moved to subdirectory

applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/files

@@ -0,0 +1,3 @@
+mdEquilibrationFoam.C
+
+EXE = $(FOAM_APPBIN)/mdEquilibrationFoam

applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/options

@@ -0,0 +1,16 @@
+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule \
+    -lpotential \
+    -lmolecularMeasurements
+

applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

@@ -0,0 +1,85 @@
+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2009 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"
+
+    potential pot(mesh);
+
+    moleculeCloud molecules(mesh, pot);
+
+#   include "temperatureAndPressureVariables.H"
+
+#   include "readmdEquilibrationDict.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.loop())
+    {
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.evolve();
+
+#       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/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H

@@ -0,0 +1,18 @@
+Info<< nl << "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/solvers/discreteMethods/molecularDynamics/mdFoam/Make/files

@@ -0,0 +1,3 @@
+mdFoam.C
+
+EXE = $(FOAM_APPBIN)/mdFoam

applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/options

@@ -0,0 +1,16 @@
+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule \
+    -lpotential \
+    -lmolecularMeasurements
+

applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C

@@ -0,0 +1,81 @@
+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2009 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
+    mdFoam
+
+Description
+    molecular dynamics solver for fluid dynamics
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    potential pot(mesh);
+
+    moleculeCloud molecules(mesh, pot);
+
+#   include "temperatureAndPressureVariables.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.loop())
+    {
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.evolve();
+
+#       include "meanMomentumEnergyAndNMols.H"
+
+#       include "temperatureAndPressure.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;
+}