geochemical package update

Allwclean

@@ -22,5 +22,4 @@ then
     rm -f $FOAM_USER_LIBBIN/libporousModels.so
     rm -f $FOAM_USER_LIBBIN/libtoolsGIS.so
     rm -f $FOAM_USER_LIBBIN/liboherModelsGIS.so
-    rm -f $FOAM_USER_LIBBIN/libgeochemicalModels.so
 fi

libraries/porousModels/Make/files

@@ -41,6 +41,8 @@ unsaturatedPorousModels/unsaturatedPorousModel.C
 
 geochemicalModels/basicGeochemicalModel/basicGeochemicalModel.C
 geochemicalModels/basicGeochemicalModel/basicGeochemicalModelNew.C
+geochemicalModels/flowOnly/flowOnly.C
+
 
 geochemicalModels/geochemicalModel.C
 

libraries/porousModels/geochemicalModels/basicGeochemicalModel/basicGeochemicalModel.C

@@ -41,11 +41,85 @@ Foam::basicGeochemicalModel::basicGeochemicalModel
     const dictionary& dict
 )
 :
-//      basicGeochemicalModel(mesh, dict.subDict("geochemicalProperties")),
       mesh_(mesh),
-      mineralList_(dict.lookup("mineral"))
+      mineralList_(dict.lookup("mineral")),
+      Ys_(mineralList_.size() ),
+      inertMineral_
+      (
+          IOobject
+          (
+              "inertMineral",
+              mesh.time().timeName(),
+              mesh,
+              IOobject::READ_IF_PRESENT,
+              IOobject::AUTO_WRITE
+          ),
+          mesh,
+          dimensionedScalar("inertMineral",dimless,0.0),
+          "zeroGradient"
+      ),
+      eps_
+      (
+          IOobject
+          (
+              "eps",
+              mesh.time().timeName(),
+              mesh,
+              IOobject::NO_READ,
+              IOobject::AUTO_WRITE
+          ),
+          mesh,
+          dimensionedScalar("eps",dimless,1.0),
+          "zeroGradient"
+      ),
+      porousMedia_(mineralList_.size()),
+      absolutePermeabilityModelPtr_
+      (
+          absolutePermeabilityModel::New(mesh, dict)
+      )
 ///      rhol_(dict.lookup("rhol"))
 {
+
+    forAll(mineralList_,s)
+    {
+      word currentMineral = mineralList_[s];
+      Info << " Doing stuff for mineral: " << currentMineral << endl;
+
+      Ys_.set
+      (
+        s,
+        new volScalarField
+        (
+          IOobject
+          (
+            "Ys."+mineralList_[s],
+            mesh_.time().timeName(),
+            mesh_,
+            IOobject::MUST_READ, //READ_IF_PRESENT,  //MUST_READ ??
+            IOobject::AUTO_WRITE
+          ),
+          mesh_ //,
+          //		dimensionedScalar(currentMineral,dimless,0.0),
+          //		"zeroGradient"
+        )
+      );
+      Ys_[s].write();
+
+      porousMedia_.set
+      (
+        s,
+        new porousModel
+        (
+          mesh,
+          mineralList_[s],
+          Ys_[s],
+          dict
+        )
+      );
+    }
+    updatePorosity();
+
+
 }
 
 // -------------------------------------------------------------------------//
@@ -77,4 +151,17 @@ Foam::volScalarField Foam::basicGeochemicalModel::rhol() const
     return rhol_;
 }
 */
+
+void Foam::basicGeochemicalModel::updatePorosity()
+{
+    eps_ = 0.0*eps_;
+    forAll(mineralList_,s)
+    {
+        eps_+=Ys_[s];
+    }
+    eps_ = 1.-eps_-inertMineral_;
+}
+
+
+
 // ************************************************************************* //

libraries/porousModels/geochemicalModels/basicGeochemicalModel/basicGeochemicalModel.H

@@ -62,21 +62,19 @@ class basicGeochemicalModel
     const fvMesh &mesh_;
 
     speciesTable mineralList_;
-/*
+
     PtrList<volScalarField> Ys_;
 
     volScalarField inertMineral_;
 
     volScalarField eps_;
-*/
 
-
-//    autoPtr<surfaceAreaModel> surfaceAreaModelPtr_;
+    PtrList<porousModel> porousMedia_;
 
 //    tmp<volScalarField> Ae_;
 //    volScalarField Ae_;
 
-//    autoPtr<permeabilityModel> permeabilityModelPtr_;
+    autoPtr<absolutePermeabilityModel> absolutePermeabilityModelPtr_;
 /*
     tmp<volScalarField> invK_;
 */
@@ -145,7 +143,8 @@ class basicGeochemicalModel
 
     virtual void updatePermeability();
 */
-/*
+/*    rm -f $FOAM_USER_LIBBIN/libgeochemicalModels.so
+
     tmp<volScalarField> surfaceArea() const
 //    volScalarField surfaceArea() const
     {
@@ -187,9 +186,24 @@ class basicGeochemicalModel
 
 */
 
-    virtual void updatePorosity() = 0;
+    void updatePorosity();
+
+  //  virtual volScalarField dMs() const = 0;
 
-    virtual volScalarField dMs() const = 0;
+    tmp<volScalarField> porosity() const
+    {
+        return eps_;
+    }
+
+    tmp<volScalarField> absolutePermeability() const
+    {
+        return absolutePermeabilityModelPtr_->absolutePermeability();
+    }
+
+    tmp<volScalarField> inversePermeability() const
+    {
+        return absolutePermeabilityModelPtr_->inversePermeability();
+    }
 
     void coucou()
     {

libraries/porousModels/geochemicalModels/flowOnly/flowOnly.C

@@ -0,0 +1,90 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Copyright (C) 2011-2018 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 <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "flowOnly.H"
+#include "addToRunTimeSelectionTable.H"
+
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    namespace geochemicalModels
+    {
+        defineTypeNameAndDebug(flowOnly, 0);
+
+        addToRunTimeSelectionTable
+        (
+            basicGeochemicalModel,
+            flowOnly,
+            dictionary
+        );
+    }
+}
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::geochemicalModels::flowOnly::flowOnly
+(
+    const fvMesh& mesh,
+    const dictionary& dict
+)
+:
+      basicGeochemicalModel(mesh, dict)
+///      rhol_(dict.lookup("rhol"))
+{
+    Info << " flowOnly, no geochemistry " << nl << endl;
+}
+
+// -------------------------------------------------------------------------//
+
+/*
+Foam::volScalarField Foam::flowOnly::dMl() const
+{
+
+    volScalarField dMl_(0.0*fvc::ddt(Y_[0])/this->rhol());
+    forAll(Y_,s)
+    {
+        dMl_ = dMl_ + fvc::ddt(Y_[s])/this->rhol();
+    }
+
+    return dMl_;
+}
+*/
+
+/*
+Foam::volScalarField Foam::flowOnly::rhol() const
+{
+
+    volScalarField rhol_(0.0*Y_[0]);
+    forAll(Y_,s)
+    {
+        rhol_ = rhol_ + Y_[s];
+    }
+
+    return rhol_;
+}
+*/
+// ************************************************************************* //