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Merge branch 'master' of ssh://noisy/home/noisy2/OpenFOAM/OpenFOAM-dev

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henry
2008-06-24 17:01:14 +01:00
parent 7639571b4b 2e51c93821
commit da76e14229
228 changed files with 51748 additions and 2373 deletions
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165
src/OpenFOAM/db/IOstreams/gzstream/gzstream.C.1.7
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@ -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 //

121
src/OpenFOAM/db/IOstreams/gzstream/gzstream.h.1.5
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@ -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 //

2
src/autoMesh/autoHexMesh/autoHexMeshDriver/autoHexMeshDriver.H
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@ -803,7 +803,7 @@ public:
(
const dictionary& shrinkDict,
const dictionary& motionDict,
const scalar nAllowableErrors,
const label nAllowableErrors,
motionSmoother&
);

2
src/autoMesh/autoHexMesh/autoHexMeshDriver/autoHexMeshDriverLayers.C
View File

@ -2346,7 +2346,7 @@ void Foam::autoHexMeshDriver::addLayers
(
const dictionary& shrinkDict,
const dictionary& motionDict,
const scalar nAllowableErrors,
const label nAllowableErrors,
motionSmoother& meshMover
)
{

2
src/finiteVolume/Make/files
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@ -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

139
src/finiteVolume/cfdTools/general/porousMedia/porousZone.C
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@ -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"

2
src/finiteVolume/cfdTools/general/porousMedia/porousZone.H
View File

@ -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>

4
src/lagrangian/Allwmake
View File

@ -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)

10
src/lagrangian/molecule/Make/files → src/lagrangian/molecularDynamics/molecule/Make/files
View File

@ -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

4
src/lagrangian/molecule/Make/options → src/lagrangian/molecularDynamics/molecule/Make/options
View File

@ -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

0
src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C → src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C Executable file → Normal file
View File

0
src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H → src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H Executable file → Normal file
View File

0
src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H → src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H Executable file → Normal file
View File

0
src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C → src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C Executable file → Normal file
View File

0
src/lagrangian/molecule/correlationFunction/correlationFunction.C → src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.C
View File

0
src/lagrangian/molecule/correlationFunction/correlationFunction.H → src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.H
View File

0
src/lagrangian/molecule/correlationFunction/correlationFunctionI.H → src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionI.H
View File

0
src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C → src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionIO.C
View File

12
src/lagrangian/molecule/distribution/distribution.C → src/lagrangian/molecularDynamics/molecule/distribution/distribution.C Executable file → Normal file
View 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
View 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
View File

0
src/lagrangian/molecule/distribution/distributionIO.C → src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C Executable file → Normal file
View File

0
src/lagrangian/molecule/mdTools/averageMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H Executable file → Normal file
View File

24
src/lagrangian/molecule/mdTools/calculateAutoCorrelationFunctions.H → src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
View 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
View File

21
src/lagrangian/molecule/mdTools/calculateTransportProperties.H → src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
View 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;

0
src/lagrangian/molecule/mdTools/createAutoCorrelationFunctions.H → src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
View File

74
src/lagrangian/molecule/mdTools/createMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H Executable file → Normal file
View 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/createRefUnits.H → src/lagrangian/molecularDynamics/molecule/mdTools/createRefUnits.H
View File

0
src/lagrangian/molecule/mdTools/md.H → src/lagrangian/molecularDynamics/molecule/mdTools/md.H Executable file → Normal file
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0
src/lagrangian/molecule/mdTools/meanMomentumEnergyAndNMols.H → src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H Executable file → Normal file
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8
src/lagrangian/molecule/mdTools/resetMDFields.H → src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H Executable file → Normal file
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@ -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)
);
}

2
src/lagrangian/molecule/mdTools/temperatureAndPressure.H → src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H Executable file → Normal file
View File

@ -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;

0
src/lagrangian/molecule/mdTools/temperatureAndPressureVariables.H → src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H Executable file → Normal file
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0
src/lagrangian/molecule/mdTools/temperatureEquilibration.H → src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H Executable file → Normal file
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3
src/lagrangian/molecule/molecule/molecule.C → src/lagrangian/molecularDynamics/molecule/molecule/molecule.C Executable file → Normal file
View 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
View 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
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@ -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
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloud.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C Executable file → Normal file
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22
src/lagrangian/molecule/moleculeCloud/moleculeCloud.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H Executable file → Normal file
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@ -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;

0
src/lagrangian/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C Executable file → Normal file
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18
src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C Executable file → Normal file
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@ -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
// ************************************************************************* //

0
src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateForce.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H Executable file → Normal file
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2
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H Executable file → Normal file
View File

@ -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
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H Executable file → Normal file
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0
src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C Executable file → Normal file
View File

193
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H Normal file
View File

@ -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
View 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
src/lagrangian/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C Executable file → Normal file
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177
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H Normal file
View File

@ -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;

0
src/lagrangian/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C Executable file → Normal file
View File

0
src/lagrangian/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C Executable file → Normal file
View File

2
src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C Executable file → Normal file
View File

@ -34,7 +34,7 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
forAll(removalOrder_, rO)
{
Info << " " << idList_[removalOrder_[rO]];
Info << " " << pairPotentials_.idList()[removalOrder_[rO]];
}
Info << nl ;

0
src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H Executable file → Normal file
View File

15
src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H Executable file → Normal file
View File

@ -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;
}
}

12
src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H Executable file → Normal file
View File

@ -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)
{

2
src/lagrangian/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C Executable file → Normal file
View File

@ -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()
);
}

12
src/lagrangian/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C → src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C Executable file → Normal file
View File

@ -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()
);
}

0
src/lagrangian/molecule/reducedUnits/reducedUnits.C → src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
View File

2
src/lagrangian/molecule/reducedUnits/reducedUnits.H → src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
View File

@ -105,7 +105,7 @@ public:
//- Construct with no argument, uses default values:
// length = 1nm
// mass = 1.660538782e−27kg (unified atomic mass unit)
// mass = 1.660538782e−27kg (unified atomic mass unit)
// temperature = 1K (therefore, energy = 1*kb)
reducedUnits();

0
src/lagrangian/molecule/reducedUnits/reducedUnitsI.H → src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
View File

0
src/lagrangian/molecule/reducedUnits/reducedUnitsIO.C → src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
View File

0
src/lagrangian/molecule/referralLists/receivingReferralList.C → src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C Executable file → Normal file
View File

0
src/lagrangian/molecule/referralLists/receivingReferralList.H → src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referralLists/receivingReferralListI.H → src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referralLists/sendingReferralList.C → src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C Executable file → Normal file
View File

0
src/lagrangian/molecule/referralLists/sendingReferralList.H → src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referralLists/sendingReferralListI.H → src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referredCell/referredCell.C → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C Executable file → Normal file
View File

0
src/lagrangian/molecule/referredCell/referredCell.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referredCell/referredCellI.H → src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H Executable file → Normal file
View File

0
src/lagrangian/molecule/referredCellList/referredCellList.C → src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C Executable file → Normal file
View File

0
src/lagrangian/molecule/referredCellList/referredCellList.H → src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H Executable file → Normal file
View File

7
src/lagrangian/molecule/referredCellList/referredCellListI.H → src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H Executable file → Normal file
View 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
// ************************************************************************* //

0
src/lagrangian/molecule/referredMolecule/referredMolecule.C → src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C Executable file → Normal file
View File

1
src/lagrangian/molecule/referredMolecule/referredMolecule.H → src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H Executable file → Normal file
View File

@ -98,6 +98,7 @@ public:
const referredMolecule& b
);
// IOstream Operators
friend Istream& operator>>

0
src/lagrangian/molecule/referredMolecule/referredMoleculeI.H → src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H Executable file → Normal file
View File

35
src/lagrangian/molecularDynamics/potential/Make/files Normal file
View File

@ -0,0 +1,35 @@
pairPotential = pairPotential
$(pairPotential)/pairPotentialList/pairPotentialList.C
$(pairPotential)/basic/pairPotential.C
$(pairPotential)/basic/pairPotentialIO.C
$(pairPotential)/basic/newPairPotential.C
$(pairPotential)/derived/lennardJones/lennardJones.C
$(pairPotential)/derived/maitlandSmith/maitlandSmith.C
$(pairPotential)/derived/azizChen/azizChen.C
energyScalingFunction = energyScalingFunction
$(energyScalingFunction)/basic/energyScalingFunction.C
$(energyScalingFunction)/basic/newEnergyScalingFunction.C
$(energyScalingFunction)/derived/shifted/shifted.C
$(energyScalingFunction)/derived/shiftedForce/shiftedForce.C
$(energyScalingFunction)/derived/noScaling/noScaling.C
$(energyScalingFunction)/derived/sigmoid/sigmoid.C
$(energyScalingFunction)/derived/doubleSigmoid/doubleSigmoid.C
tetherPotential = tetherPotential
$(tetherPotential)/tetherPotentialList/tetherPotentialList.C
$(tetherPotential)/basic/tetherPotential.C
$(tetherPotential)/basic/newTetherPotential.C
$(tetherPotential)/derived/harmonicSpring/harmonicSpring.C
$(tetherPotential)/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
LIB = $(FOAM_LIBBIN)/libpotential

6
src/lagrangian/molecularDynamics/potential/Make/options Normal file
View File

@ -0,0 +1,6 @@
EXE_INC = \
-I.. \
-I$(LIB_SRC)/finiteVolume/lnInclude
LIB_LIBS = \
-lfiniteVolume

76
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C Normal file
View File

@ -0,0 +1,76 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
energyScalingFunction
\*---------------------------------------------------------------------------*/
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(energyScalingFunction, 0);
defineRunTimeSelectionTable(energyScalingFunction, dictionary);
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::energyScalingFunction::energyScalingFunction
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
name_(name),
energyScalingFunctionProperties_(energyScalingFunctionProperties),
pairPot_(pairPot)
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
bool Foam::energyScalingFunction::read
(
const dictionary& energyScalingFunctionProperties
)
{
energyScalingFunctionProperties_ = energyScalingFunctionProperties;
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //

151
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H Normal file
View File

@ -0,0 +1,151 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunction
Description
SourceFiles
energyScalingFunction.C
newEnergyScalingFunction.C
\*---------------------------------------------------------------------------*/
#ifndef energyScalingFunction_H
#define energyScalingFunction_H
#include "IOdictionary.H"
#include "typeInfo.H"
#include "runTimeSelectionTables.H"
#include "autoPtr.H"
#include "pairPotential.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
/*---------------------------------------------------------------------------*\
Class energyScalingFunction Declaration
\*---------------------------------------------------------------------------*/
class energyScalingFunction
{
protected:
// Protected data
word name_;
dictionary energyScalingFunctionProperties_;
const pairPotential& pairPot_;
// Private Member Functions
//- Disallow copy construct
energyScalingFunction(const energyScalingFunction&);
//- Disallow default bitwise assignment
void operator=(const energyScalingFunction&);
public:
//- Runtime type information
TypeName("energyScalingFunction");
// Declare run-time constructor selection table
declareRunTimeSelectionTable
(
autoPtr,
energyScalingFunction,
dictionary,
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
),
(name, energyScalingFunctionProperties, pairPot)
);
// Selectors
//- Return a reference to the selected viscosity model
static autoPtr<energyScalingFunction> New
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Constructors
//- Construct from components
energyScalingFunction
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
virtual ~energyScalingFunction()
{}
// Member Functions
virtual void scaleEnergy(scalar& e, const scalar r) const = 0;
const dictionary& energyScalingFunctionProperties() const
{
return energyScalingFunctionProperties_;
}
//- Read energyScalingFunction dictionary
virtual bool read(const dictionary& energyScalingFunctionProperties) = 0;
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

79
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C Normal file
View File

@ -0,0 +1,79 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
energyScalingFunction
\*---------------------------------------------------------------------------*/
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
autoPtr<energyScalingFunction> energyScalingFunction::New
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
{
word energyScalingFunctionTypeName
(
energyScalingFunctionProperties.lookup("energyScalingFunction")
);
Info<< "Selecting energy scaling function "
<< energyScalingFunctionTypeName << " for "
<< name << " potential energy." << endl;
dictionaryConstructorTable::iterator cstrIter =
dictionaryConstructorTablePtr_->find(energyScalingFunctionTypeName);
if (cstrIter == dictionaryConstructorTablePtr_->end())
{
FatalErrorIn
(
"energyScalingFunction::New()"
) << "Unknown energyScalingFunction type "
<< energyScalingFunctionTypeName << endl << endl
<< "Valid energyScalingFunctions are : " << endl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}
return autoPtr<energyScalingFunction>
(cstrIter()(name, energyScalingFunctionProperties, pairPot));
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //

104
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C Normal file
View File

@ -0,0 +1,104 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
\*---------------------------------------------------------------------------*/
#include "doubleSigmoid.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(doubleSigmoid, 0);
addToRunTimeSelectionTable
(
energyScalingFunction,
doubleSigmoid,
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
scalar doubleSigmoid::sigmoidScale
(
const scalar r,
const scalar shift,
const scalar scale
) const
{
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
doubleSigmoid::doubleSigmoid
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
doubleSigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
shift1_(readScalar(doubleSigmoidCoeffs_.lookup("shift1"))),
scale1_(readScalar(doubleSigmoidCoeffs_.lookup("scale1"))),
shift2_(readScalar(doubleSigmoidCoeffs_.lookup("shift2"))),
scale2_(readScalar(doubleSigmoidCoeffs_.lookup("scale2")))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void doubleSigmoid::scaleEnergy(scalar& e, const scalar r) const
{
e *= sigmoidScale(r, shift1_, scale1_) * sigmoidScale(r, shift2_, scale2_);
}
bool doubleSigmoid::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
doubleSigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
doubleSigmoidCoeffs_.lookup("shift1") >> shift1_;
doubleSigmoidCoeffs_.lookup("scale1") >> scale1_;
doubleSigmoidCoeffs_.lookup("shift2") >> shift2_;
doubleSigmoidCoeffs_.lookup("scale2") >> scale2_;
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// ************************************************************************* //

115
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H Normal file
View File

@ -0,0 +1,115 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunctions::doubleSigmoid
Description
SourceFiles
doubleSigmoid.C
\*---------------------------------------------------------------------------*/
#ifndef doubleSigmoid_H
#define doubleSigmoid_H
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class doubleSigmoid Declaration
\*---------------------------------------------------------------------------*/
class doubleSigmoid
:
public energyScalingFunction
{
// Private data
dictionary doubleSigmoidCoeffs_;
scalar shift1_;
scalar scale1_;
scalar shift2_;
scalar scale2_;
// Private Member Functions
scalar sigmoidScale
(
const scalar r,
const scalar shift,
const scalar scale
) const;
public:
//- Runtime type information
TypeName("doubleSigmoid");
// Constructors
//- Construct from components
doubleSigmoid
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
~doubleSigmoid()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

81
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C Normal file
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@ -0,0 +1,81 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
\*---------------------------------------------------------------------------*/
#include "noScaling.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(noScaling, 0);
addToRunTimeSelectionTable
(
energyScalingFunction,
noScaling,
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
noScaling::noScaling
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot)
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void noScaling::scaleEnergy(scalar& e, const scalar r) const
{}
bool noScaling::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// ************************************************************************* //

97
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H Normal file
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@ -0,0 +1,97 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunctions::noScaling
Description
SourceFiles
noScaling.C
\*---------------------------------------------------------------------------*/
#ifndef noScaling_H
#define noScaling_H
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class noScaling Declaration
\*---------------------------------------------------------------------------*/
class noScaling
:
public energyScalingFunction
{
public:
//- Runtime type information
TypeName("noScaling");
// Constructors
//- Construct from components
noScaling
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
~noScaling()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

90
src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.C → src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C Executable file → Normal file
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@ -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
@ -22,73 +22,63 @@ License
along with OpenFOAM; if not, write to the Free Software Foundation,
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
\*----------------------------------------------------------------------------*/
\*---------------------------------------------------------------------------*/
#include "tetherPotential.H"
#include "shifted.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(shifted, 0);
addToRunTimeSelectionTable
(
energyScalingFunction,
shifted,
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
tetherPotential::tetherPotential()
{}
tetherPotential::tetherPotential
shifted::shifted
(
const word& tetherPotentialName,
const word& tetherPotentialType,
const scalar springConstant
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
tetherPotentialName_(tetherPotentialName),
tetherPotentialType_(tetherPotentialType),
springConstant_(springConstant)
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
e_at_rCut_(pairPot.unscaledEnergy(pairPot.rCut()))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
tetherPotential::~tetherPotential()
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
void tetherPotential::write(Ostream& os) const
void shifted::scaleEnergy(scalar& e, const scalar r) const
{
os << tetherPotentialName_
<< nl << tetherPotentialType_
<< nl << springConstant_
<< endl;
e -= e_at_rCut_;
}
bool shifted::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
return true;
}
scalar tetherPotential::force(const scalar rITMag) const
{
return -springConstant_ * rITMag;
}
scalar tetherPotential::energy(const scalar rITMag) const
{
return 0.5*springConstant_*rITMag*rITMag;
}
// * * * * * * * * * * * * * * * Friend Functions * * * * * * * * * * * * * //
Ostream& operator<<(Ostream& os, const tetherPotential& pot)
{
pot.write(os);
os.check("Ostream& operator<<(Ostream& f, const tetherPotential& pot");
return os;
}
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// ************************************************************************* //

101
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H Normal file
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@ -0,0 +1,101 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunctions::shifted
Description
SourceFiles
shifted.C
\*---------------------------------------------------------------------------*/
#ifndef shifted_H
#define shifted_H
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class shifted Declaration
\*---------------------------------------------------------------------------*/
class shifted
:
public energyScalingFunction
{
// Private data
scalar e_at_rCut_;
public:
//- Runtime type information
TypeName("shifted");
// Constructors
//- Construct from components
shifted
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
~shifted()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

86
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C Normal file
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@ -0,0 +1,86 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
\*---------------------------------------------------------------------------*/
#include "shiftedForce.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(shiftedForce, 0);
addToRunTimeSelectionTable
(
energyScalingFunction,
shiftedForce,
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
shiftedForce::shiftedForce
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
rCut_(pairPot.rCut()),
e_at_rCut_(pairPot.unscaledEnergy(rCut_)),
de_dr_at_rCut_(pairPot.energyDerivative(rCut_, false))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void shiftedForce::scaleEnergy(scalar& e, const scalar r) const
{
e -= ( e_at_rCut_ + de_dr_at_rCut_ * (r - rCut_) );
}
bool shiftedForce::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// ************************************************************************* //

106
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H Normal file
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@ -0,0 +1,106 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunctions::shiftedForce
Description
SourceFiles
shiftedForce.C
\*---------------------------------------------------------------------------*/
#ifndef shiftedForce_H
#define shiftedForce_H
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class shiftedForce Declaration
\*---------------------------------------------------------------------------*/
class shiftedForce
:
public energyScalingFunction
{
// Private data
scalar rCut_;
scalar e_at_rCut_;
scalar de_dr_at_rCut_;
public:
//- Runtime type information
TypeName("shiftedForce");
// Constructors
//- Construct from components
shiftedForce
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
~shiftedForce()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

100
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C Normal file
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@ -0,0 +1,100 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
\*---------------------------------------------------------------------------*/
#include "sigmoid.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(sigmoid, 0);
addToRunTimeSelectionTable
(
energyScalingFunction,
sigmoid,
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
scalar sigmoid::sigmoidScale
(
const scalar r,
const scalar shift,
const scalar scale
) const
{
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
sigmoid::sigmoid
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
sigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
shift_(readScalar(sigmoidCoeffs_.lookup("shift"))),
scale_(readScalar(sigmoidCoeffs_.lookup("scale")))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void sigmoid::scaleEnergy(scalar& e, const scalar r) const
{
e *= sigmoidScale(r, shift_, scale_);
}
bool sigmoid::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
sigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
sigmoidCoeffs_.lookup("shift") >> shift_;
sigmoidCoeffs_.lookup("scale") >> shift_;
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// ************************************************************************* //

115
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H Normal file
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@ -0,0 +1,115 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / 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
Class
Foam::energyScalingFunctions::sigmoid
Description
SourceFiles
sigmoid.C
\*---------------------------------------------------------------------------*/
#ifndef sigmoid_H
#define sigmoid_H
#include "energyScalingFunction.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class sigmoid Declaration
\*---------------------------------------------------------------------------*/
class sigmoid
:
public energyScalingFunction
{
// Private data
dictionary sigmoidCoeffs_;
scalar shift_;
scalar scale_;
// Private Member Functions
scalar sigmoidScale
(
const scalar r,
const scalar shift,
const scalar scale
) const;
public:
//- Runtime type information
TypeName("sigmoid");
// Constructors
//- Construct from components
sigmoid
(
const word& name,
const dictionary& energyScalingFunctionProperties,
const pairPotential& pairPot
);
// Destructor
~sigmoid()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace energyScalingFunctions
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

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