porousMediaProperties -{ - absolutePermeabilityModel KozenyCarman; - KozenyCarmanCoeffs - { - K0 K0 [0 2 0 0 0 0 0] 1e-14; - } - dispersionModel none; - surfaceAreaModel none; -} // ************************************************************************* // diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/transportProperties b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/physicalProperties similarity index 88% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/transportProperties rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/physicalProperties index d087ce3..29d3ece 100755 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/transportProperties +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/physicalProperties @@ -27,12 +27,20 @@ fluidProperties rho0 rho0 [ 1 -3 0 0 0 0 0 ] 1000; } + viscosityModel constantViscosity; + + constantViscosityCoeffs + { + nu0 nu0 [ 0 2 -1 0 0 0 0 ] 1e-6; + } + + } transportModel Newtonian; -mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; -nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; +//mu mu [ 1 -1 -1 0 0 0 0 ] 1e-3; +//nu nu [ 0 2 -1 0 0 0 0 ] 1e-6; geochemicalModel simpleFirstOrderKineticMole; @@ -63,7 +71,7 @@ geochemicalProperties KozenyCarmanCoeffs { K0 K0 [ 0 2 0 0 0 0 0 ] 1e-11; - updateFromInitialValue off; + updateFromInitialValue on; } dispersionModel archiesLaw; diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/turbulenceProperties b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/turbulenceProperties similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/turbulenceProperties rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/turbulenceProperties diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/blockMeshDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/blockMeshDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/blockMeshDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/blockMeshDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict similarity index 98% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict index b980518..04d7300 100755 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/controlDict @@ -15,7 +15,7 @@ FoamFile } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -application icoFoam; +application dbsFoam; startFrom latestTime; diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/decomposeParDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/decomposeParDict similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/decomposeParDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/decomposeParDict diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSchemes b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSchemes similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSchemes rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSchemes diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSolution b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSolution similarity index 100% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSolution rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/fvSolution diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict similarity index 96% rename from tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict rename to tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict index ef3661b..fb98f98 100755 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict +++ b/tutorials-pM4F/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/system/setFieldsDict @@ -20,7 +20,7 @@ valueAlpha 0.99; //0.9999; defaultFieldValues ( volScalarFieldValue Ys.Calcite 0//0.9999 - volScalarFieldValue Ci 0 // 1e-2 //0.9999 +// volScalarFieldValue Ci 0 // 1e-2 //0.9999 ); diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Sb b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Sb similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Sb rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Sb diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ua b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ua similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ua rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ua diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ub b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ub similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ub rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/Ub diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/p b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/p similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/0/p rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/0/p diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/12000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/12000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/12000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/12000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/20000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/20000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/20000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/20000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/6000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/6000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/6000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case1/6000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/10000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/10000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/10000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/10000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/15000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/15000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/15000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/15000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/5000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/5000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/5000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/5000s diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/resultBL2 b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/resultBL2 similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/resultBL2 rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/analytical/case2/resultBL2 diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/clean b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/clean similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/clean rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/clean diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/K b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/K similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/K rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/K diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case1 b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case1 similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case1 rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case1 diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case2 b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case2 similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case2 rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/g.case2 diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/transportProperties b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/transportProperties similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/transportProperties rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/constant/transportProperties diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseGravity.gp b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseGravity.gp similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseGravity.gp rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseGravity.gp diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseNoGravity.gp b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseNoGravity.gp similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseNoGravity.gp rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/plot_caseNoGravity.gp diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/run b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/run similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/run rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/run diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/run.gravityCase b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/run.gravityCase similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/run.gravityCase rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/run.gravityCase diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/blockMeshDict b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/blockMeshDict similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/blockMeshDict rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/blockMeshDict diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/controlDict b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/controlDict similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/controlDict rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/controlDict diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSchemes b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSchemes similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSchemes rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSchemes diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSolution b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSolution similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSolution rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/fvSolution diff --git a/tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/graphCell b/tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/graphCell similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/BrooksAndCorey/system/graphCell rename to tutorials-pM4F/impesFoam/Buckley-Leverett/BrooksAndCorey/system/graphCell diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Sa b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Sa similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Sa rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Sa diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Sb b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Sb similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Sb rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Sb diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Ua b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Ua similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Ua rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Ua diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Ub b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Ub similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/Ub rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/Ub diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/p b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/p similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/0/p rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/0/p diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/12000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/12000s similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/12000s rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/12000s diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/20000s b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/analytical/case1/20000s similarity index 100% rename from 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tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/K.old diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case1 b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case1 similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case1 rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case1 diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case2 b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case2 similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case2 rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/g.case2 diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/constant/transportProperties b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/constant/transportProperties similarity index 100% rename from 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--git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseGravity.gp b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseGravity.gp similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseGravity.gp rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseGravity.gp diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseNoGravity.gp b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseNoGravity.gp similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseNoGravity.gp rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/plot_caseNoGravity.gp diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/run b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/run similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/run rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/run diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/run.gravityCase b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/run.gravityCase similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/run.gravityCase rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/run.gravityCase diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/system/blockMeshDict b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/system/blockMeshDict similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/system/blockMeshDict rename to tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/system/blockMeshDict diff --git a/tutorials/impesFoam/Buckley-Leverett/VanGenuchten/system/controlDict b/tutorials-pM4F/impesFoam/Buckley-Leverett/VanGenuchten/system/controlDict similarity index 100% rename from tutorials/impesFoam/Buckley-Leverett/VanGenuchten/system/controlDict rename to 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a/tutorials/impesFoam/capillaryValidation/VanGenuchten/system/setFieldsDict b/tutorials-pM4F/impesFoam/capillaryValidation/VanGenuchten/system/setFieldsDict similarity index 100% rename from tutorials/impesFoam/capillaryValidation/VanGenuchten/system/setFieldsDict rename to tutorials-pM4F/impesFoam/capillaryValidation/VanGenuchten/system/setFieldsDict diff --git a/tutorials/impesFoam/capillaryValidation/linear/0/Sb.org b/tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Sb.org similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/0/Sb.org rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Sb.org diff --git a/tutorials/impesFoam/capillaryValidation/linear/0/Ua b/tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Ua similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/0/Ua rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Ua diff --git a/tutorials/impesFoam/capillaryValidation/linear/0/Ub b/tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Ub similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/0/Ub rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/0/Ub diff --git a/tutorials/impesFoam/capillaryValidation/linear/0/p b/tutorials-pM4F/impesFoam/capillaryValidation/linear/0/p similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/0/p rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/0/p diff --git a/tutorials/impesFoam/capillaryValidation/linear/clean b/tutorials-pM4F/impesFoam/capillaryValidation/linear/clean similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/clean rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/clean diff --git a/tutorials/impesFoam/capillaryValidation/linear/constant/K b/tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/K similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/constant/K rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/K diff --git a/tutorials/impesFoam/capillaryValidation/linear/constant/g b/tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/g similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/constant/g rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/g diff --git a/tutorials/impesFoam/capillaryValidation/linear/constant/transportProperties b/tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/transportProperties similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/constant/transportProperties rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/constant/transportProperties diff --git a/tutorials/impesFoam/capillaryValidation/linear/plot.gp b/tutorials-pM4F/impesFoam/capillaryValidation/linear/plot.gp similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/plot.gp rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/plot.gp diff --git a/tutorials/impesFoam/capillaryValidation/linear/run b/tutorials-pM4F/impesFoam/capillaryValidation/linear/run similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/run rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/run diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/blockMeshDict b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/blockMeshDict similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/blockMeshDict rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/blockMeshDict diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/controlDict b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/controlDict similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/controlDict rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/controlDict diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/fvSchemes b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/fvSchemes similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/fvSchemes rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/fvSchemes diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/fvSolution b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/fvSolution similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/fvSolution rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/fvSolution diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/graphCell b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/graphCell similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/graphCell rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/graphCell diff --git a/tutorials/impesFoam/capillaryValidation/linear/system/setFieldsDict b/tutorials-pM4F/impesFoam/capillaryValidation/linear/system/setFieldsDict similarity index 100% rename from tutorials/impesFoam/capillaryValidation/linear/system/setFieldsDict rename to tutorials-pM4F/impesFoam/capillaryValidation/linear/system/setFieldsDict diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/clean b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/clean deleted file mode 100755 index 1fa0658..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/clean +++ /dev/null @@ -1,6 +0,0 @@ -rm -r postProcessing constant/polyMesh - -foamListTimes -rm - - -rm log.* *.eps 0/Y.* 0/pH diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/run b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/run deleted file mode 100755 index bd1853b..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionDolomitePrecipitation/run +++ /dev/null @@ -1,19 +0,0 @@ -#Script to mesh, run the benchmark case (B1. M Xie - Calcite dissolution), post process output data, plot results - - - -echo Building mesh -blockMesh > log.blockMesh - -echo Running the case -constantVelocityFoam > log.constantVelocityFoam -echo End of the run - - - -#Output data at 20, 40 and 60 min. -postProcess -time 1200,2400,3600 -func graphCell - -gnuplot plot.gp - -echo END diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Ca b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Ca deleted file mode 100755 index a4bd45a..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Ca +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.Ca; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0.0005113; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Cl b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Cl deleted file mode 100755 index 7da152a..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.Cl +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.Cl; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 9.97e-16; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0.01095; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.H b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.H deleted file mode 100755 index 1247351..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.H +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.H; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 110.7; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 110.7; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.O b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.O deleted file mode 100755 index 49dcbdb..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/Y.O +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.O; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 55.34; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 55.33; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/pH b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/pH deleted file mode 100755 index 518fcdc..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/0/pH +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object pH; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 8.246; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/clean b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/clean deleted file mode 100755 index 27a70fa..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/clean +++ /dev/null @@ -1,7 +0,0 @@ -foamListTimes -rm - -rm -r postProcessing constant/polyMesh - -rm log.* - -rm *.eps diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/run b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/run deleted file mode 100755 index f8067ec..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithKineticReactions/run +++ /dev/null @@ -1,8 +0,0 @@ -blockMesh > log.blockMesh - -constantVelocityFoam > log.constantVelocityFoam - -postProcess -func graphCell > log.postProcess - - -gnuplot plot.gp diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.C b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.C deleted file mode 100755 index 0069d20..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.C +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.C; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0.001018; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Ca b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Ca deleted file mode 100755 index a4bd45a..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Ca +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.Ca; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0.0005113; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Charge b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Charge deleted file mode 100755 index 8f5bdf9..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Charge +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.Charge; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform -4.832e-12; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform -6.397e-11; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Cl b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Cl deleted file mode 100755 index 7da152a..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.Cl +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.Cl; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 9.97e-16; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 0.01095; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.H b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.H deleted file mode 100755 index 1247351..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.H +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.H; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 110.7; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 110.7; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.O b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.O deleted file mode 100755 index 49dcbdb..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/Y.O +++ /dev/null @@ -1,39 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Y.O; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 55.34; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type fixedValue; - value uniform 55.33; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/pH b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/pH deleted file mode 100755 index 518fcdc..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/0/pH +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object pH; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 8.246; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/clean b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/clean deleted file mode 100755 index 53a99f2..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/clean +++ /dev/null @@ -1,5 +0,0 @@ -foamListTimes -rm - -rm -r postProcessing constant/polyMesh - -rm *.eps log.* diff --git a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/run b/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/run deleted file mode 100755 index 5389adc..0000000 --- a/tutorials/constantVelocityFoam/phreeqcRM/calciteDissolutionWithThermEquilibrium/run +++ /dev/null @@ -1,7 +0,0 @@ -blockMesh > log.blockMesh - -constantVelocityFoam > log.constantVelocityFoam - -postProcess -func graphCell > log.postProcess - -gnuplot plot.gp diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/clean b/tutorials/constantVelocityFoam/transportOnly/linearDispersion/clean deleted file mode 100755 index 8f6340e..0000000 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/clean +++ /dev/null @@ -1,7 +0,0 @@ -foamListTimes -rm - -rm -r postProcessing - -rm *.eps - -rm -r constant/polyMesh diff --git a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/run b/tutorials/constantVelocityFoam/transportOnly/linearDispersion/run deleted file mode 100755 index d50428c..0000000 --- a/tutorials/constantVelocityFoam/transportOnly/linearDispersion/run +++ /dev/null @@ -1,10 +0,0 @@ -blockMesh - -constantVelocityFoam - -postProcess -func "probes(points=((10 0 0)), fields=(Ci))" - -## postProcess -func "boundaryProbes(points=((10 0 0)),maxDistance=1e-3 fields=(Ci))" - - -gnuplot plot.gp diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/clean b/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/clean deleted file mode 100755 index 1ac5deb..0000000 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/clean +++ /dev/null @@ -1,9 +0,0 @@ -rm -r postProcessing constant/polyMesh - -foamListTimes -rm - - -rm log.* *.eps - - -cp 0/K.Orig 0/K diff --git a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/run b/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/run deleted file mode 100755 index 2a967a5..0000000 --- a/tutorials/darcyFoam/flowOnly/heterogeneousPermeability/run +++ /dev/null @@ -1,13 +0,0 @@ - -blockMesh > log.blockMesh - - -setFields > log.setFields - - -darcyFoam > log.darcyFoam - - -postProcess -func graphCell > log.postProcess - -gnuplot plot.gp diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/clean b/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/clean deleted file mode 100755 index b45f09d..0000000 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/clean +++ /dev/null @@ -1,12 +0,0 @@ -#Script to mesh, run the benchmark case (B2. M Xie - Calcite dissolution, Gypsum precipitation - dissolution), post process output data, plot results - -echo "Clean case" - -#Remove any previous output files and run the case from 0 -foamListTimes -rm - -rm -r constant/polyMesh postProcessing - -rm 0/Y.* 0/pH log.* *.eps - -echo END diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/run b/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/run deleted file mode 100755 index 6fccba7..0000000 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionGypsumPrecipitationPorosityClogging/run +++ /dev/null @@ -1,26 +0,0 @@ -#Script to mesh, run the benchmark case (B2. M Xie - Calcite dissolution, Gypsum precipitation - dissolution), post process output data, plot results - -echo Building mesh -blockMesh > log.blockMesh - -echo Running the case -darcyFoam > log.darcyFoam -echo End of the run - -#Output cell center data at 10, 100 years -#Data written for - -#porosity, -#hydraulic head (pressure), -#gypsum volume fraction, -#hydraulic conductivity (permeability), -#calcite volume fraction and -#flux -echo Postprocessing output data - check postProcess folder -postProcess -time 3.149928e+08,3.1499928e+09 -func graphCell - -#Output flux -postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' - -gnuplot plot.gp - -echo END diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean b/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean deleted file mode 100755 index 1fa0658..0000000 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean +++ /dev/null @@ -1,6 +0,0 @@ -rm -r postProcessing constant/polyMesh - -foamListTimes -rm - - -rm log.* *.eps 0/Y.* 0/pH diff --git a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run b/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run deleted file mode 100755 index 4a053a2..0000000 --- a/tutorials/darcyFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run +++ /dev/null @@ -1,24 +0,0 @@ -#Script to mesh, run the benchmark case (B1. M Xie - Calcite dissolution), post process output data, plot results - -#Remove any previous output files and run the case from 0 -#foamListTimes -rm - -echo Building mesh -blockMesh > log.blockMesh - -echo Running the case -darcyFoam > log.darcyFoam -echo End of the run - -#Output cell center data at 10, 100, 120 years -#Data written for - porosity, calcite volume fraction and pressure -echo Postprocessing output data - check postProcess folder -postProcess -time 3.149928e+08,3.1499928e+09,3.78e+09 -func graphCell - -#Output flux -postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' - - -gnuplot plot.gp - -echo END diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K b/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K deleted file mode 100644 index 084a6db..0000000 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object K; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 2 0 0 0 0 0]; - -internalField uniform 1e-11; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K.Orig b/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K.Orig deleted file mode 100644 index 084a6db..0000000 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/0/K.Orig +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object K; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 2 0 0 0 0 0]; - -internalField uniform 1e-11; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/clean b/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/clean deleted file mode 100755 index 1ac5deb..0000000 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/clean +++ /dev/null @@ -1,9 +0,0 @@ -rm -r postProcessing constant/polyMesh - -foamListTimes -rm - - -rm log.* *.eps - - -cp 0/K.Orig 0/K diff --git a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/run b/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/run deleted file mode 100755 index a7f40ed..0000000 --- a/tutorials/dbsFoam/flowOnly/heterogeneousPermeability/run +++ /dev/null @@ -1,13 +0,0 @@ - -blockMesh > log.blockMesh - - -setFields > log.setFields - - -dbsFoam > log.dbsFoam - - -postProcess -func graphCell > log.postProcess - -gnuplot plot.gp diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite b/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite deleted file mode 100644 index 2af1aeb..0000000 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/Ys.Calcite +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Ys.Calcite; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0.3; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/pH b/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/pH deleted file mode 100644 index 45514e2..0000000 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/0/pH +++ /dev/null @@ -1,38 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object pH; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 9.375; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean b/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean deleted file mode 100755 index e70d35f..0000000 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/clean +++ /dev/null @@ -1,6 +0,0 @@ -rm -r postProcessing constant/polyMesh - -foamListTimes -rm - - -rm log.* *.eps diff --git a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run b/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run deleted file mode 100755 index 3ed06d7..0000000 --- a/tutorials/dbsFoam/phreeqcRM/calciteDissolutionWithPorosityChange/run +++ /dev/null @@ -1,24 +0,0 @@ -#Script to mesh, run the benchmark case (B1. M Xie - Calcite dissolution), post process output data, plot results - -#Remove any previous output files and run the case from 0 -#foamListTimes -rm - -echo Building mesh -blockMesh > log.blockMesh - -echo Running the case -dbsFoam > log.dbsFoam -echo End of the run - -#Output cell center data at 10, 100, 120 years -#Data written for - porosity, calcite volume fraction and pressure -echo Postprocessing output data - check postProcess folder -postProcess -time 3.149928e+08,3.1499928e+09,3.78e+09 -func graphCell - -#Output flux -postProcess -time 0:6e+09 -func 'patchFlowRate(patch=outlet)' - - -gnuplot plot.gp - -echo END diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite.Orig b/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite.Orig deleted file mode 100755 index 0e5b388..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/0/Ys.Calcite.Orig +++ /dev/null @@ -1,46 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 10 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - format ascii; - class volScalarField; - location "0"; - object Ys.Calcite; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0.8; - -boundaryField -{ - outlet - { - type zeroGradient; - } - inlet - { - type zeroGradient; - } - frontAndBack - { - type empty; - } - bottom - { - type zeroGradient; - } - top - { - type zeroGradient; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/clean b/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/clean deleted file mode 100755 index ff7e285..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/clean +++ /dev/null @@ -1,10 +0,0 @@ -foamListTimes -rm - - -rm -r constant/polyMesh - - -rm log.* 0/randomise* - - -cp 0/Ys.Calcite.Orig 0/Ys.Calcite diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties b/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties deleted file mode 100755 index fa2b0b3..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/constant/physicalProperties +++ /dev/null @@ -1,41 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: 2.2.2 | -| \\ / A nd | Web: www.OpenFOAM.org | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - location "constant"; - object physicalProperties; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -transportModel Newtonian; - -//mu mu [1 -1 -1 0 0 0 0] 1e-3; -rho rho [1 -3 0 0 0 0 0] 1000; -nu nu [0 2 -1 0 0 0 0] 1e-6; - -Di Di [0 2 -1 0 0 0 0] 1e-9; - - -K0 K0 [0 2 0 0 0 0 0] 1.e-12; - - -Vm Vm [0 3 0 0 -1 0 0] 36.9e-6; - - -alpha alpha [0 1 -1 0 0 0 0] -1e-3; - - -A0 A0 [0 -1 0 0 0 0 0] 1e3; - - -// ************************************************************************* // - - diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/run b/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/run deleted file mode 100755 index 13ab3db..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/dissolutionWormholing/run +++ /dev/null @@ -1,14 +0,0 @@ - - -blockMesh > log.blockMesh - -postProcess -func "randomise(field=Ys.Calcite, magPerturbation=0.04)" > log.postProcessRandomise - - -cp 0/'randomise(Ys.Calcite)' 0/Ys.Calcite - - -dbsFoam > log.dbsFoam - - - diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite.Orig b/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite.Orig deleted file mode 100755 index e94e89a..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/0/Ys.Calcite.Orig +++ /dev/null @@ -1,47 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 7 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class volScalarField; - location "0"; - object Ys.Calcite; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 0 0 0 0 0 0]; - -internalField uniform 0; - -boundaryField -{ - right - { - type zeroGradient; - } - left - { - type zeroGradient; - } - bottom - { - type zeroGradient; - } - top - { - type zeroGradient; - } - frontAndBack - { - type empty; - } -} - - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/clean b/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/clean deleted file mode 100755 index 5e29a83..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/clean +++ /dev/null @@ -1,11 +0,0 @@ - -foamListTimes -rm - - -rm -r constant/polyMesh postProcessing - - -rm log.* 0/Y.* 0/pH - - -cp 0/Ys.Calcite.Orig 0/Ys.Calcite diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/turbulenceProperties b/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/turbulenceProperties deleted file mode 100755 index b882bea..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/constant/turbulenceProperties +++ /dev/null @@ -1,34 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | Website: https://openfoam.org - \\ / A nd | Version: 6 - \\/ M anipulation | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - object turbulenceProperties; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -simulationType laminar; - -/* -laminar -{ - laminarModel Stokes; //Maxwell; - - MaxwellCoeffs - { - nuM 1; - lambda 5; - } - - printCoeffs on; -} -*/ - -// ************************************************************************* // diff --git a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/run b/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/run deleted file mode 100755 index cc901b7..0000000 --- a/tutorials/dbsFoam/simpleFirstOrderKineticMole/poreScaleCalciteDissolution/run +++ /dev/null @@ -1,8 +0,0 @@ - -blockMesh > log.blockMesh - - -setFields > log.setFields - - -dbsFoam > log.dbsFoam diff --git a/tutorials/dbsSimpleFoam/constrictedTube/clean b/tutorials/dbsSimpleFoam/constrictedTube/clean deleted file mode 100755 index 68f699a..0000000 --- a/tutorials/dbsSimpleFoam/constrictedTube/clean +++ /dev/null @@ -1,7 +0,0 @@ -foamListTimes -rm - - -rm -r constant/polyMesh - - -rm 0/eps 0/K log.* diff --git a/tutorials/dbsSimpleFoam/constrictedTube/constant/transportProperties b/tutorials/dbsSimpleFoam/constrictedTube/constant/transportProperties deleted file mode 100755 index 31ea0d8..0000000 --- a/tutorials/dbsSimpleFoam/constrictedTube/constant/transportProperties +++ /dev/null @@ -1,41 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - location "constant"; - object transportProperties; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -transportModel Newtonian; - -nu [0 2 -1 0 0 0 0] 0.1; // kinematic -> 0.002 dynamic - - -porousMediaProperties -{ - absolutePermeabilityModel KozenyCarman; - KozenyCarmanCoeffs - {} - - - surfaceAreaModel none; - dispersionModel none; - -} - -activateHeleShaw false; -HeleShawCoeffs -{ - h h [0 1 0 0 0 0 0] 10e-6; -} - -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/constrictedTube/run b/tutorials/dbsSimpleFoam/constrictedTube/run deleted file mode 100755 index 63c31b0..0000000 --- a/tutorials/dbsSimpleFoam/constrictedTube/run +++ /dev/null @@ -1,15 +0,0 @@ -cp 0/eps.org 0/eps -cp 0/K.org 0/K - - -blockMesh > log.blockMesh - -##topoSet > log.blockMesh -##refineMesh -overwrite -##refineMesh -overwrite -##refineMesh -overwrite - -setFields > log.setFields - - -dbsSimpleFoam > log.dbsSimpleFoam diff --git a/tutorials/dbsSimpleFoam/constrictedTube/system/fvSolution b/tutorials/dbsSimpleFoam/constrictedTube/system/fvSolution deleted file mode 100755 index edadbef..0000000 --- a/tutorials/dbsSimpleFoam/constrictedTube/system/fvSolution +++ /dev/null @@ -1,69 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - location "system"; - object fvSolution; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // -solvers -{ - p - { - solver GAMG; - smoother DIC; - tolerance 1e-6; - relTol 0.05; - } - - U - { - solver smoothSolver; - smoother symGaussSeidel; - tolerance 1e-6; - relTol 0.1; - } - - pFinal - { - $p; - relTol 0; - } - - UFinal - { - $U; - relTol 0; - } -} - - -SIMPLE -{ - nNonOrthogonalCorrectors 0; - consistent yes; - - residualControl - { - p 1e-5; - U 1e-5; - } -} - -relaxationFactors -{ - equations - { - U 0.9; // 0.9 is more stable but 0.95 more convergent - ".*" 0.9; // 0.9 is more stable but 0.95 more convergent - } -} -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/0/U b/tutorials/dbsSimpleFoam/planarPoiseuille/0/U deleted file mode 100755 index 472aede..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/0/U +++ /dev/null @@ -1,51 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class volVectorField; - object U; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -dimensions [0 1 -1 0 0 0 0]; - -internalField uniform (0 0 0); - -boundaryField -{ - left - { - type fixedValue; - value uniform (1 0 0); - } - - right - { - type zeroGradient; - } - - top - { - type symmetryPlane; - } - - bottom - { - type fixedValue; - value uniform (0 0 0); - } - - frontAndBack - { - type empty; - } -} - -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/clean b/tutorials/dbsSimpleFoam/planarPoiseuille/clean deleted file mode 100755 index f5c432d..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/clean +++ /dev/null @@ -1,3 +0,0 @@ -rm -r constant/polyMesh log.* - -foamListTimes -rm diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/run b/tutorials/dbsSimpleFoam/planarPoiseuille/run deleted file mode 100755 index be71322..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/run +++ /dev/null @@ -1,4 +0,0 @@ -blockMesh > log.blockMesh - - -dbsSimpleFoam > log.dbsSimpleFoam diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/system/blockMeshDict b/tutorials/dbsSimpleFoam/planarPoiseuille/system/blockMeshDict deleted file mode 100755 index 779a125..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/system/blockMeshDict +++ /dev/null @@ -1,89 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - object blockMeshDict; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -scale 1e-3; - -vertices -( - (0 0 0) - (20 0 0) - (20 1 0) - (0 1 0) - (0 0 0.1) - (20 0 0.1) - (20 1 0.1) - (0 1 0.1) -); - -blocks -( - hex (0 1 2 3 4 5 6 7) (100 20 1) simpleGrading (1 5 1) -); - -edges -( -); - -boundary -( - top - { - type symmetryPlane; - faces - ( - (3 7 6 2) - ); - } - left - { - type patch; - faces - ( - (0 4 7 3) - ); - } - right - { - type patch; - faces - ( - (2 6 5 1) - ); - } - bottom - { - type wall; - faces - ( - (1 5 4 0) - ); - } - frontAndBack - { - type empty; - faces - ( - (0 3 2 1) - (4 5 6 7) - ); - } -); - -mergePatchPairs -( -); - -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/system/controlDict b/tutorials/dbsSimpleFoam/planarPoiseuille/system/controlDict deleted file mode 100755 index b41b14d..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/system/controlDict +++ /dev/null @@ -1,54 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - location "system"; - object controlDict; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -application simpleFoam; - -startFrom startTime; - -startTime 0; - -stopAt endTime; - -endTime 1000; - -deltaT 1; - -writeControl runTime; - -writeInterval 1000; - -purgeWrite 0; - -writeFormat ascii; - -writePrecision 6; - -writeCompression off; - -timeFormat general; - -timePrecision 6; - -runTimeModifiable true; - -/* -functions -{ - #includeFunc streamlines -} -*/ -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSchemes b/tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSchemes deleted file mode 100755 index e197ba1..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/system/fvSchemes +++ /dev/null @@ -1,54 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ -| ========= | | -| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | -| \\ / O peration | Version: plus | -| \\ / A nd | Web: www.OpenFOAM.com | -| \\/ M anipulation | | -\*---------------------------------------------------------------------------*/ -FoamFile -{ - version 2.0; - format ascii; - class dictionary; - location "system"; - object fvSchemes; -} -// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // - -ddtSchemes -{ -// default backward; - default steadyState; -} - -gradSchemes -{ - default Gauss linear; -} - -divSchemes -{ - default none; - - div(phi,U) Gauss linearUpwind grad(U); - div((nu*dev2(T(grad(U))))) Gauss linear; - div((nuEff*dev2(T(grad(U))))) Gauss linear; - div((nuM*grad(U))) Gauss linear; -} - -laplacianSchemes -{ - default Gauss linear uncorrected; -} - -interpolationSchemes -{ - default linear; -} - -snGradSchemes -{ - default uncorrected; -} - -// ************************************************************************* // diff --git a/tutorials/dbsSimpleFoam/planarPoiseuille/system/streamlines b/tutorials/dbsSimpleFoam/planarPoiseuille/system/streamlines deleted file mode 100755 index bcf7a7d..0000000 --- a/tutorials/dbsSimpleFoam/planarPoiseuille/system/streamlines +++ /dev/null @@ -1,22 +0,0 @@ -/*--------------------------------*- C++ -*----------------------------------*\ - ========= | - \\ / F ield | OpenFOAM: The Open Source CFD Toolbox - \\ / O peration | - \\ / A nd | Web: www.OpenFOAM.com - \\/ M anipulation | -------------------------------------------------------------------------------- -Description - Writes out files of streamlines with interpolated field data in VTK format. - -\*---------------------------------------------------------------------------*/ - -nLines 10; -start (-0.0205 0.001 0.00001); -end (-0.0205 0.0251 0.00001); -fields (p k U); -U U; - -// Must be last entry -#includeEtc "caseDicts/postProcessing/visualization/streamlines.cfg" - -// ************************************************************************* //