From b03f3a97d19ef474859577c41a59f0ead324765d Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Mon, 4 Aug 2008 14:54:02 +0100
Subject: [PATCH] Adding mdTransportProperitesFoam solver

---
 .../mdTransportProperitesFoam/Make/files      |  3 +
 .../mdTransportProperitesFoam/Make/options    | 13 +++
 .../mdTransportProperitesFoam.C               | 92 +++++++++++++++++++
 3 files changed, 108 insertions(+)
 create mode 100755 applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/files
 create mode 100755 applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/options
 create mode 100755 applications/solvers/molecularDynamics/mdTransportProperitesFoam/mdTransportProperitesFoam.C

diff --git a/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/files b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/files
new file mode 100755
index 0000000000..242cbcf407
--- /dev/null
+++ b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/files
@@ -0,0 +1,3 @@
+mdTransportProperitesFoam.C
+
+EXE = $(FOAM_APPBIN)/mdTransportProperitesFoam
diff --git a/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/options b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/options
new file mode 100755
index 0000000000..89431d0625
--- /dev/null
+++ b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/Make/options
@@ -0,0 +1,13 @@
+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule \
+    -lpotential
diff --git a/applications/solvers/molecularDynamics/mdTransportProperitesFoam/mdTransportProperitesFoam.C b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/mdTransportProperitesFoam.C
new file mode 100755
index 0000000000..61c94d81d4
--- /dev/null
+++ b/applications/solvers/molecularDynamics/mdTransportProperitesFoam/mdTransportProperitesFoam.C
@@ -0,0 +1,92 @@
+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   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
+    mdTransportProperitesFoam
+
+Description
+    MD simulation to calculate continuum transport properites of a homogeneous
+    fluid at a given, stationary state.  Density and temperature defined
+    by preprocessing, pressure measured.
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+    argList::noParallel();
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    moleculeCloud molecules(mesh);
+
+    molecules.removeHighEnergyOverlaps();
+
+#   include "temperatureAndPressureVariables.H"
+
+#   include "createAutoCorrelationFunctions.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 "calculateAutoCorrelationFunctions.H"
+
+        runTime.write();
+
+        if (runTime.outputTime())
+        {
+            nAveragingSteps = 0;
+        }
+
+        Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+#   include "calculateTransportProperties.H"
+
+    Info << "End\n" << endl;
+            
+    return(0);
+}