Commit dde4ca5b authored by mattijs's avatar mattijs
Browse files

Merge branch 'master' of /home/noisy3/OpenFOAM/OpenFOAM-dev

parents 782bd24f 03c7baf7
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
......@@ -10,4 +11,6 @@ EXE_LIBS = \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential
-lpotential \
-lmolecularMeasurements
......@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Application
mdEquilibrationFOAM
mdEquilibrationFoam
Description
Equilibrates and/or preconditions MD systems
......@@ -40,9 +40,9 @@ int main(int argc, char *argv[])
# include "createTime.H"
# include "createMesh.H"
moleculeCloud molecules(mesh);
potential pot(mesh);
molecules.removeHighEnergyOverlaps();
moleculeCloud molecules(mesh, pot);
# include "temperatureAndPressureVariables.H"
......@@ -60,7 +60,7 @@ int main(int argc, char *argv[])
Info << "Time = " << runTime.timeName() << endl;
molecules.integrateEquationsOfMotion();
molecules.evolve();
# include "meanMomentumEnergyAndNMols.H"
......
Info<< "Reading MD Equilibration Dictionary" << nl << endl;
Info<< nl << "Reading MD Equilibration Dictionary" << nl << endl;
IOdictionary mdEquilibrationDict
(
......
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
......@@ -10,4 +11,6 @@ EXE_LIBS = \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential
-lpotential \
-lmolecularMeasurements
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Application
gnemdFOAM
mdFoam
Description
MD for Fluid Mechanics and hybridising with a continuum solver.
molecular dynamics solver for fluid dynamics
\*---------------------------------------------------------------------------*/
......@@ -40,11 +40,9 @@ int main(int argc, char *argv[])
# include "createTime.H"
# include "createMesh.H"
moleculeCloud molecules(mesh);
potential pot(mesh);
# include "createMDFields.H"
molecules.removeHighEnergyOverlaps();
moleculeCloud molecules(mesh, pot);
# include "temperatureAndPressureVariables.H"
......@@ -60,20 +58,14 @@ int main(int argc, char *argv[])
Info << "Time = " << runTime.timeName() << endl;
molecules.integrateEquationsOfMotion();
molecules.evolve();
# include "meanMomentumEnergyAndNMols.H"
# include "temperatureAndPressure.H"
# include "calculateMDFields.H"
# include "averageMDFields.H"
runTime.write();
# include "resetMDFields.H"
if (runTime.outputTime())
{
nAveragingSteps = 0;
......
INTERFOAM = $(FOAM_SOLVERS)/multiphase/interFoam
EXE_INC = \
-I$(LIB_SRC)/transportModels \
-I$(LIB_SRC)/transportModels/incompressible/lnInclude \
......
INTERFOAM = $(FOAM_SOLVERS)/multiphase/interFoam
EXE_INC = \
-I$(LIB_SRC)/transportModels \
-I$(LIB_SRC)/transportModels/incompressible/lnInclude \
......
mdInitialise.C
EXE = $(FOAM_APPBIN)/mdInitialise
EXE_INC = \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/dynamicMesh/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude
EXE_LIBS = \
-lmeshTools \
-ldynamicMesh \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2008 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
\*---------------------------------------------------------------------------*/
#include "md.H"
#include "fvCFD.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
int main(int argc, char *argv[])
{
# include "setRootCase.H"
# include "createTime.H"
# include "createMesh.H"
IOdictionary mdInitialiseDict
(
IOobject
(
"mdInitialiseDict",
runTime.system(),
runTime,
IOobject::MUST_READ,
IOobject::NO_WRITE,
false
)
);
IOdictionary idListDict
(
IOobject
(
"idList",
mesh.time().constant(),
mesh,
IOobject::NO_READ,
IOobject::AUTO_WRITE
)
);
potential pot(mesh, mdInitialiseDict, idListDict);
moleculeCloud molecules(mesh, pot, mdInitialiseDict);
label totalMolecules = molecules.size();
if (Pstream::parRun())
{
reduce(totalMolecules, sumOp<label>());
}
Info<< nl << "Total number of molecules added: " << totalMolecules
<< nl << endl;
IOstream::defaultPrecision(15);
if (!mesh.write())
{
FatalErrorIn(args.executable())
<< "Failed writing moleculeCloud."
<< nl << exit(FatalError);
}
Info<< nl << "ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
Info << nl << "End\n" << endl;
return 0;
}
// ************************************************************************* //
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