Merge branch 'master' of /home/noisy2/OpenFOAM/OpenFOAM-dev/

applications/solvers/molecularDynamics/gnemdFoam/Make/files

+gnemdFoam.C
+
+EXE = $(FOAM_APPBIN)/gnemdFoam

applications/solvers/molecularDynamics/gnemdFoam/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule

applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C

+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2005 OpenCFD Ltd.
+    \\/      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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    gnemdFOAM
+
+Description
+    MD for Fluid Mechanics and hybridising with a continuum solver.
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    moleculeCloud molecules(mesh);
+
+#   include "createMDFields.H"
+
+    molecules.removeHighEnergyOverlaps();
+
+#   include "temperatureAndPressureVariables.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.run())
+    {
+        runTime++;
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.integrateEquationsOfMotion();
+
+#       include "meanMomentumEnergyAndNMols.H"
+
+#       include "temperatureAndPressure.H"
+
+#       include "calculateMDFields.H"
+
+#       include "averageMDFields.H"
+
+        runTime.write();
+
+#       include "resetMDFields.H"
+
+        if (runTime.outputTime())
+        {
+            nAveragingSteps = 0;
+        }
+
+        Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info << "End\n" << endl;
+
+    return(0);
+}

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/files

+mdEquilibrationFoam.C
+
+EXE = $(FOAM_APPBIN)/mdEquilibrationFoam

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule

applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2005 OpenCFD Ltd.
+    \\/      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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    mdEquilibrationFOAM
+
+Description
+    Equilibrates and/or preconditions MD systems
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    moleculeCloud molecules(mesh);
+
+    molecules.removeHighEnergyOverlaps();
+
+#   include "temperatureAndPressureVariables.H"
+
+#   include "readmdEquilibrationDict.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.run())
+    {
+        runTime++;
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.integrateEquationsOfMotion();
+
+#       include "meanMomentumEnergyAndNMols.H"
+
+#       include "temperatureAndPressure.H"
+
+#       include "temperatureEquilibration.H"
+
+        runTime.write();
+
+        if (runTime.outputTime())
+        {
+            nAveragingSteps = 0;
+        }
+
+        Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info << "End\n" << endl;
+
+    return(0);
+}

applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H

+Info<< "Reading MD Equilibration Dictionary" << nl << endl;
+
+IOdictionary mdEquilibrationDict
+(
+    IOobject
+    (
+        "mdEquilibrationDict",
+        runTime.system(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE
+    )
+);
+
+scalar targetTemperature = readScalar
+(
+    mdEquilibrationDict.lookup("equilibrationTargetTemperature")
+);

applications/utilities/postProcessing/field/components/components.C

@@ -35,44 +35,7 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-template <class Type>
-void writeComponents
-(
-    const IOobject& header,
-    const fvMesh& mesh,
-    bool& processed
-)
-{
-    typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
-
-    if (header.headerClassName() == fieldType::typeName)
-    {
-        Info<< "    Reading " << header.name() << endl;
-        fieldType field(header, mesh);
-
-        for (direction i=0; i<Type::nComponents; i++)
-        {
-            Info<< "    Calculating " << header.name()
-                << Type::componentNames[i] << endl;
-
-            volScalarField componentField
-            (
-                IOobject
-                (
-                    header.name() + word(Type::componentNames[i]),
-                    mesh.time().timeName(),
-                    mesh,
-                    IOobject::NO_READ
-                ),
-                field.component(i)
-            );
-            componentField.write();
-        }
-
-        processed = true;
-    }
-}
-
+#include "writeComponentFields.C"
 
 int main(int argc, char *argv[])
 {
@@ -115,10 +78,15 @@ int main(int argc, char *argv[])
             mesh.readUpdate();
 
             bool processed = false;
-            writeComponents<vector>(fieldHeader, mesh, processed);
-            writeComponents<sphericalTensor>(fieldHeader, mesh, processed);
-            writeComponents<symmTensor>(fieldHeader, mesh, processed);
-            writeComponents<tensor>(fieldHeader, mesh, processed);
+            writeComponentFields<vector>(fieldHeader, mesh, processed);
+            writeComponentFields<sphericalTensor>
+            (
+                fieldHeader,
+                mesh,
+                processed
+            );
+            writeComponentFields<symmTensor>(fieldHeader, mesh, processed);
+            writeComponentFields<tensor>(fieldHeader, mesh, processed);
             if (!processed)
             {
                 FatalError

applications/utilities/postProcessing/field/components/writeComponentFields.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
+     \\/     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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    components
+
+Description
+    Writes scalar fields corresponding to each component of the supplied
+    field (name) for each time.
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+template <class Type>
+void writeComponentFields
+(
+    const IOobject& header,
+    const fvMesh& mesh,
+    bool& processed
+)
+{
+    typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
+
+    if (header.headerClassName() == fieldType::typeName)
+    {
+        Info<< "    Reading " << header.name() << endl;
+        fieldType field(header, mesh);
+
+        for (direction i=0; i<Type::nComponents; i++)
+        {
+            Info<< "    Calculating " << header.name()
+                << Type::componentNames[i] << endl;
+
+            volScalarField componentField
+            (
+                IOobject
+                (
+                    header.name() + word(Type::componentNames[i]),
+                    mesh.time().timeName(),
+                    mesh,
+                    IOobject::NO_READ
+                ),
+                field.component(i)
+            );
+            componentField.write();
+        }
+
+        processed = true;
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/utilities/postProcessing/field/mag/mag.C

@@ -34,39 +34,7 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-template<class Type>
-void writeMagField
-(
-    const IOobject& header,
-    const fvMesh& mesh,
-    bool& processed
-)
-{
-    typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
-
-    if (header.headerClassName() == fieldType::typeName)
-    {
-        Info<< "    Reading " << header.name() << endl;
-        fieldType field(header, mesh);
-
-        Info<< "    Calculating mag" << header.name() << endl;
-        volScalarField magField
-        (
-            IOobject
-            (
-                "mag" + header.name(),
-                mesh.time().timeName(),
-                mesh,
-                IOobject::NO_READ
-            ),
-            mag(field)
-        );
-        magField.write();
-
-        processed = true;
-    }
-}
-
+#include "writeMagField.C"
 
 int main(int argc, char *argv[])
 {

applications/utilities/postProcessing/field/mag/writeMagField.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
+     \\/     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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    mag
+
+Description
+    Calculates and writes the magnitude of a field for each time
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+template<class Type>
+void writeMagField
+(
+    const IOobject& header,
+    const fvMesh& mesh,
+    bool& processed
+)
+{
+    typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
+
+    if (header.headerClassName() == fieldType::typeName)
+    {
+        Info<< "    Reading " << header.name() << endl;
+        fieldType field(header, mesh);
+
+        Info<< "    Calculating mag" << header.name() << endl;
+        volScalarField magField
+        (
+            IOobject
+            (
+                "mag" + header.name(),
+                mesh.time().timeName(),
+                mesh,
+                IOobject::NO_READ
+            ),
+            mag(field)
+        );
+        magField.write();
+
+        processed = true;
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/utilities/postProcessing/field/magGrad/magGrad.C

@@ -26,23 +26,26 @@ Application
     magGrad
 
 Description
-    Calculates and writes the scalar magnitude of a scalar or vector field
-    at each time
+    Calculates and writes the magnitude of the gradient of a field for each
+    time
 
 \*---------------------------------------------------------------------------*/
 
 #include "fvCFD.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-//  Main program:
+
+#include "writeMagGradField.C"
 
 int main(int argc, char *argv[])
 {
-    argList::validArgs.append("field");
+    argList::validArgs.append("fieldName");
 
 #   include "addTimeOptions.H"
 #   include "setRootCase.H"
 
+    word fieldName(args.additionalArgs()[0]);
+
 #   include "createTime.H"
 
     // Get times list
@@ -51,8 +54,6 @@ int main(int argc, char *argv[])
     // set startTime and endTime depending on -time and -latestTime options
 #   include "checkTimeOptions.H"
 
-    const word fieldName(args.additionalArgs()[0]);
-
     runTime.setTime(Times[startTime], startTime);
 
 #   include "createMesh.H"
@@ -63,7 +64,7 @@ int main(int argc, char *argv[])
 
         Info<< "Time = " << runTime.timeName() << endl;
 
-        IOobject header
+        IOobject fieldHeader
         (
             fieldName,
             runTime.timeName(),
@@ -71,56 +72,33 @@ int main(int argc, char *argv[])
             IOobject::MUST_READ
         );
 
-        // Check U exists
-        if (header.headerOk())
+        // Check field "fieldName" exists
+        if (fieldHeader.headerOk())
         {
             mesh.readUpdate();
 
-            if (header.headerClassName() == volVectorField::typeName)
+            bool processed = false;
+            writeMagGradField<scalar>(fieldHeader, mesh, processed);
+            writeMagGradField<vector>(fieldHeader, mesh, processed);
+            if (!processed)
             {
-                Info<< "    Reading " << fieldName << endl;
-                volVectorField U(header, mesh);
-
-                volScalarField magGrad
-                (
-                    IOobject
-                    (
-                        "magGrad" + fieldName,
-                        runTime.timeName(),
-                        mesh,
-                        IOobject::NO_READ
-                    ),
-                    mag(fvc::grad(U))
-                );
-                Info<< "    Calculating " << magGrad.name() << endl;
-                magGrad.write();
-            }
-            else if (header.headerClassName() == volScalarField::typeName)
-            {
-                Info<< "    Reading " << fieldName << endl;
-                volScalarField U(header, mesh);
-
-                volScalarField magGrad
-                (
-                    IOobject
-                    (
-                        "magGrad" + fieldName,
-                        runTime.timeName(),
-                        mesh,
-                        IOobject::NO_READ
-                    ),
-                    mag(fvc::grad(U))
-                );
-                Info<< "    Calculating " << magGrad.name() << endl;
-                magGrad.write();
+                FatalError
+                    << "Unable to process " << fieldName << nl
+                    << "No call to magGrad for fields of type "
+                    << fieldHeader.headerClassName() << nl << nl
+                    << exit(FatalError);
             }
         }
         else
         {
             Info<< "    No " << fieldName