Merge branch 'master' of ssh://noisy/home/noisy2/OpenFOAM/OpenFOAM-dev
This commit is contained in:
henry
commit
da76e14229
@ -1,5 +1,6 @@
|
||||
EXE_INC = \
|
||||
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \
|
||||
-I$(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
|
||||
@ -8,4 +9,5 @@ EXE_LIBS = \
|
||||
-lmeshTools \
|
||||
-lfiniteVolume \
|
||||
-llagrangian \
|
||||
-lmolecule
|
||||
-lmolecule \
|
||||
-lpotential
|
||||
|
||||
0
applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C
Executable file → Normal file
0
applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C
Executable file → Normal file
@ -1,5 +1,6 @@
|
||||
EXE_INC = \
|
||||
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \
|
||||
-I$(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
|
||||
@ -8,4 +9,5 @@ EXE_LIBS = \
|
||||
-lmeshTools \
|
||||
-lfiniteVolume \
|
||||
-llagrangian \
|
||||
-lmolecule
|
||||
-lmolecule \
|
||||
-lpotential
|
||||
|
||||
0
applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
Executable file → Normal file
0
applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
Executable file → Normal file
0
applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
Executable file → Normal file
0
applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
Executable file → Normal file
@ -1 +0,0 @@
|
||||
quit
|
||||
@ -405,64 +405,71 @@ bool doCommand
|
||||
backup(mesh, setName, currentSet, setName + "_old");
|
||||
}
|
||||
|
||||
if (action == topoSetSource::CLEAR)
|
||||
switch (action)
|
||||
{
|
||||
// Already handled above by not reading
|
||||
}
|
||||
else if (action == topoSetSource::INVERT)
|
||||
{
|
||||
currentSet.invert(currentSet.maxSize(mesh));
|
||||
}
|
||||
else if (action == topoSetSource::LIST)
|
||||
{
|
||||
currentSet.writeDebug(Pout, mesh, 100);
|
||||
Pout<< endl;
|
||||
}
|
||||
else if (action == topoSetSource::SUBSET)
|
||||
{
|
||||
if (is >> sourceType)
|
||||
case topoSetSource::CLEAR:
|
||||
{
|
||||
autoPtr<topoSetSource> setSource
|
||||
(
|
||||
topoSetSource::New
|
||||
(
|
||||
sourceType,
|
||||
mesh,
|
||||
is
|
||||
)
|
||||
);
|
||||
|
||||
// Backup current set.
|
||||
topoSet oldSet
|
||||
(
|
||||
mesh,
|
||||
currentSet.name() + "_old2",
|
||||
currentSet
|
||||
);
|
||||
|
||||
currentSet.clear();
|
||||
currentSet.resize(oldSet.size());
|
||||
setSource().applyToSet(topoSetSource::NEW, currentSet);
|
||||
|
||||
// Combine new value of currentSet with old one.
|
||||
currentSet.subset(oldSet);
|
||||
// Already handled above by not reading
|
||||
break;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
if (is >> sourceType)
|
||||
case topoSetSource::INVERT:
|
||||
{
|
||||
autoPtr<topoSetSource> setSource
|
||||
(
|
||||
topoSetSource::New
|
||||
currentSet.invert(currentSet.maxSize(mesh));
|
||||
break;
|
||||
}
|
||||
case topoSetSource::LIST:
|
||||
{
|
||||
currentSet.writeDebug(Pout, mesh, 100);
|
||||
Pout<< endl;
|
||||
break;
|
||||
}
|
||||
case topoSetSource::SUBSET:
|
||||
{
|
||||
if (is >> sourceType)
|
||||
{
|
||||
autoPtr<topoSetSource> setSource
|
||||
(
|
||||
sourceType,
|
||||
mesh,
|
||||
is
|
||||
)
|
||||
);
|
||||
topoSetSource::New
|
||||
(
|
||||
sourceType,
|
||||
mesh,
|
||||
is
|
||||
)
|
||||
);
|
||||
|
||||
setSource().applyToSet(action, currentSet);
|
||||
// Backup current set.
|
||||
topoSet oldSet
|
||||
(
|
||||
mesh,
|
||||
currentSet.name() + "_old2",
|
||||
currentSet
|
||||
);
|
||||
|
||||
currentSet.clear();
|
||||
currentSet.resize(oldSet.size());
|
||||
setSource().applyToSet(topoSetSource::NEW, currentSet);
|
||||
|
||||
// Combine new value of currentSet with old one.
|
||||
currentSet.subset(oldSet);
|
||||
}
|
||||
break;
|
||||
}
|
||||
default:
|
||||
{
|
||||
if (is >> sourceType)
|
||||
{
|
||||
autoPtr<topoSetSource> setSource
|
||||
(
|
||||
topoSetSource::New
|
||||
(
|
||||
sourceType,
|
||||
mesh,
|
||||
is
|
||||
)
|
||||
);
|
||||
|
||||
setSource().applyToSet(action, currentSet);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -532,7 +539,7 @@ bool doCommand
|
||||
}
|
||||
}
|
||||
|
||||
return error;
|
||||
return !error;
|
||||
}
|
||||
|
||||
|
||||
@ -612,31 +619,36 @@ commandStatus parseType
|
||||
switch(stat)
|
||||
{
|
||||
case polyMesh::UNCHANGED:
|
||||
{
|
||||
Pout<< " mesh not changed." << endl;
|
||||
break;
|
||||
|
||||
break;
|
||||
}
|
||||
case polyMesh::POINTS_MOVED:
|
||||
{
|
||||
Pout<< " points moved; topology unchanged." << endl;
|
||||
break;
|
||||
|
||||
break;
|
||||
}
|
||||
case polyMesh::TOPO_CHANGE:
|
||||
{
|
||||
Pout<< " topology changed; patches unchanged." << nl
|
||||
<< " ";
|
||||
printMesh(runTime, mesh);
|
||||
|
||||
break;
|
||||
|
||||
break;
|
||||
}
|
||||
case polyMesh::TOPO_PATCH_CHANGE:
|
||||
{
|
||||
Pout<< " topology changed and patches changed." << nl
|
||||
<< " ";
|
||||
printMesh(runTime, mesh);
|
||||
|
||||
break;
|
||||
|
||||
break;
|
||||
}
|
||||
default:
|
||||
{
|
||||
FatalErrorIn("parseType") << "Illegal mesh update state "
|
||||
<< stat << abort(FatalError);
|
||||
break;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return INVALID;
|
||||
|
||||
@ -0,0 +1,3 @@
|
||||
patchSummary.C
|
||||
|
||||
EXE = $(FOAM_USER_APPBIN)/patchSummary
|
||||
@ -0,0 +1,5 @@
|
||||
EXE_INC = \
|
||||
-I$(LIB_SRC)/finiteVolume/lnInclude
|
||||
|
||||
EXE_LIBS = \
|
||||
-lfiniteVolume
|
||||
117
applications/utilities/miscellaneous/patchSummary/patchSummary.C
Normal file
117
applications/utilities/miscellaneous/patchSummary/patchSummary.C
Normal file
@ -0,0 +1,117 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / 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
|
||||
patchSummary
|
||||
|
||||
Description
|
||||
Writes fields and boundary condition info for each patch at each requested
|
||||
time instance.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "fvCFD.H"
|
||||
#include "volFields.H"
|
||||
#include "IOobjectList.H"
|
||||
#include "patchSummaryTemplates.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
|
||||
# include "addTimeOptions.H"
|
||||
# include "setRootCase.H"
|
||||
# include "createTime.H"
|
||||
|
||||
// Get times list
|
||||
instantList Times = runTime.times();
|
||||
|
||||
// set startTime and endTime depending on -time and -latestTime options
|
||||
# include "checkTimeOptions.H"
|
||||
|
||||
runTime.setTime(Times[startTime], startTime);
|
||||
|
||||
# include "createMesh.H"
|
||||
|
||||
for (label i=startTime; i<endTime; i++)
|
||||
{
|
||||
runTime.setTime(Times[i], i);
|
||||
|
||||
Info<< "Time = " << runTime.timeName() << nl << endl;
|
||||
|
||||
const IOobjectList fieldObjs(mesh, runTime.timeName());
|
||||
|
||||
const wordList objNames = fieldObjs.names();
|
||||
|
||||
PtrList<volScalarField> vsf(objNames.size());
|
||||
PtrList<volVectorField> vvf(objNames.size());
|
||||
PtrList<volSphericalTensorField> vsptf(objNames.size());
|
||||
PtrList<volSymmTensorField> vsytf(objNames.size());
|
||||
PtrList<volTensorField> vtf(objNames.size());
|
||||
|
||||
Info<< "Valid fields:" << endl;
|
||||
|
||||
forAll(objNames, objI)
|
||||
{
|
||||
IOobject obj
|
||||
(
|
||||
objNames[objI],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::MUST_READ
|
||||
);
|
||||
|
||||
if (obj.headerOk())
|
||||
{
|
||||
addToFieldList<scalar>(vsf, obj, objI, mesh);
|
||||
addToFieldList<vector>(vvf, obj, objI, mesh);
|
||||
addToFieldList<sphericalTensor>(vsptf, obj, objI, mesh);
|
||||
addToFieldList<symmTensor>(vsytf, obj, objI, mesh);
|
||||
addToFieldList<tensor>(vtf, obj, objI, mesh);
|
||||
}
|
||||
}
|
||||
|
||||
Info<< endl;
|
||||
|
||||
const polyBoundaryMesh& bm = mesh.boundaryMesh();
|
||||
forAll(bm, patchI)
|
||||
{
|
||||
Info<< "Patch: " << bm[patchI].name() << nl;
|
||||
outputFieldList<scalar>(vsf, patchI);
|
||||
outputFieldList<vector>(vvf, patchI);
|
||||
outputFieldList<sphericalTensor>(vsptf, patchI);
|
||||
outputFieldList<symmTensor>(vsytf, patchI);
|
||||
outputFieldList<tensor>(vtf, patchI);
|
||||
Info << endl;
|
||||
}
|
||||
}
|
||||
|
||||
Info << "End\n" << endl;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -2,7 +2,7 @@
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 1991-2005 OpenCFD Ltd.
|
||||
\\ / A nd | Copyright (C) 1991-2007 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
@ -22,80 +22,53 @@ License
|
||||
along with OpenFOAM; if not, write to the Free Software Foundation,
|
||||
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::m() const
|
||||
{
|
||||
return m_;
|
||||
}
|
||||
#include "patchSummaryTemplates.H"
|
||||
#include "IOmanip.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::gamma() const
|
||||
{
|
||||
return gamma_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::rm() const
|
||||
{
|
||||
return rm_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::epsilon() const
|
||||
{
|
||||
return epsilon_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::rCut() const
|
||||
{
|
||||
return rCut_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::rCutSqr() const
|
||||
{
|
||||
return rCutSqr_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::rMin() const
|
||||
{
|
||||
return rMin_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::pairPotential::dr() const
|
||||
{
|
||||
return dr_;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
|
||||
|
||||
inline bool Foam::operator==
|
||||
template<class Type>
|
||||
void Foam::addToFieldList
|
||||
(
|
||||
const pairPotential& a,
|
||||
const pairPotential& b
|
||||
PtrList<GeometricField<Type, fvPatchField, volMesh> >& fieldList,
|
||||
const IOobject& obj,
|
||||
const label fieldI,
|
||||
const fvMesh& mesh
|
||||
)
|
||||
{
|
||||
return
|
||||
(a.m() == b.m())
|
||||
&& (a.gamma() == b.gamma())
|
||||
&& (a.rm() == b.rm())
|
||||
&& (a.epsilon() == b.epsilon())
|
||||
&& (a.rCut() == b.rCut());
|
||||
typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
|
||||
|
||||
if (obj.headerClassName() == fieldType::typeName)
|
||||
{
|
||||
fieldList.set
|
||||
(
|
||||
fieldI,
|
||||
new fieldType(obj, mesh)
|
||||
);
|
||||
Info<< " " << fieldType::typeName << tab << obj.name() << endl;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
inline bool Foam::operator!=
|
||||
template<class Type>
|
||||
void Foam::outputFieldList
|
||||
(
|
||||
const pairPotential& a,
|
||||
const pairPotential& b
|
||||
PtrList<GeometricField<Type, fvPatchField, volMesh> >& fieldList,
|
||||
const label patchI
|
||||
)
|
||||
{
|
||||
return !(a == b);
|
||||
forAll(fieldList, fieldI)
|
||||
{
|
||||
if (fieldList.set(fieldI))
|
||||
{
|
||||
Info<< " " << pTraits<Type>::typeName << tab << tab
|
||||
<< fieldList[fieldI].name() << tab << tab
|
||||
<< fieldList[fieldI].boundaryField()[patchI].type() << nl;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 1991-2005 OpenCFD Ltd.
|
||||
\\ / A nd | Copyright (C) 1991-2007 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
@ -24,33 +24,42 @@ License
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef patchSummaryTemplates_H
|
||||
#define patchSummaryTemplates_H
|
||||
|
||||
#include "fvCFD.H"
|
||||
#include "volFields.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
template<class Type>
|
||||
void addToFieldList
|
||||
(
|
||||
PtrList<GeometricField<Type, fvPatchField, volMesh> >& fieldList,
|
||||
const IOobject& obj,
|
||||
const label fieldI,
|
||||
const fvMesh& mesh
|
||||
);
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
inline const word& tetherPotential::tetherPotentialName() const
|
||||
{
|
||||
return tetherPotentialName_;
|
||||
}
|
||||
|
||||
|
||||
inline const word& tetherPotential::tetherPotentialType() const
|
||||
{
|
||||
return tetherPotentialType_;
|
||||
}
|
||||
|
||||
|
||||
inline scalar tetherPotential::springConstant() const
|
||||
{
|
||||
return springConstant_;
|
||||
}
|
||||
template<class Type>
|
||||
void outputFieldList
|
||||
(
|
||||
PtrList<GeometricField<Type, fvPatchField, volMesh> >& fieldList,
|
||||
const label patchI
|
||||
);
|
||||
} // End namespace Foam
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
#ifdef NoRepository
|
||||
# include "patchSummaryTemplates.C"
|
||||
#endif
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -3,7 +3,8 @@ EXE_INC = \
|
||||
-I$(velocityDistributions) \
|
||||
-I$(LIB_SRC)/meshTools/lnInclude \
|
||||
-I$(LIB_SRC)/dynamicMesh/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
|
||||
-I$(LIB_SRC)/finiteVolume/lnInclude
|
||||
|
||||
@ -12,4 +13,5 @@ EXE_LIBS = \
|
||||
-ldynamicMesh \
|
||||
-lfiniteVolume \
|
||||
-llagrangian \
|
||||
-lmolecule
|
||||
-lmolecule \
|
||||
-lpotential
|
||||
|
||||
45
bin/foamLog
45
bin/foamLog
@ -47,7 +47,7 @@ printUsage() {
|
||||
cat <<LABUSAGE
|
||||
$PROGNAME - extracts xy files from Foam logs.
|
||||
|
||||
Usage: $PROGNAME [-n][-s] <root> <case> <log>
|
||||
Usage: $PROGNAME [-n][-s] <log>
|
||||
extracts xy files from log
|
||||
$PROGNAME -l <log>
|
||||
lists but does not extract
|
||||
@ -82,11 +82,11 @@ files with the extracted data only.
|
||||
|
||||
The query database is a simple text format with three entries per line,
|
||||
separated with '/'. Column 1 is the name of the variable (cannot contain
|
||||
spaces), column 2 is the regular expression to select the line and
|
||||
column 3 is the string to select the column inside the line. The value
|
||||
taken will be the first (non-space)word after this column.
|
||||
The database will either be \$HOME/.${PROGNAME}.db or if not found
|
||||
$PROGDIR/${PROGNAME}.db.
|
||||
spaces), column 2 is the extended regular expression (egrep) to select
|
||||
the line and column 3 is the string (fgrep) to select the column inside the
|
||||
line. The value taken will be the first (non-space)word after this
|
||||
column. The database will either be \$HOME/.${PROGNAME}.db or if not
|
||||
found $PROGDIR/${PROGNAME}.db.
|
||||
|
||||
Option -s suppresses the default information and only prints the extracted
|
||||
variables.
|
||||
@ -105,7 +105,7 @@ myEcho() {
|
||||
# getSolvedVars logFile
|
||||
# Prints names of all 'solved for' variables in the log file.
|
||||
getSolvedVars() {
|
||||
grep ' Solving for ' $1 | fgrep ',' | sed -e 's/.* Solving for \([^,]*\)[,:].*/\1/' | sort -u
|
||||
fgrep ' Solving for ' $1 | fgrep ',' | sed -e 's/.* Solving for \([^,]*\)[,:].*/\1/' | sort -u
|
||||
}
|
||||
|
||||
|
||||
@ -163,7 +163,7 @@ getAllQueries() {
|
||||
for var in $dbQueries
|
||||
do
|
||||
getQueries $1 "$var"
|
||||
line=`grep "$LINEQ" $2`
|
||||
line=`egrep "$LINEQ" $2`
|
||||
if [ "$line" ]; then
|
||||
column=`echo "$line" | fgrep "$NUMQ"`
|
||||
if [ "$column" ]; then
|
||||
@ -228,14 +228,13 @@ if [ "$LISTONLY" ]; then
|
||||
exit 0
|
||||
fi
|
||||
|
||||
if [ $# -ne 3 ]; then
|
||||
if [ $# -ne 1 ]; then
|
||||
printUsage
|
||||
exit 1
|
||||
fi
|
||||
|
||||
ROOT=$1
|
||||
CASE=$2
|
||||
LOG=$3
|
||||
CASEDIR=.
|
||||
LOG=$1
|
||||
if [ ! -r $LOG ]; then
|
||||
echo "$PROGNAME: Cannot read log $LOG"
|
||||
exit 1
|
||||
@ -244,13 +243,13 @@ fi
|
||||
QUERYNAMES=`getAllQueries $DBFILE $LOG`
|
||||
|
||||
|
||||
if [ ! "$ROOT" -o ! "$CASE" ]; then
|
||||
if [ ! "$CASEDIR" ]; then
|
||||
printUsage
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if [ ! -d "$ROOT/$CASE" ]; then
|
||||
echo "$PROGNAME: Cannot read $ROOT/$CASE"
|
||||
if [ ! -d "$CASEDIR" ]; then
|
||||
echo "$PROGNAME: Cannot read $CASEDIR"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
@ -262,16 +261,14 @@ fi
|
||||
|
||||
#-- Make logs dir in case directory and put awk file there.
|
||||
|
||||
mkdir -p $ROOT/$CASE/logs
|
||||
AWKFILE=$ROOT/$CASE/logs/$PROGNAME.awk
|
||||
mkdir -p $CASEDIR/logs
|
||||
AWKFILE=$CASEDIR/logs/$PROGNAME.awk
|
||||
|
||||
myEcho "Using:"
|
||||
myEcho " root : $ROOT"
|
||||
myEcho " case : $CASE"
|
||||
myEcho " log : $LOG"
|
||||
myEcho " database : $DBFILE"
|
||||
myEcho " awk file : $AWKFILE"
|
||||
myEcho " files to : $ROOT/$CASE/logs"
|
||||
myEcho " files to : $CASEDIR/logs"
|
||||
myEcho ""
|
||||
|
||||
|
||||
@ -364,19 +361,19 @@ cat <<LABSOLVE >> $AWKFILE
|
||||
|
||||
varName=varNameVal[1]
|
||||
file=varName "_" subIter[varName]++
|
||||
file="$ROOT/$CASE/logs/" file
|
||||
file="$CASEDIR/logs/" file
|
||||
extract(\$0, "Initial residual = ", val)
|
||||
print $TIMENAME "\t" val[1] > file
|
||||
|
||||
varName=varNameVal[1] "FinalRes"
|
||||
file=varName "_" subIter[varName]++
|
||||
file="$ROOT/$CASE/logs/" file
|
||||
file="$CASEDIR/logs/" file
|
||||
extract(\$0, "Final residual = ", val)
|
||||
print $TIMENAME "\t" val[1] > file
|
||||
|
||||
varName=varNameVal[1] "Iters"
|
||||
file=varName "_" subIter[varName]++
|
||||
file="$ROOT/$CASE/logs/" file
|
||||
file="$CASEDIR/logs/" file
|
||||
extract(\$0, "No Iterations ", val)
|
||||
print $TIMENAME "\t" val[1] > file
|
||||
}
|
||||
@ -393,7 +390,7 @@ do
|
||||
echo "#-- Extraction of $queryName" >> $AWKFILE
|
||||
echo "/$LINEQ/ {" >> $AWKFILE
|
||||
echo " extract(\$0, \"$NUMQ\", val)" >> $AWKFILE
|
||||
echo " file=\"$ROOT/$CASE/logs/${queryName}_\" ${counter}" >> $AWKFILE
|
||||
echo " file=\"$CASEDIR/logs/${queryName}_\" ${counter}" >> $AWKFILE
|
||||
echo " print $TIMENAME \"\\t\" val[1] > file" >> $AWKFILE
|
||||
echo " ${counter}++" >> $AWKFILE
|
||||
echo "}" >> $AWKFILE
|
||||
|
||||
@ -48,6 +48,6 @@ epsMax/bounding epsilon,/max:
|
||||
epsAvg/bounding epsilon,/average:
|
||||
|
||||
#- gamma bounding
|
||||
gammaMin/Min\(gamma\) =/Min(gamma) =
|
||||
gammaMax/Max\(gamma\) =/Max(gamma) =
|
||||
gammaMin/Min\(gamma\) =/Min(gamma) =
|
||||
gammaMax/Max\(gamma\) =/Max(gamma) =
|
||||
|
||||
|
||||
85
bin/upgradeTurbulenceProperties
Executable file
85
bin/upgradeTurbulenceProperties
Executable file
@ -0,0 +1,85 @@
|
||||
#!/bin/sh
|
||||
#------------------------------------------------------------------------------
|
||||
# ========= |
|
||||
# \\ / 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
|
||||
#
|
||||
# Script
|
||||
# upgradeTurbulenceProperties
|
||||
#
|
||||
# Description
|
||||
# Upgrade the turbulenceProperties dictionary to the new format employed
|
||||
# in OpenFOAM version 1.5
|
||||
# - RAS turbulence models now defined by the RASProperties dictionary,
|
||||
# and RASModel keyword, and
|
||||
# - LES turbulence models now defined by the LESProperties dictionary,
|
||||
# and LESModel keyword.
|
||||
#
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
printUsage()
|
||||
{
|
||||
echo "Usage: `basename $0` <turbulenceProperties>"
|
||||
echo " Where <turbulenceProperties> is the full path to the"
|
||||
echo " turbulenceProperties dictionary"
|
||||
}
|
||||
|
||||
convertDict()
|
||||
{
|
||||
echo " Identified $1 turbulence model"
|
||||
|
||||
sed -e "s/turbulenceProperties/$1Properties/" \
|
||||
-e "s/$2/$1Model/" \
|
||||
-e "s/[a-zA-Z0-9]* [ ]*\[[0-9 ]*\]//" \
|
||||
$3 > "$outputPath/$1Properties"
|
||||
|
||||
echo " written $1Properties to $outputPath/"
|
||||
}
|
||||
|
||||
outputPath=`dirname $1`
|
||||
|
||||
if [ $# -ne 1 ]; then
|
||||
printUsage
|
||||
exit 1
|
||||
elif [ ! -e $1 ]; then
|
||||
echo " Error: file $1 does not exist"
|
||||
echo ""
|
||||
printUsage
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# Identify type of turbulence model
|
||||
RAS=`grep turbulenceModel $1`
|
||||
LES=`grep LESmodel $1`
|
||||
|
||||
if [ -n "$RAS" ]; then
|
||||
convertDict "RAS" "turbulenceModel" $1
|
||||
elif [ -n "$LES" ]; then
|
||||
convertDict "LES" "LESmodel" $1
|
||||
else
|
||||
echo "Unable to determine turbulence model type - nothing changed"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "done."
|
||||
|
||||
exit 0
|
||||
@ -11,4 +11,5 @@ Misc Tools
|
||||
1. find-templateInComments
|
||||
2. find-its
|
||||
3. find-junkFiles
|
||||
4. find-longlines
|
||||
|
||||
|
||||
46
doc/Doxygen/tools/find-longlines
Executable file
46
doc/Doxygen/tools/find-longlines
Executable file
@ -0,0 +1,46 @@
|
||||
#!/usr/bin/perl -w
|
||||
use strict;
|
||||
use File::Find ();
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
#
|
||||
# Script
|
||||
# find-longlines
|
||||
#
|
||||
# Description
|
||||
# Search for *.[CH] files that exceed the 80-column width
|
||||
#
|
||||
# - print filename lineNumber and offending line (with truncation point)
|
||||
#
|
||||
# -----------------------------------------------------------------------------
|
||||
|
||||
my $maxlen = 80;
|
||||
my $re_filespec = qr{^.+\.[CH]$};
|
||||
my $count;
|
||||
|
||||
sub wanted {
|
||||
unless ( lstat($_) and -f _ and -r _ and not -l _ and /$re_filespec/ ) {
|
||||
return;
|
||||
}
|
||||
|
||||
local @ARGV = $_;
|
||||
while (<>) {
|
||||
chomp;
|
||||
s{\s+$}{}; # trim
|
||||
|
||||
if ( $maxlen < length ) {
|
||||
$count++;
|
||||
substr( $_, $maxlen, 0 ) = "||->>"; # show truncation point
|
||||
print "$ARGV $. $_\n";
|
||||
}
|
||||
}
|
||||
close ARGV;
|
||||
}
|
||||
|
||||
## Traverse desired filesystems
|
||||
for my $dir (@ARGV) {
|
||||
no warnings 'File::Find';
|
||||
warn "(**) checking '$dir' ...\n";
|
||||
File::Find::find( { wanted => \&wanted }, $dir );
|
||||
}
|
||||
|
||||
@ -1,165 +0,0 @@
|
||||
// ============================================================================
|
||||
// gzstream, C++ iostream classes wrapping the zlib compression library.
|
||||
// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
|
||||
//
|
||||
// This library is free software; you can redistribute it and/or
|
||||
// modify it under the terms of the GNU Lesser General Public
|
||||
// License as published by the Free Software Foundation; either
|
||||
// version 2.1 of the License, or (at your option) any later version.
|
||||
//
|
||||
// This library 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
|
||||
// Lesser General Public License for more details.
|
||||
//
|
||||
// You should have received a copy of the GNU Lesser General Public
|
||||
// License along with this library; if not, write to the Free Software
|
||||
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
||||
// ============================================================================
|
||||
//
|
||||
// File : gzstream.C
|
||||
// Revision : $Revision: 1.7 $
|
||||
// Revision_date : $Date: 2003/01/08 14:41:27 $
|
||||
// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
|
||||
//
|
||||
// Standard streambuf implementation following Nicolai Josuttis, "The
|
||||
// Standard C++ Library".
|
||||
// ============================================================================
|
||||
|
||||
#include <gzstream.h>
|
||||
#include <iostream>
|
||||
#include <string.h> // for memcpy
|
||||
|
||||
#ifdef GZSTREAM_NAMESPACE
|
||||
namespace GZSTREAM_NAMESPACE {
|
||||
#endif
|
||||
|
||||
// ----------------------------------------------------------------------------
|
||||
// Internal classes to implement gzstream. See header file for user classes.
|
||||
// ----------------------------------------------------------------------------
|
||||
|
||||
// --------------------------------------
|
||||
// class gzstreambuf:
|
||||
// --------------------------------------
|
||||
|
||||
gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
|
||||
if ( is_open())
|
||||
return reinterpret_cast<gzstreambuf*>(0);
|
||||
mode = open_mode;
|
||||
// no append nor read/write mode
|
||||
if ((mode & std::ios::ate) || (mode & std::ios::app)
|
||||
|| ((mode & std::ios::in) && (mode & std::ios::out)))
|
||||
return reinterpret_cast<gzstreambuf*>(0);
|
||||
char fmode[10];
|
||||
char* fmodeptr = fmode;
|
||||
if ( mode & std::ios::in)
|
||||
*fmodeptr++ = 'r';
|
||||
else if ( mode & std::ios::out)
|
||||
*fmodeptr++ = 'w';
|
||||
*fmodeptr++ = 'b';
|
||||
*fmodeptr = '\0';
|
||||
file = gzopen( name, fmode);
|
||||
if (file == 0)
|
||||
return reinterpret_cast<gzstreambuf*>(0);
|
||||
opened = 1;
|
||||
return this;
|
||||
}
|
||||
|
||||
gzstreambuf * gzstreambuf::close() {
|
||||
if ( is_open()) {
|
||||
sync();
|
||||
opened = 0;
|
||||
if ( gzclose( file) == Z_OK)
|
||||
return this;
|
||||
}
|
||||
return reinterpret_cast<gzstreambuf*>(0);
|
||||
}
|
||||
|
||||
int gzstreambuf::underflow() { // used for input buffer only
|
||||
if ( gptr() && ( gptr() < egptr()))
|
||||
return * reinterpret_cast<unsigned char *>( gptr());
|
||||
|
||||
if ( ! (mode & std::ios::in) || ! opened)
|
||||
return EOF;
|
||||
// Josuttis' implementation of inbuf
|
||||
int n_putback = gptr() - eback();
|
||||
if ( n_putback > 4)
|
||||
n_putback = 4;
|
||||
memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
|
||||
|
||||
int num = gzread( file, buffer+4, bufferSize-4);
|
||||
if (num <= 0) // ERROR or EOF
|
||||
return EOF;
|
||||
|
||||
// reset buffer pointers
|
||||
setg( buffer + (4 - n_putback), // beginning of putback area
|
||||
buffer + 4, // read position
|
||||
buffer + 4 + num); // end of buffer
|
||||
|
||||
// return next character
|
||||
return * reinterpret_cast<unsigned char *>( gptr());
|
||||
}
|
||||
|
||||
int gzstreambuf::flush_buffer() {
|
||||
// Separate the writing of the buffer from overflow() and
|
||||
// sync() operation.
|
||||
int w = pptr() - pbase();
|
||||
if ( gzwrite( file, pbase(), w) != w)
|
||||
return EOF;
|
||||
pbump( -w);
|
||||
return w;
|
||||
}
|
||||
|
||||
int gzstreambuf::overflow( int c) { // used for output buffer only
|
||||
if ( ! ( mode & std::ios::out) || ! opened)
|
||||
return EOF;
|
||||
if (c != EOF) {
|
||||
*pptr() = c;
|
||||
pbump(1);
|
||||
}
|
||||
if ( flush_buffer() == EOF)
|
||||
return EOF;
|
||||
return c;
|
||||
}
|
||||
|
||||
int gzstreambuf::sync() {
|
||||
// Changed to use flush_buffer() instead of overflow( EOF)
|
||||
// which caused improper behavior with std::endl and flush(),
|
||||
// bug reported by Vincent Ricard.
|
||||
if ( pptr() && pptr() > pbase()) {
|
||||
if ( flush_buffer() == EOF)
|
||||
return -1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
// --------------------------------------
|
||||
// class gzstreambase:
|
||||
// --------------------------------------
|
||||
|
||||
gzstreambase::gzstreambase( const char* name, int mode) {
|
||||
init( &buf);
|
||||
open( name, mode);
|
||||
}
|
||||
|
||||
gzstreambase::~gzstreambase() {
|
||||
buf.close();
|
||||
}
|
||||
|
||||
void gzstreambase::open( const char* name, int open_mode) {
|
||||
if ( ! buf.open( name, open_mode))
|
||||
clear( rdstate() | std::ios::badbit);
|
||||
}
|
||||
|
||||
void gzstreambase::close() {
|
||||
if ( buf.is_open())
|
||||
if ( ! buf.close())
|
||||
clear( rdstate() | std::ios::badbit);
|
||||
}
|
||||
|
||||
#ifdef GZSTREAM_NAMESPACE
|
||||
} // namespace GZSTREAM_NAMESPACE
|
||||
#endif
|
||||
|
||||
// ============================================================================
|
||||
// EOF //
|
||||
@ -1,121 +0,0 @@
|
||||
// ============================================================================
|
||||
// gzstream, C++ iostream classes wrapping the zlib compression library.
|
||||
// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
|
||||
//
|
||||
// This library is free software; you can redistribute it and/or
|
||||
// modify it under the terms of the GNU Lesser General Public
|
||||
// License as published by the Free Software Foundation; either
|
||||
// version 2.1 of the License, or (at your option) any later version.
|
||||
//
|
||||
// This library 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
|
||||
// Lesser General Public License for more details.
|
||||
//
|
||||
// You should have received a copy of the GNU Lesser General Public
|
||||
// License along with this library; if not, write to the Free Software
|
||||
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
||||
// ============================================================================
|
||||
//
|
||||
// File : gzstream.h
|
||||
// Revision : $Revision: 1.5 $
|
||||
// Revision_date : $Date: 2002/04/26 23:30:15 $
|
||||
// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
|
||||
//
|
||||
// Standard streambuf implementation following Nicolai Josuttis, "The
|
||||
// Standard C++ Library".
|
||||
// ============================================================================
|
||||
|
||||
#ifndef GZSTREAM_H
|
||||
#define GZSTREAM_H 1
|
||||
|
||||
// standard C++ with new header file names and std:: namespace
|
||||
#include <iostream>
|
||||
#include <fstream>
|
||||
#include <zlib.h>
|
||||
|
||||
#ifdef GZSTREAM_NAMESPACE
|
||||
namespace GZSTREAM_NAMESPACE {
|
||||
#endif
|
||||
|
||||
// ----------------------------------------------------------------------------
|
||||
// Internal classes to implement gzstream. See below for user classes.
|
||||
// ----------------------------------------------------------------------------
|
||||
|
||||
class gzstreambuf : public std::streambuf {
|
||||
private:
|
||||
static const int bufferSize = 47+256; // size of data buff
|
||||
// totals 512 bytes under g++ for igzstream at the end.
|
||||
|
||||
gzFile file; // file handle for compressed file
|
||||
char buffer[bufferSize]; // data buffer
|
||||
char opened; // open/close state of stream
|
||||
int mode; // I/O mode
|
||||
|
||||
int flush_buffer();
|
||||
public:
|
||||
gzstreambuf() : opened(0) {
|
||||
setp( buffer, buffer + (bufferSize-1));
|
||||
setg( buffer + 4, // beginning of putback area
|
||||
buffer + 4, // read position
|
||||
buffer + 4); // end position
|
||||
// ASSERT: both input & output capabilities will not be used together
|
||||
}
|
||||
int is_open() { return opened; }
|
||||
gzstreambuf* open( const char* name, int open_mode);
|
||||
gzstreambuf* close();
|
||||
~gzstreambuf() { close(); }
|
||||
|
||||
virtual int overflow( int c = EOF);
|
||||
virtual int underflow();
|
||||
virtual int sync();
|
||||
};
|
||||
|
||||
class gzstreambase : virtual public std::ios {
|
||||
protected:
|
||||
gzstreambuf buf;
|
||||
public:
|
||||
gzstreambase() { init(&buf); }
|
||||
gzstreambase( const char* name, int open_mode);
|
||||
~gzstreambase();
|
||||
void open( const char* name, int open_mode);
|
||||
void close();
|
||||
gzstreambuf* rdbuf() { return &buf; }
|
||||
};
|
||||
|
||||
// ----------------------------------------------------------------------------
|
||||
// User classes. Use igzstream and ogzstream analogously to ifstream and
|
||||
// ofstream respectively. They read and write files based on the gz*
|
||||
// function interface of the zlib. Files are compatible with gzip compression.
|
||||
// ----------------------------------------------------------------------------
|
||||
|
||||
class igzstream : public gzstreambase, public std::istream {
|
||||
public:
|
||||
igzstream() : std::istream( &buf) {}
|
||||
igzstream( const char* name, int open_mode = std::ios::in)
|
||||
: gzstreambase( name, open_mode), std::istream( &buf) {}
|
||||
gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
|
||||
void open( const char* name, int open_mode = std::ios::in) {
|
||||
gzstreambase::open( name, open_mode);
|
||||
}
|
||||
};
|
||||
|
||||
class ogzstream : public gzstreambase, public std::ostream {
|
||||
public:
|
||||
ogzstream() : std::ostream( &buf) {}
|
||||
ogzstream( const char* name, int mode = std::ios::out)
|
||||
: gzstreambase( name, mode), std::ostream( &buf) {}
|
||||
gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
|
||||
void open( const char* name, int open_mode = std::ios::out) {
|
||||
gzstreambase::open( name, open_mode);
|
||||
}
|
||||
};
|
||||
|
||||
#ifdef GZSTREAM_NAMESPACE
|
||||
} // namespace GZSTREAM_NAMESPACE
|
||||
#endif
|
||||
|
||||
#endif // GZSTREAM_H
|
||||
// ============================================================================
|
||||
// EOF //
|
||||
|
||||
@ -803,7 +803,7 @@ public:
|
||||
(
|
||||
const dictionary& shrinkDict,
|
||||
const dictionary& motionDict,
|
||||
const scalar nAllowableErrors,
|
||||
const label nAllowableErrors,
|
||||
motionSmoother&
|
||||
);
|
||||
|
||||
|
||||
@ -2346,7 +2346,7 @@ void Foam::autoHexMeshDriver::addLayers
|
||||
(
|
||||
const dictionary& shrinkDict,
|
||||
const dictionary& motionDict,
|
||||
const scalar nAllowableErrors,
|
||||
const label nAllowableErrors,
|
||||
motionSmoother& meshMover
|
||||
)
|
||||
{
|
||||
|
||||
@ -103,8 +103,6 @@ $(derivedFvPatchFields)/timeVaryingUniformTotalPressure/timeVaryingUniformTotalP
|
||||
$(derivedFvPatchFields)/totalTemperature/totalTemperatureFvPatchScalarField.C
|
||||
$(derivedFvPatchFields)/turbulentInlet/turbulentInletFvPatchFields.C
|
||||
$(derivedFvPatchFields)/turbulentIntensityKineticEnergyInlet/turbulentIntensityKineticEnergyInletFvPatchScalarField.C
|
||||
$(derivedFvPatchFields)/turbulentMixingLengthDissipationRateInlet/turbulentMixingLengthDissipationRateInletFvPatchScalarField.C
|
||||
$(derivedFvPatchFields)/turbulentMixingLengthFrequencyInlet/turbulentMixingLengthFrequencyInletFvPatchScalarField.C
|
||||
$(derivedFvPatchFields)/uniformFixedValue/uniformFixedValueFvPatchFields.C
|
||||
$(derivedFvPatchFields)/waveTransmissive/waveTransmissiveFvPatchFields.C
|
||||
|
||||
|
||||
@ -32,15 +32,28 @@ License
|
||||
// * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
// adjust negative resistance values to be multiplier of max value
|
||||
void Foam::porousZone::adjustNegativeResistance(vector& resist)
|
||||
void Foam::porousZone::adjustNegativeResistance(dimensionedVector& resist)
|
||||
{
|
||||
scalar maxCmpt = max(0, cmptMax(resist));
|
||||
scalar maxCmpt = max(0, cmptMax(resist.value()));
|
||||
|
||||
for (label cmpt=0; cmpt < vector::nComponents; ++cmpt)
|
||||
if (maxCmpt < 0)
|
||||
{
|
||||
if (resist[cmpt] < 0)
|
||||
FatalErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone::adjustNegativeResistance"
|
||||
"(dimensionedVector&)"
|
||||
) << "negative resistances! " << resist
|
||||
<< exit(FatalError);
|
||||
}
|
||||
else
|
||||
{
|
||||
vector& val = resist.value();
|
||||
for (label cmpt=0; cmpt < vector::nComponents; ++cmpt)
|
||||
{
|
||||
resist[cmpt] *= -maxCmpt;
|
||||
if (val[cmpt] < 0)
|
||||
{
|
||||
val[cmpt] *= -maxCmpt;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -71,24 +84,20 @@ Foam::porousZone::porousZone
|
||||
FatalErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone"
|
||||
"(const fvMesh&, const Istream&)"
|
||||
"(const fvMesh&, const word&, const dictionary&)"
|
||||
) << "cannot find porous cellZone " << name_
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
// local-to-global transformation tensor
|
||||
const tensor& E = coordSys_.R();
|
||||
|
||||
// porosity
|
||||
if (dict_.found("porosity"))
|
||||
if (dict_.readIfPresent("porosity", porosity_))
|
||||
{
|
||||
dict_.lookup("porosity") >> porosity_;
|
||||
|
||||
if (porosity_ <= 0.0 || porosity_ > 1.0)
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone(const fvMesh&, const Istream&)",
|
||||
"Foam::porousZone::porousZone"
|
||||
"(const fvMesh&, const word&, const dictionary&)",
|
||||
dict_
|
||||
)
|
||||
<< "out-of-range porosity value " << porosity_
|
||||
@ -97,73 +106,64 @@ Foam::porousZone::porousZone
|
||||
}
|
||||
|
||||
// powerLaw coefficients
|
||||
if (dict_.found("powerLaw"))
|
||||
if (const dictionary* dictPtr = dict_.subDictPtr("powerLaw"))
|
||||
{
|
||||
const dictionary& subDict = dict_.subDict("powerLaw");
|
||||
if (subDict.found("C0"))
|
||||
{
|
||||
subDict.lookup("C0") >> C0_;
|
||||
}
|
||||
if (subDict.found("C1"))
|
||||
{
|
||||
subDict.lookup("C1") >> C1_;
|
||||
}
|
||||
dictPtr->readIfPresent("C0", C0_);
|
||||
dictPtr->readIfPresent("C1", C1_);
|
||||
}
|
||||
|
||||
// Darcy-Forchheimer coefficients
|
||||
if (dict_.found("Darcy"))
|
||||
if (const dictionary* dictPtr = dict_.subDictPtr("Darcy"))
|
||||
{
|
||||
const dictionary& subDict = dict_.subDict("Darcy");
|
||||
// local-to-global transformation tensor
|
||||
const tensor& E = coordSys_.R();
|
||||
|
||||
dimensionedVector d("d", D_.dimensions(), vector::zero);
|
||||
dimensionedVector f("f", F_.dimensions(), vector::zero);
|
||||
|
||||
if (subDict.found("d"))
|
||||
dimensionedVector d(vector::zero);
|
||||
if (dictPtr->readIfPresent("d", d))
|
||||
{
|
||||
// d = dimensionedVector("d", subDict.lookup("d"));
|
||||
subDict.lookup("d") >> d;
|
||||
adjustNegativeResistance(d.value());
|
||||
if (D_.dimensions() != d.dimensions())
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone"
|
||||
"(const fvMesh&, const word&, const dictionary&)",
|
||||
dict_
|
||||
) << "incorrect dimensions for d: " << d.dimensions()
|
||||
<< " should be " << D_.dimensions()
|
||||
<< exit(FatalIOError);
|
||||
}
|
||||
|
||||
}
|
||||
if (subDict.found("f"))
|
||||
{
|
||||
// f = dimensionedVector("f", subDict.lookup("f"));
|
||||
subDict.lookup("f") >> f;
|
||||
adjustNegativeResistance(f.value());
|
||||
adjustNegativeResistance(d);
|
||||
|
||||
D_.value().xx() = d.value().x();
|
||||
D_.value().yy() = d.value().y();
|
||||
D_.value().zz() = d.value().z();
|
||||
D_.value() = (E & D_ & E.T()).value();
|
||||
}
|
||||
|
||||
if (D_.dimensions() != d.dimensions())
|
||||
dimensionedVector f(vector::zero);
|
||||
if (dictPtr->readIfPresent("f", f))
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone(const fvMesh&, const Istream&)",
|
||||
dict_
|
||||
) << "incorrect dimensions for d: " << d.dimensions()
|
||||
<< " should be " << D_.dimensions()
|
||||
<< exit(FatalIOError);
|
||||
if (F_.dimensions() != f.dimensions())
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone"
|
||||
"(const fvMesh&, const word&, const dictionary&)",
|
||||
dict_
|
||||
) << "incorrect dimensions for f: " << f.dimensions()
|
||||
<< " should be " << F_.dimensions()
|
||||
<< exit(FatalIOError);
|
||||
}
|
||||
|
||||
adjustNegativeResistance(f);
|
||||
|
||||
// leading 0.5 is from 1/2 * rho
|
||||
F_.value().xx() = 0.5*f.value().x();
|
||||
F_.value().yy() = 0.5*f.value().y();
|
||||
F_.value().zz() = 0.5*f.value().z();
|
||||
F_.value() = (E & F_ & E.T()).value();
|
||||
}
|
||||
|
||||
if (F_.dimensions() != f.dimensions())
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone(const fvMesh&, const Istream&)",
|
||||
dict_
|
||||
) << "incorrect dimensions for f: " << f.dimensions()
|
||||
<< " should be " << F_.dimensions()
|
||||
<< exit(FatalIOError);
|
||||
}
|
||||
|
||||
D_.value().xx() = d.value().x();
|
||||
D_.value().yy() = d.value().y();
|
||||
D_.value().zz() = d.value().z();
|
||||
D_.value() = (E & D_ & E.T()).value();
|
||||
|
||||
// leading 0.5 is from 1/2 * rho
|
||||
F_.value().xx() = 0.5*f.value().x();
|
||||
F_.value().yy() = 0.5*f.value().y();
|
||||
F_.value().zz() = 0.5*f.value().z();
|
||||
F_.value() = (E & F_ & E.T()).value();
|
||||
}
|
||||
|
||||
// provide some feedback for the user
|
||||
@ -179,7 +179,8 @@ Foam::porousZone::porousZone
|
||||
{
|
||||
FatalIOErrorIn
|
||||
(
|
||||
"Foam::porousZone::porousZone(const fvMesh&, const Istream&)",
|
||||
"Foam::porousZone::porousZone"
|
||||
"(const fvMesh&, const word&, const dictionary&)",
|
||||
dict_
|
||||
) << "neither powerLaw (C0/C1) "
|
||||
"nor Darcy-Forchheimer law (d/f) specified"
|
||||
|
||||
@ -128,7 +128,7 @@ class porousZone
|
||||
// Private Member Functions
|
||||
|
||||
//- adjust negative resistance values to be multiplier of max value
|
||||
static void adjustNegativeResistance(vector& resist);
|
||||
static void adjustNegativeResistance(dimensionedVector& resist);
|
||||
|
||||
//- Power-law resistance
|
||||
template<class RhoFieldType>
|
||||
|
||||
@ -5,4 +5,6 @@ wmake libso basic
|
||||
wmake libso solidParticle
|
||||
wmake libso intermediate
|
||||
wmake libso dieselSpray
|
||||
wmake libso molecule
|
||||
(cd molecularDynamics && wmake libso potential)
|
||||
(cd molecularDynamics && wmake libso molecule)
|
||||
|
||||
|
||||
@ -11,11 +11,6 @@ referredMolecule = referredMolecule
|
||||
referredCellList = referredCellList
|
||||
referredCell = referredCell
|
||||
referralLists = referralLists
|
||||
|
||||
potentials = potentials
|
||||
pairPotential = $(potentials)/pairPotential
|
||||
tetherPotential = $(potentials)/tetherPotential
|
||||
|
||||
$(distribution)/distribution.C
|
||||
|
||||
$(reducedUnits)/reducedUnits.C
|
||||
@ -42,11 +37,6 @@ $(moleculeCloud)/moleculeCloudIntegrateEquationsOfMotion.C
|
||||
$(moleculeCloud)/moleculeCloudRemoveHighEnergyOverlaps.C
|
||||
$(moleculeCloud)/moleculeCloudApplyConstraintsAndThermostats.C
|
||||
|
||||
$(pairPotential)/basic/pairPotential.C
|
||||
$(pairPotential)/basic/pairPotentialList.C
|
||||
$(tetherPotential)/tetherPotential.C
|
||||
$(tetherPotential)/tetherPotentialList.C
|
||||
|
||||
$(referralLists)/receivingReferralList.C
|
||||
$(referralLists)/sendingReferralList.C
|
||||
$(referredCellList)/referredCellList.C
|
||||
@ -1,8 +1,10 @@
|
||||
EXE_INC = \
|
||||
-I$(LIB_SRC)/finiteVolume/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
|
||||
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude
|
||||
|
||||
EXE_LIBS = \
|
||||
-lfiniteVolume \
|
||||
-llagrangian
|
||||
-llagrangian \
|
||||
-lpotential
|
||||
|
||||
12
src/lagrangian/molecule/distribution/distribution.C → src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
Executable file → Normal file
12
src/lagrangian/molecule/distribution/distribution.C → src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
Executable file → Normal file
@ -135,7 +135,7 @@ scalar distribution::median()
|
||||
|
||||
scalar runningSum = 0.0;
|
||||
|
||||
List< Pair<scalar> > normDist(normalised());
|
||||
List<Pair<scalar> > normDist(normalised());
|
||||
|
||||
if (normDist.size())
|
||||
{
|
||||
@ -259,7 +259,7 @@ List< Pair<scalar> > distribution::normalised()
|
||||
|
||||
sort(keys);
|
||||
|
||||
List< Pair<scalar> > normDist(size());
|
||||
List<Pair<scalar> > normDist(size());
|
||||
|
||||
forAll(keys,k)
|
||||
{
|
||||
@ -282,9 +282,9 @@ List< Pair<scalar> > distribution::normalisedMinusMean()
|
||||
|
||||
List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
|
||||
{
|
||||
List< Pair<scalar> > oldDist(normalised());
|
||||
List<Pair<scalar> > oldDist(normalised());
|
||||
|
||||
List< Pair<scalar> > newDist(oldDist.size());
|
||||
List<Pair<scalar> > newDist(oldDist.size());
|
||||
|
||||
forAll(oldDist,u)
|
||||
{
|
||||
@ -383,7 +383,7 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
|
||||
}
|
||||
|
||||
|
||||
List< Pair<scalar> > distribution::raw()
|
||||
List<Pair<scalar> > distribution::raw()
|
||||
{
|
||||
insertMissingKeys();
|
||||
|
||||
@ -391,7 +391,7 @@ List< Pair<scalar> > distribution::raw()
|
||||
|
||||
sort(keys);
|
||||
|
||||
List< Pair<scalar> > rawDist(size());
|
||||
List<Pair<scalar> > rawDist(size());
|
||||
|
||||
forAll(keys,k)
|
||||
{
|
||||
1
src/lagrangian/molecule/distribution/distribution.H → src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
Executable file → Normal file
1
src/lagrangian/molecule/distribution/distribution.H → src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
Executable file → Normal file
@ -102,6 +102,7 @@ public:
|
||||
|
||||
List<Pair<scalar> > raw();
|
||||
|
||||
|
||||
// Access
|
||||
|
||||
inline scalar binWidth() const;
|
||||
0
src/lagrangian/molecule/distribution/distributionI.H → src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
Executable file → Normal file
0
src/lagrangian/molecule/distribution/distributionI.H → src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
Executable file → Normal file
0
src/lagrangian/molecule/distribution/distributionIO.C → src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
Executable file → Normal file
0
src/lagrangian/molecule/distribution/distributionIO.C → src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
Executable file → Normal file
0
src/lagrangian/molecule/mdTools/averageMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
Executable file → Normal file
0
src/lagrangian/molecule/mdTools/averageMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
Executable file → Normal file
@ -79,5 +79,27 @@ if (mesh.time().timeIndex() % pacf.sampleSteps() == 0)
|
||||
|
||||
if (mesh.time().timeIndex() % hfacf.sampleSteps() == 0)
|
||||
{
|
||||
// hFacf.calculateCorrelationFunction();
|
||||
|
||||
IDLList<molecule>::iterator mol(molecules.begin());
|
||||
|
||||
vector s = vector::zero;
|
||||
|
||||
for
|
||||
(
|
||||
mol = molecules.begin();
|
||||
mol != molecules.end();
|
||||
++mol
|
||||
)
|
||||
{
|
||||
s +=
|
||||
(
|
||||
0.5 * mol().mass() * magSqr(mol().U())
|
||||
+
|
||||
mol().potentialEnergy()
|
||||
) * mol().U()
|
||||
+
|
||||
0.5 * ( mol().rf() & mol().U() );
|
||||
}
|
||||
|
||||
hfacf.calculateCorrelationFunction(s);
|
||||
}
|
||||
0
src/lagrangian/molecule/mdTools/calculateMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
Executable file → Normal file
0
src/lagrangian/molecule/mdTools/calculateMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
Executable file → Normal file
@ -59,7 +59,24 @@ Info<< "Viscosity = "
|
||||
|
||||
if(writeHFacf)
|
||||
{
|
||||
|
||||
OFstream hfacfFile
|
||||
(
|
||||
runTime.path()/ + "hfacf"
|
||||
);
|
||||
|
||||
if (!hfacf.writeAveraged(hfacfFile))
|
||||
{
|
||||
FatalErrorIn(args.executable())
|
||||
<< "Failed writing to "
|
||||
<< hfacfFile.name()
|
||||
<< abort(FatalError);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Info << "Thermal conductivity = "
|
||||
<< hfacf.integral()
|
||||
/averageTemperature
|
||||
/averageTemperature
|
||||
/moleculeCloud::kb
|
||||
/ meshVolume
|
||||
<< endl;
|
||||
74
src/lagrangian/molecule/mdTools/createMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
Executable file → Normal file
74
src/lagrangian/molecule/mdTools/createMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
Executable file → Normal file
@ -2,25 +2,25 @@
|
||||
|
||||
List< scalarField > allSpeciesN_RU
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
|
||||
List< scalarField > allSpeciesM_RU
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
|
||||
List< vectorField > allSpeciesVelocitySum_RU
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
vectorField (mesh.nCells(), vector::zero)
|
||||
);
|
||||
|
||||
List< scalarField > allSpeciesVelocityMagSquaredSum_RU
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
|
||||
@ -34,13 +34,13 @@ Info << nl << "Creating fields." << endl;
|
||||
|
||||
PtrList<volScalarField> allSpeciesRhoN
|
||||
(
|
||||
molecules.nIds()
|
||||
molecules.pairPotentials().nIds()
|
||||
);
|
||||
|
||||
forAll (allSpeciesRhoN, rN)
|
||||
{
|
||||
Info << " Creating number density field for "
|
||||
<< molecules.idList()[rN] << endl;
|
||||
<< molecules.pairPotentials().idList()[rN] << endl;
|
||||
|
||||
allSpeciesRhoN.set
|
||||
(
|
||||
@ -49,7 +49,7 @@ forAll (allSpeciesRhoN, rN)
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"rhoN_" + molecules.idList()[rN],
|
||||
"rhoN_" + molecules.pairPotentials().idList()[rN],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
@ -89,13 +89,13 @@ totalRhoN.correctBoundaryConditions();
|
||||
|
||||
PtrList<volScalarField> allSpeciesRhoM
|
||||
(
|
||||
molecules.nIds()
|
||||
molecules.pairPotentials().nIds()
|
||||
);
|
||||
|
||||
forAll (allSpeciesRhoM, rM)
|
||||
{
|
||||
Info << " Creating mass density field for "
|
||||
<< molecules.idList()[rM] << endl;
|
||||
<< molecules.pairPotentials().idList()[rM] << endl;
|
||||
|
||||
allSpeciesRhoM.set
|
||||
(
|
||||
@ -104,7 +104,7 @@ forAll (allSpeciesRhoM, rM)
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"rhoM_" + molecules.idList()[rM],
|
||||
"rhoM_" + molecules.pairPotentials().idList()[rM],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
@ -144,13 +144,13 @@ totalRhoM.correctBoundaryConditions();
|
||||
|
||||
PtrList<volVectorField> allSpeciesVelocity
|
||||
(
|
||||
molecules.nIds()
|
||||
molecules.pairPotentials().nIds()
|
||||
);
|
||||
|
||||
forAll (allSpeciesVelocity, v)
|
||||
{
|
||||
Info << " Creating velocity field for "
|
||||
<< molecules.idList()[v] << endl;
|
||||
<< molecules.pairPotentials().idList()[v] << endl;
|
||||
|
||||
allSpeciesVelocity.set
|
||||
(
|
||||
@ -159,7 +159,7 @@ forAll (allSpeciesVelocity, v)
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"velocity_" + molecules.idList()[v],
|
||||
"velocity_" + molecules.pairPotentials().idList()[v],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
@ -177,22 +177,40 @@ forAll (allSpeciesVelocity, v)
|
||||
|
||||
Info << " Creating total velocity field" << endl;
|
||||
|
||||
// volVectorField totalVelocity
|
||||
// (
|
||||
// IOobject
|
||||
// (
|
||||
// "velocity_total",
|
||||
// runTime.timeName(),
|
||||
// mesh,
|
||||
// IOobject::NO_READ,
|
||||
// IOobject::AUTO_WRITE
|
||||
// ),
|
||||
// mesh,
|
||||
// dimVelocity,
|
||||
// "zeroGradient"
|
||||
// );
|
||||
// totalVelocity.internalField() = vectorField (mesh.nCells(), vector::zero);
|
||||
// totalVelocity.correctBoundaryConditions();
|
||||
|
||||
|
||||
volVectorField totalVelocity
|
||||
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"velocity_total",
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
IOobject::AUTO_WRITE
|
||||
|
||||
"velocity_total",
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
IOobject::AUTO_WRITE
|
||||
|
||||
),
|
||||
mesh,
|
||||
dimVelocity,
|
||||
"zeroGradient"
|
||||
dimensionedVector("zero", dimVelocity, vector::zero)
|
||||
);
|
||||
totalVelocity.internalField() = vectorField (mesh.nCells(), vector::zero);
|
||||
totalVelocity.correctBoundaryConditions();
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Kinetic temperature
|
||||
@ -200,13 +218,13 @@ totalVelocity.correctBoundaryConditions();
|
||||
|
||||
PtrList<volScalarField> allSpeciesTemperature
|
||||
(
|
||||
molecules.nIds()
|
||||
molecules.pairPotentials().nIds()
|
||||
);
|
||||
|
||||
forAll (allSpeciesTemperature, t)
|
||||
{
|
||||
Info << " Creating temperature field for "
|
||||
<< molecules.idList()[t] << endl;
|
||||
<< molecules.pairPotentials().idList()[t] << endl;
|
||||
|
||||
allSpeciesTemperature.set
|
||||
(
|
||||
@ -215,7 +233,7 @@ forAll (allSpeciesTemperature, t)
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"temperature_" + molecules.idList()[t],
|
||||
"temperature_" + molecules.pairPotentials().idList()[t],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
@ -256,13 +274,13 @@ totalTemperature.correctBoundaryConditions();
|
||||
|
||||
PtrList<volScalarField> allSpeciesMeanKE
|
||||
(
|
||||
molecules.nIds()
|
||||
molecules.pairPotentials().nIds()
|
||||
);
|
||||
|
||||
forAll (allSpeciesMeanKE, mKE)
|
||||
{
|
||||
Info << " Creating mean kinetic energy field for "
|
||||
<< molecules.idList()[mKE] << endl;
|
||||
<< molecules.pairPotentials().idList()[mKE] << endl;
|
||||
|
||||
allSpeciesMeanKE.set
|
||||
(
|
||||
@ -271,7 +289,7 @@ forAll (allSpeciesMeanKE, mKE)
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"meanKE_" + molecules.idList()[mKE],
|
||||
"meanKE_" + molecules.pairPotentials().idList()[mKE],
|
||||
runTime.timeName(),
|
||||
mesh,
|
||||
IOobject::NO_READ,
|
||||
0
src/lagrangian/molecule/mdTools/md.H → src/lagrangian/molecularDynamics/molecule/mdTools/md.H
Executable file → Normal file
0
src/lagrangian/molecule/mdTools/md.H → src/lagrangian/molecularDynamics/molecule/mdTools/md.H
Executable file → Normal file
8
src/lagrangian/molecule/mdTools/resetMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
Executable file → Normal file
8
src/lagrangian/molecule/mdTools/resetMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
Executable file → Normal file
@ -2,25 +2,25 @@ if (runTime.outputTime())
|
||||
{
|
||||
allSpeciesN_RU = List< scalarField >
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
|
||||
allSpeciesM_RU = List< scalarField >
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
|
||||
allSpeciesVelocitySum_RU = List< vectorField >
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
vectorField (mesh.nCells(), vector::zero)
|
||||
);
|
||||
|
||||
allSpeciesVelocityMagSquaredSum_RU = List< scalarField >
|
||||
(
|
||||
molecules.nIds(),
|
||||
molecules.pairPotentials().nIds(),
|
||||
scalarField (mesh.nCells(), 0.0)
|
||||
);
|
||||
}
|
||||
@ -86,6 +86,8 @@ if (runTime.outputTime())
|
||||
<< " m/s" << nl
|
||||
<< "Average temperature = "
|
||||
<< averageTemperature << " K" << nl
|
||||
<< "accumulatedTotalrDotfSum = "
|
||||
<< accumulatedTotalrDotfSum << nl
|
||||
<< "Average pressure = "
|
||||
<< averagePressure << " N/m^2" << nl
|
||||
<< "----------------------------------------" << endl;
|
||||
3
src/lagrangian/molecule/molecule/molecule.C → src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
Executable file → Normal file
3
src/lagrangian/molecule/molecule/molecule.C → src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
Executable file → Normal file
@ -54,7 +54,7 @@ bool molecule::move(molecule::trackData& td)
|
||||
U_ += 0.5*deltaT*A_;
|
||||
}
|
||||
|
||||
while (td.keepParticle && !td.switchProcessor && tEnd > SMALL)
|
||||
while (td.keepParticle && !td.switchProcessor && tEnd > (SMALL*SMALL))
|
||||
{
|
||||
// set the lagrangian time-step
|
||||
scalar dt = min(dtMax, tEnd);
|
||||
@ -178,6 +178,7 @@ void molecule::hitWallPatch
|
||||
{
|
||||
U_ -= 2*Un*nw;
|
||||
}
|
||||
|
||||
// }
|
||||
|
||||
}
|
||||
4
src/lagrangian/molecule/molecule/molecule.H → src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
Executable file → Normal file
4
src/lagrangian/molecule/molecule/molecule.H → src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
Executable file → Normal file
@ -23,10 +23,9 @@ License
|
||||
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
|
||||
Class
|
||||
Foam::molecule
|
||||
molecule
|
||||
|
||||
Description
|
||||
Foam::molecule
|
||||
|
||||
SourceFiles
|
||||
moleculeI.H
|
||||
@ -192,6 +191,7 @@ public:
|
||||
|
||||
//- Return tetherPosition
|
||||
inline const vector& tetherPosition() const;
|
||||
inline vector& tetherPosition();
|
||||
|
||||
|
||||
//- Tracking
|
||||
45
src/lagrangian/molecule/molecule/moleculeI.H → src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
Executable file → Normal file
45
src/lagrangian/molecule/molecule/moleculeI.H → src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
Executable file → Normal file
@ -24,9 +24,12 @@ License
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
inline Foam::molecule::molecule
|
||||
inline molecule::molecule
|
||||
(
|
||||
const Cloud<molecule>& c,
|
||||
const vector& position,
|
||||
@ -51,7 +54,7 @@ inline Foam::molecule::molecule
|
||||
{}
|
||||
|
||||
|
||||
inline Foam::molecule::trackData::trackData
|
||||
inline molecule::trackData::trackData
|
||||
(
|
||||
moleculeCloud& molCloud,
|
||||
label part
|
||||
@ -65,88 +68,98 @@ inline Foam::molecule::trackData::trackData
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
inline Foam::label Foam::molecule::id() const
|
||||
inline label molecule::id() const
|
||||
{
|
||||
return id_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::molecule::mass() const
|
||||
inline scalar molecule::mass() const
|
||||
{
|
||||
return mass_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::vector& Foam::molecule::U() const
|
||||
inline const vector& molecule::U() const
|
||||
{
|
||||
return U_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::vector& Foam::molecule::U()
|
||||
inline vector& molecule::U()
|
||||
{
|
||||
return U_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::vector& Foam::molecule::A() const
|
||||
inline const vector& molecule::A() const
|
||||
{
|
||||
return A_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::vector& Foam::molecule::A()
|
||||
inline vector& molecule::A()
|
||||
{
|
||||
return A_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar Foam::molecule::potentialEnergy() const
|
||||
inline scalar molecule::potentialEnergy() const
|
||||
{
|
||||
return potentialEnergy_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::scalar& Foam::molecule::potentialEnergy()
|
||||
inline scalar& molecule::potentialEnergy()
|
||||
{
|
||||
return potentialEnergy_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::tensor& Foam::molecule::rf() const
|
||||
inline const tensor& molecule::rf() const
|
||||
{
|
||||
return rf_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::tensor& Foam::molecule::rf()
|
||||
inline tensor& molecule::rf()
|
||||
{
|
||||
return rf_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::label Foam::molecule::tethered() const
|
||||
inline label molecule::tethered() const
|
||||
{
|
||||
return tethered_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::vector& Foam::molecule::tetherPosition() const
|
||||
inline const vector& molecule::tetherPosition() const
|
||||
{
|
||||
return tetherPosition_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::moleculeCloud& Foam::molecule::trackData::molCloud()
|
||||
inline vector& molecule::tetherPosition()
|
||||
{
|
||||
return tetherPosition_;
|
||||
}
|
||||
|
||||
|
||||
inline moleculeCloud& molecule::trackData::molCloud()
|
||||
{
|
||||
return molCloud_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::label Foam::molecule::trackData::part() const
|
||||
inline label molecule::trackData::part() const
|
||||
{
|
||||
return part_;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// ************************************************************************* //
|
||||
0
src/lagrangian/molecule/molecule/moleculeIO.C → src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
Executable file → Normal file
0
src/lagrangian/molecule/molecule/moleculeIO.C → src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
Executable file → Normal file
0
src/lagrangian/molecule/moleculeCloud/moleculeCloud.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
Executable file → Normal file
0
src/lagrangian/molecule/moleculeCloud/moleculeCloud.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
Executable file → Normal file
22
src/lagrangian/molecule/moleculeCloud/moleculeCloud.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
Executable file → Normal file
22
src/lagrangian/molecule/moleculeCloud/moleculeCloud.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
Executable file → Normal file
@ -97,18 +97,6 @@ private:
|
||||
|
||||
scalar potentialEnergyLimit_;
|
||||
|
||||
scalar guardRadius_;
|
||||
|
||||
scalar rCutMax_;
|
||||
|
||||
//- storing rCutMaxSqr in class as well as rCutMax to
|
||||
//- avoid needing to calculate it often.
|
||||
//- Possibilty of inconsistency if tinkered with.
|
||||
|
||||
scalar rCutMaxSqr_;
|
||||
|
||||
List<word> idList_;
|
||||
|
||||
labelList removalOrder_;
|
||||
|
||||
labelListList directInteractionList_;
|
||||
@ -189,20 +177,10 @@ public:
|
||||
|
||||
inline scalar potentialEnergyLimit() const;
|
||||
|
||||
inline scalar guardRadius() const;
|
||||
|
||||
inline scalar rCutMax() const;
|
||||
|
||||
inline scalar rCutMaxSqr() const;
|
||||
|
||||
inline const List<word>& idList() const;
|
||||
|
||||
inline const labelList& removalOrder() const;
|
||||
|
||||
inline label nPairPotentials() const;
|
||||
|
||||
inline label nIds() const;
|
||||
|
||||
inline const labelListList& directInteractionList() const;
|
||||
|
||||
inline const referredCellList& referredInteractionList() const;
|
||||
@ -22,13 +22,21 @@ License
|
||||
along with OpenFOAM; if not, write to the Free Software Foundation,
|
||||
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
|
||||
Class
|
||||
moleculeCloud
|
||||
|
||||
Description
|
||||
|
||||
\*----------------------------------------------------------------------------*/
|
||||
|
||||
#include "moleculeCloud.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
void Foam::moleculeCloud::buildCellOccupancy()
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
void moleculeCloud::buildCellOccupancy()
|
||||
{
|
||||
forAll(cellOccupancy_, cO)
|
||||
{
|
||||
@ -37,7 +45,12 @@ void Foam::moleculeCloud::buildCellOccupancy()
|
||||
|
||||
iterator mol(this->begin());
|
||||
|
||||
for (mol = this->begin(); mol != this->end(); ++mol)
|
||||
for
|
||||
(
|
||||
mol = this->begin();
|
||||
mol != this->end();
|
||||
++mol
|
||||
)
|
||||
{
|
||||
cellOccupancy_[mol().cell()].append(&mol());
|
||||
}
|
||||
@ -50,5 +63,6 @@ void Foam::moleculeCloud::buildCellOccupancy()
|
||||
referredInteractionList_.referMolecules();
|
||||
}
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -6,7 +6,7 @@ rIJ = molI->position() - molJ->position();
|
||||
|
||||
rIJMagSq = magSqr(rIJ);
|
||||
|
||||
if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
|
||||
if(pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
|
||||
{
|
||||
rIJMag = mag(rIJ);
|
||||
|
||||
@ -0,0 +1,193 @@
|
||||
// Parallel coding to access boundary information to build up interaction cell info
|
||||
|
||||
// See preservePatchTypes for how to read the boundary file.
|
||||
|
||||
// Read faceProcAddressing, as per reconstructPar, to get hold of the original,
|
||||
// undecomposed face label from a face on a processor mesh. See email from Mattijs:
|
||||
|
||||
// > Is it a case of reading the faceProcAddressing file, in the same way as
|
||||
// > something like reconstructPar?
|
||||
// Correct.
|
||||
//
|
||||
// Note that faceProcAddressing is a bit weird since it also includes which side
|
||||
// of an internal face we have. If I remember correctly:
|
||||
//
|
||||
// faceI == 0 illegal
|
||||
// faceI > 0 we have the original owner of faceI-1 i.e. we have the face in the
|
||||
// original order.
|
||||
// faceI < 0 we have the original neighbour of -faceI-1 so the face is flipped.
|
||||
|
||||
// Use the same functionality as
|
||||
// label polyBoundaryMesh::whichPatch(const label faceIndex) const
|
||||
// To determine which patch a face was on originally.
|
||||
|
||||
if (Pstream::parRun())
|
||||
{
|
||||
// if (Pstream::myProcNo() == Pstream::masterNo())
|
||||
// // {
|
||||
// dictionary patchDictionary;
|
||||
//
|
||||
// DynamicList<word> patchNames;
|
||||
//
|
||||
// {
|
||||
// IOobject undecomposedBoundaryHeader
|
||||
// (
|
||||
// "undecomposedBoundary",
|
||||
// mesh_.time().constant(),
|
||||
// polyMesh::meshSubDir,
|
||||
// mesh_,
|
||||
// IOobject::MUST_READ,
|
||||
// IOobject::NO_WRITE,
|
||||
// false
|
||||
// );
|
||||
//
|
||||
// if (undecomposedBoundaryHeader.headerOk())
|
||||
// {
|
||||
// polyBoundaryMeshEntries undecomposedPatchEntries
|
||||
// (
|
||||
// undecomposedBoundaryHeader
|
||||
// );
|
||||
//
|
||||
// forAll(undecomposedPatchEntries, patchi)
|
||||
// {
|
||||
// patchNames.append
|
||||
// (
|
||||
// undecomposedPatchEntries[patchi].keyword()
|
||||
// );
|
||||
//
|
||||
// patchDictionary.add
|
||||
// (
|
||||
// undecomposedPatchEntries[patchi]
|
||||
// );
|
||||
// }
|
||||
// }
|
||||
// else
|
||||
// {
|
||||
// FatalErrorIn
|
||||
// (
|
||||
// "moleculeCloudBuildCellInteractionLists.C\n"
|
||||
// )
|
||||
// << "undecomposedBoundary file not found in "
|
||||
// "constant/polyMesh"
|
||||
// << abort(FatalError);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// labelIOList faceProcAddressing
|
||||
// (
|
||||
// IOobject
|
||||
// (
|
||||
// "faceProcAddressing",
|
||||
// mesh_.time().constant(),
|
||||
// polyMesh::meshSubDir,
|
||||
// mesh_,
|
||||
// IOobject::MUST_READ,
|
||||
// IOobject::NO_WRITE,
|
||||
// false
|
||||
// )
|
||||
// );
|
||||
|
||||
labelList procPatches(mesh_.globalData().processorPatches());
|
||||
|
||||
forAll(procPatches,pP)
|
||||
{
|
||||
const processorPolyPatch& patch =
|
||||
refCast<const processorPolyPatch>
|
||||
(
|
||||
mesh_.boundaryMesh()[procPatches[pP]]
|
||||
);
|
||||
//
|
||||
// Pout << nl << "name: " << patch.name() << nl
|
||||
// << "start: " << patch.start() << nl
|
||||
// << "size: " << patch.size() << nl
|
||||
// << "separated: " << Switch(patch.separated()) << nl
|
||||
// << "parallel: " << Switch(patch.parallel()) << nl << endl;
|
||||
//
|
||||
// forAll (patch, pI)
|
||||
// {
|
||||
// label decomposedMeshFace = patch.start() + pI;
|
||||
//
|
||||
// label faceProcAdd = faceProcAddressing[decomposedMeshFace];
|
||||
//
|
||||
// label globalFace = abs(faceProcAdd)-1;
|
||||
//
|
||||
// Pout << "Patch index: " << pI
|
||||
// << " " << patch[pI]
|
||||
// << " Mesh index: " << decomposedMeshFace
|
||||
// << " faceProcAdd: " << faceProcAdd
|
||||
// << " globalFace:" << globalFace;
|
||||
//
|
||||
// label minStart = -1;
|
||||
//
|
||||
// // Scanning the dictionary each time is a very ugly way of
|
||||
// // finding out what patch a face originally belonged to, but
|
||||
// // it proves the concept. Read the patch info a container
|
||||
// // class and have a neat way of tell which patch a face is from
|
||||
// // embedded in that. Split each processor face down into
|
||||
// // separate lists for each different originiating patch.
|
||||
//
|
||||
// forAll(patchNames, patchi)
|
||||
// {
|
||||
// if (patchDictionary.found(patchNames[patchi]))
|
||||
// {
|
||||
// const dictionary& patchDict =
|
||||
// patchDictionary.subDict(patchNames[patchi]);
|
||||
//
|
||||
// word faceName(patchNames[patchi]);
|
||||
// label startFace(readLabel(patchDict.lookup("startFace")));
|
||||
// label nFaces(readLabel(patchDict.lookup("nFaces")));
|
||||
//
|
||||
// if
|
||||
// (
|
||||
// minStart < 0
|
||||
// || startFace < minStart
|
||||
// )
|
||||
// {
|
||||
// minStart = startFace;
|
||||
// }
|
||||
//
|
||||
// if
|
||||
// (
|
||||
// globalFace >= startFace
|
||||
// && globalFace < startFace + nFaces
|
||||
// )
|
||||
// {
|
||||
// Pout << " original patch: " << faceName << endl;
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// if (globalFace < minStart)
|
||||
// {
|
||||
// Pout << " originally an internal face" << endl;
|
||||
// }
|
||||
// }
|
||||
//
|
||||
if (patch.separated())
|
||||
{
|
||||
Pout << patch.separation();
|
||||
}
|
||||
|
||||
if (!patch.parallel())
|
||||
{
|
||||
Pout << patch.forwardT();
|
||||
}
|
||||
}
|
||||
// }
|
||||
// else
|
||||
// {
|
||||
//
|
||||
// }
|
||||
|
||||
// Get coords of my shared points
|
||||
// vector sharedPoints(vector::one*(Pstream::myProcNo()+1));
|
||||
// label testRedLab(Pstream::myProcNo()+1);
|
||||
|
||||
// Pout << testRedLab << endl;
|
||||
|
||||
// Append from all processors
|
||||
// combineReduce(sharedPoints, plusEqOp<vector>());
|
||||
// reduce(testRedLab, plusOp<label>());
|
||||
|
||||
// Pout << testRedLab << endl;
|
||||
}
|
||||
30
src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
Executable file → Normal file
30
src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
Executable file → Normal file
@ -50,42 +50,12 @@ inline scalar moleculeCloud::potentialEnergyLimit() const
|
||||
}
|
||||
|
||||
|
||||
inline scalar moleculeCloud::guardRadius() const
|
||||
{
|
||||
return guardRadius_;
|
||||
}
|
||||
|
||||
|
||||
inline scalar moleculeCloud::rCutMax() const
|
||||
{
|
||||
return rCutMax_;
|
||||
}
|
||||
|
||||
|
||||
inline scalar moleculeCloud::rCutMaxSqr() const
|
||||
{
|
||||
return rCutMaxSqr_;
|
||||
}
|
||||
|
||||
|
||||
inline const List<word>& moleculeCloud::idList() const
|
||||
{
|
||||
return idList_;
|
||||
}
|
||||
|
||||
|
||||
inline label moleculeCloud::nPairPotentials() const
|
||||
{
|
||||
return pairPotentials_.size();
|
||||
}
|
||||
|
||||
|
||||
inline label moleculeCloud::nIds() const
|
||||
{
|
||||
return idList_.size();
|
||||
}
|
||||
|
||||
|
||||
inline const labelList& moleculeCloud::removalOrder() const
|
||||
{
|
||||
return removalOrder_;
|
||||
@ -0,0 +1,177 @@
|
||||
Info<< nl << "Reading MD solution parameters:" << endl;
|
||||
|
||||
IOdictionary mdSolution
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"mdSolution",
|
||||
mesh_.time().system(),
|
||||
mesh_,
|
||||
IOobject::MUST_READ,
|
||||
IOobject::NO_WRITE
|
||||
)
|
||||
);
|
||||
|
||||
integrationMethod_ = integrationMethodNames_.read
|
||||
(
|
||||
mdSolution.lookup("integrationMethod")
|
||||
);
|
||||
|
||||
potentialEnergyLimit_ = readScalar
|
||||
(
|
||||
mdSolution.lookup("potentialEnergyLimit")
|
||||
);
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
IOdictionary potentialDict
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"potentialDict",
|
||||
mesh_.time().system(),
|
||||
mesh_,
|
||||
IOobject::MUST_READ,
|
||||
IOobject::NO_WRITE
|
||||
)
|
||||
);
|
||||
|
||||
IOdictionary idListDict
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
"idList",
|
||||
mesh_.time().constant(),
|
||||
mesh_,
|
||||
IOobject::MUST_READ,
|
||||
IOobject::NO_WRITE
|
||||
)
|
||||
);
|
||||
|
||||
// ****************************************************************************
|
||||
// Pair potentials
|
||||
|
||||
if (!potentialDict.found("pair"))
|
||||
{
|
||||
FatalErrorIn("moleculeCloudReadPotentials.H") << nl
|
||||
<< "pair potential specification subDict not found"
|
||||
<< abort(FatalError);
|
||||
}
|
||||
|
||||
const dictionary& pairDict = potentialDict.subDict("pair");
|
||||
|
||||
pairPotentials_.buildPotentials(idListDict, pairDict, mesh_);
|
||||
|
||||
if (potentialDict.found("removalOrder"))
|
||||
{
|
||||
List<word> remOrd = potentialDict.lookup("removalOrder");
|
||||
|
||||
removalOrder_.setSize(remOrd.size());
|
||||
|
||||
forAll(removalOrder_, rO)
|
||||
{
|
||||
removalOrder_[rO] = findIndex(pairPotentials_.idList(), remOrd[rO]);
|
||||
}
|
||||
}
|
||||
|
||||
// ****************************************************************************
|
||||
// Tether potentials
|
||||
|
||||
iterator mol(this->begin());
|
||||
|
||||
DynamicList<label> tetherIds;
|
||||
|
||||
for
|
||||
(
|
||||
mol = this->begin();
|
||||
mol != this->end();
|
||||
++mol
|
||||
)
|
||||
{
|
||||
if (mol().tethered())
|
||||
{
|
||||
if (findIndex(tetherIds, mol().id()) == -1)
|
||||
{
|
||||
tetherIds.append
|
||||
(
|
||||
mol().id()
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (Pstream::parRun())
|
||||
{
|
||||
List< labelList > allTetherIds(Pstream::nProcs());
|
||||
|
||||
allTetherIds[Pstream::myProcNo()] = tetherIds;
|
||||
|
||||
Pstream::gatherList(allTetherIds);
|
||||
|
||||
if (Pstream::master())
|
||||
{
|
||||
DynamicList<label> globalTetherIds;
|
||||
|
||||
forAll(allTetherIds, procN)
|
||||
{
|
||||
const labelList& procNTetherIds = allTetherIds[procN];
|
||||
|
||||
forAll(procNTetherIds, id)
|
||||
{
|
||||
if (findIndex(globalTetherIds, procNTetherIds[id]) == -1)
|
||||
{
|
||||
globalTetherIds.append
|
||||
(
|
||||
procNTetherIds[id]
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
globalTetherIds.shrink();
|
||||
|
||||
tetherIds = globalTetherIds;
|
||||
}
|
||||
|
||||
Pstream::scatter(tetherIds);
|
||||
}
|
||||
|
||||
tetherIds.shrink();
|
||||
|
||||
if (tetherIds.size())
|
||||
{
|
||||
if (!potentialDict.found("tether"))
|
||||
{
|
||||
FatalErrorIn("moleculeCloudReadPotentials.H") << nl
|
||||
<< "tether potential specification subDict not found"
|
||||
<< abort(FatalError);
|
||||
}
|
||||
|
||||
const dictionary& tetherDict = potentialDict.subDict("tether");
|
||||
|
||||
tetherPotentials_.buildPotentials(idListDict, tetherDict, tetherIds);
|
||||
}
|
||||
|
||||
// ****************************************************************************
|
||||
// External Forces
|
||||
|
||||
gravity_ = vector::zero;
|
||||
|
||||
if (potentialDict.found("external"))
|
||||
{
|
||||
|
||||
Info << nl << "Reading external forces:" << endl;
|
||||
|
||||
const dictionary& externalDict = potentialDict.subDict("external");
|
||||
|
||||
// ************************************************************************
|
||||
// gravity
|
||||
|
||||
if (externalDict.found("gravity"))
|
||||
{
|
||||
gravity_ = externalDict.lookup("gravity");
|
||||
}
|
||||
}
|
||||
|
||||
Info << nl << tab << "gravity = " << gravity_ << endl;
|
||||
|
||||
@ -34,7 +34,7 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
|
||||
forAll(removalOrder_, rO)
|
||||
{
|
||||
Info << " " << idList_[removalOrder_[rO]];
|
||||
Info << " " << pairPotentials_.idList()[removalOrder_[rO]];
|
||||
}
|
||||
|
||||
Info << nl ;
|
||||
@ -12,6 +12,10 @@ if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
|
||||
|
||||
bool remove = false;
|
||||
|
||||
// Guard against pairPotentials_.energy being evaluated
|
||||
// if rIJMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
|
||||
if (rIJMag < SMALL)
|
||||
{
|
||||
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
|
||||
@ -30,10 +34,14 @@ if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
|
||||
|
||||
remove = true;
|
||||
}
|
||||
|
||||
|
||||
// Guard against pairPotentials_.energy being evaluated
|
||||
// if rIJMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
// if rIJMag < rMin. A tabulation lookup error will occur otherwise.
|
||||
|
||||
if (rIJMag < pairPotentials_.rMin(idI, idJ))
|
||||
{
|
||||
remove = true;
|
||||
}
|
||||
|
||||
if (!remove)
|
||||
{
|
||||
@ -42,6 +50,7 @@ if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
|
||||
pairPotentials_.energy(idI, idJ, rIJMag) > potentialEnergyLimit_
|
||||
)
|
||||
{
|
||||
|
||||
remove = true;
|
||||
}
|
||||
}
|
||||
@ -47,6 +47,10 @@
|
||||
|
||||
bool remove = false;
|
||||
|
||||
// Guard against pairPotentials_.energy being evaluated
|
||||
// if rKLMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
|
||||
if (rKLMag < SMALL)
|
||||
{
|
||||
WarningIn
|
||||
@ -72,8 +76,12 @@
|
||||
}
|
||||
|
||||
// Guard against pairPotentials_.energy being evaluated
|
||||
// if rKLMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
// if rIJMag < rMin. A tubulation lookup error will occur otherwise.
|
||||
|
||||
if (rKLMag < pairPotentials_.rMin(idK, idL))
|
||||
{
|
||||
remove = true;
|
||||
}
|
||||
|
||||
if (!remove)
|
||||
{
|
||||
@ -75,7 +75,7 @@ bool Foam::moleculeCloud::testEdgeEdgeDistance
|
||||
&& s <= 1
|
||||
&& t >= 0
|
||||
&& t <= 1
|
||||
&& magSqr(eIs + a*s - eJs - b*t) <= rCutMaxSqr()
|
||||
&& magSqr(eIs + a*s - eJs - b*t) <= pairPotentials_.rCutMaxSqr()
|
||||
);
|
||||
}
|
||||
|
||||
@ -128,14 +128,14 @@ bool Foam::moleculeCloud::testPointFaceDistance
|
||||
|
||||
scalar perpDist((p - faceC) & faceN);
|
||||
|
||||
if (mag(perpDist) > rCutMax())
|
||||
if (mag(perpDist) > pairPotentials_.rCutMax())
|
||||
{
|
||||
return false;
|
||||
}
|
||||
|
||||
vector pointOnPlane = (p - faceN * perpDist);
|
||||
|
||||
if (magSqr(faceC - pointOnPlane) < rCutMaxSqr()*1e-8)
|
||||
if (magSqr(faceC - pointOnPlane) < pairPotentials_.rCutMaxSqr()*1e-8)
|
||||
{
|
||||
// If pointOnPlane is very close to the face centre
|
||||
// then defining the local axes will be inaccurate
|
||||
@ -143,7 +143,7 @@ bool Foam::moleculeCloud::testPointFaceDistance
|
||||
// inside the face, so return true if the points
|
||||
// are in range to be safe
|
||||
|
||||
return (magSqr(pointOnPlane - p) <= rCutMaxSqr());
|
||||
return (magSqr(pointOnPlane - p) <= pairPotentials_.rCutMaxSqr());
|
||||
}
|
||||
|
||||
vector xAxis = (faceC - pointOnPlane)/mag(faceC - pointOnPlane);
|
||||
@ -158,7 +158,7 @@ bool Foam::moleculeCloud::testPointFaceDistance
|
||||
{
|
||||
const vector& V(points[faceToTest[fTT]]);
|
||||
|
||||
if (magSqr(V-p) <= rCutMaxSqr())
|
||||
if (magSqr(V-p) <= pairPotentials_.rCutMaxSqr())
|
||||
{
|
||||
return true;
|
||||
}
|
||||
@ -206,7 +206,7 @@ bool Foam::moleculeCloud::testPointFaceDistance
|
||||
if (la_valid < 0)
|
||||
{
|
||||
// perpendicular point inside face, nearest point is pointOnPlane;
|
||||
return (magSqr(pointOnPlane-p) <= rCutMaxSqr());
|
||||
return (magSqr(pointOnPlane-p) <= pairPotentials_.rCutMaxSqr());
|
||||
}
|
||||
else
|
||||
{
|
||||
@ -215,7 +215,7 @@ bool Foam::moleculeCloud::testPointFaceDistance
|
||||
return
|
||||
(
|
||||
magSqr(pointOnPlane + la_valid*(faceC - pointOnPlane) - p)
|
||||
<= rCutMaxSqr()
|
||||
<= pairPotentials_.rCutMaxSqr()
|
||||
);
|
||||
}
|
||||
|
||||
@ -105,7 +105,7 @@ public:
|
||||
|
||||
//- Construct with no argument, uses default values:
|
||||
// length = 1nm
|
||||
// mass = 1.660538782e−27kg (unified atomic mass unit)
|
||||
// mass = 1.660538782eâ27kg (unified atomic mass unit)
|
||||
// temperature = 1K (therefore, energy = 1*kb)
|
||||
reducedUnits();
|
||||
|
||||
0
src/lagrangian/molecule/referredCell/referredCell.C → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
Executable file → Normal file
0
src/lagrangian/molecule/referredCell/referredCell.C → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
Executable file → Normal file
0
src/lagrangian/molecule/referredCell/referredCell.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
Executable file → Normal file
0
src/lagrangian/molecule/referredCell/referredCell.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
Executable file → Normal file
0
src/lagrangian/molecule/referredCell/referredCellI.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
Executable file → Normal file
0
src/lagrangian/molecule/referredCell/referredCellI.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
Executable file → Normal file
@ -24,9 +24,6 @@ License
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
|
||||
|
||||
inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
|
||||
@ -35,8 +32,4 @@ inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// ************************************************************************* //
|
||||
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Reference in New Issue
Block a user