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ENH: Templated MolecularCloud.

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This commit is contained in:
graham
2011-07-04 16:17:52 +01:00
parent aaad626afe
commit d3ddb37480
20 changed files with 667 additions and 303 deletions
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21
applications/solvers/discreteMethods/molecularDynamics/mdFoam/createFields.H
View File

@ -12,6 +12,23 @@
mesh
);
potential pot(mesh);
word cloudName("polyatomicCloud");
polyatomicCloud molecules(mesh, pot);
potential pot
(
mesh,
IOdictionary
(
IOobject
(
cloudName + "Properties",
mesh.time().constant(),
mesh,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE,
false
)
)
);
polyatomicCloud molecules(cloudName, mesh, pot);

4
applications/utilities/preProcessing/mdInitialise/Make/options
View File

@ -3,7 +3,6 @@ EXE_INC = \
-I$(LIB_SRC)/dynamicMesh/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude
@ -13,6 +12,5 @@ EXE_LIBS = \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
-lpotential

23
applications/utilities/preProcessing/mdInitialise/mdInitialise.C
View File

@ -62,11 +62,28 @@ int main(int argc, char *argv[])
)
);
potential pot(mesh, mdInitialiseDict, idListDict);
word cloudName("polyatomicCloud");
polyatomicCloud molecules(mesh, pot, mdInitialiseDict);
potential pot
(
mesh,
mdInitialiseDict,
IOdictionary
(
IOobject
(
cloudName + "Properties",
mesh.time().constant(),
mesh,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE,
false
)
),
idListDict
);
Info<< "Cloud is called " << molecules.name() << endl;
polyatomicCloud molecules(cloudName, mesh, pot, mdInitialiseDict);
label totalMolecules = molecules.size();

8
src/lagrangian/molecularDynamics/molecule/Make/files
View File

@ -1,9 +1,9 @@
constPropSite/constPropSite.C
clouds/baseClasses/moleculeCloud/moleculeCloud.C
polyatomic/polyatomic/polyatomic.C
polyatomic/polyatomic/polyatomicIO.C
molecules/constPropSite/constPropSite.C
polyatomic/polyatomicCloud/polyatomicCloud.C
molecules/polyatomic/polyatomic.C
molecules/polyatomic/polyatomicIO.C
/* controllers/basic/controllers/controllers.C
controllers/basic/stateController/stateController.C

6
src/lagrangian/molecularDynamics/molecule/Make/options
View File

@ -2,13 +2,11 @@ EXE_INC = \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude
LIB_LIBS = \
-lfiniteVolume \
-lmeshTools \
-llagrangian \
-lpotential \
-lmolecularMeasurements
-lpotential

281
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloud.C → src/lagrangian/molecularDynamics/molecule/clouds/Templates/MoleculeCloud/MoleculeCloud.C
View File

@ -23,36 +23,29 @@ License
\*----------------------------------------------------------------------------*/
#include "polyatomicCloud.H"
#include "MoleculeCloud.H"
#include "fvMesh.H"
#include "mathematicalConstants.H"
using namespace Foam::constant::mathematical;
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
namespace Foam
{
defineTemplateTypeNameAndDebug(Cloud<polyatomic>, 0);
}
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::polyatomicCloud::buildConstProps()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::buildConstProps()
{
Info<< nl << "Reading mdProperties dictionary." << endl;
const List<word>& idList(pot_.idList());
constPropList_.setSize(idList.size());
const List<word>& siteIdList(pot_.siteIdList());
IOdictionary mdPropertiesDict
IOdictionary molPropertiesDict
(
IOobject
(
"mdProperties",
this->name() + "Properties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
@ -61,11 +54,13 @@ void Foam::polyatomicCloud::buildConstProps()
)
);
Info<< nl << "Reading " << molPropertiesDict.name() << endl;
forAll(idList, i)
{
const word& id = idList[i];
const dictionary& molDict(mdPropertiesDict.subDict(id));
const dictionary& molDict(molPropertiesDict.subDict(id));
List<word> siteIdNames = molDict.lookup("siteIds");
@ -81,17 +76,14 @@ void Foam::polyatomicCloud::buildConstProps()
{
FatalErrorIn
(
"Foam::polyatomic::constantProperties::constantProperties"
"("
"const dictionary& dict"
")"
"void Foam::MoleculeCloud<MoleculeType>::buildConstProps()"
)
<< siteId << " site not found."
<< nl << abort(FatalError);
}
}
constPropList_[i] = polyatomic::constantProperties
constPropList_[i] = typename MoleculeType::constantProperties
(
molDict,
siteIds
@ -100,11 +92,15 @@ void Foam::polyatomicCloud::buildConstProps()
}
void Foam::polyatomicCloud::setSiteSizesAndPositions()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::setSiteSizesAndPositions()
{
forAllIter(polyatomicCloud, *this, mol)
forAllIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
const polyatomic::constantProperties& cP = constProps(mol().id());
const typename MoleculeType::constantProperties& cP
(
constProps(mol().id())
);
mol().setSiteSizes(cP.nSites());
@ -113,14 +109,15 @@ void Foam::polyatomicCloud::setSiteSizesAndPositions()
}
void Foam::polyatomicCloud::buildCellOccupancy()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::buildCellOccupancy()
{
forAll(cellOccupancy_, cO)
{
cellOccupancy_[cO].clear();
}
forAllIter(polyatomicCloud, *this, mol)
forAllIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
cellOccupancy_[mol().cell()].append(&mol());
}
@ -132,15 +129,16 @@ void Foam::polyatomicCloud::buildCellOccupancy()
}
void Foam::polyatomicCloud::calculatePairForce()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::calculatePairForce()
{
PstreamBuffers pBufs(Pstream::nonBlocking);
// Start sending referred data
il_.sendReferredData(cellOccupancy(), pBufs);
polyatomic* molI = NULL;
polyatomic* molJ = NULL;
MoleculeType* molI = NULL;
MoleculeType* molJ = NULL;
{
// Real-Real interactions
@ -155,7 +153,7 @@ void Foam::polyatomicCloud::calculatePairForce()
forAll(dil[d], interactingCells)
{
List<polyatomic*> cellJ =
List<MoleculeType*> cellJ =
cellOccupancy_[dil[d][interactingCells]];
forAll(cellJ, cellJMols)
@ -187,24 +185,24 @@ void Foam::polyatomicCloud::calculatePairForce()
const labelListList& ril = il_.ril();
List<IDLList<polyatomic> >& referredMols = il_.referredParticles();
List<IDLList<MoleculeType> >& referredMols = il_.referredParticles();
forAll(ril, r)
{
const List<label>& realCells = ril[r];
IDLList<polyatomic>& refMols = referredMols[r];
IDLList<MoleculeType>& refMols = referredMols[r];
forAllIter
(
IDLList<polyatomic>,
typename IDLList<MoleculeType>,
refMols,
refMol
)
{
forAll(realCells, rC)
{
List<polyatomic*> cellI = cellOccupancy_[realCells[rC]];
List<MoleculeType*> cellI = cellOccupancy_[realCells[rC]];
forAll(cellI, cellIMols)
{
@ -219,11 +217,12 @@ void Foam::polyatomicCloud::calculatePairForce()
}
void Foam::polyatomicCloud::calculateTetherForce()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::calculateTetherForce()
{
const tetherPotentialList& tetherPot(pot_.tetherPotentials());
forAllIter(polyatomicCloud, *this, mol)
forAllIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
if (mol().tethered())
{
@ -246,16 +245,18 @@ void Foam::polyatomicCloud::calculateTetherForce()
}
void Foam::polyatomicCloud::calculateExternalForce()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::calculateExternalForce()
{
forAllIter(polyatomicCloud, *this, mol)
forAllIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
mol().a() += pot_.gravity();
}
}
void Foam::polyatomicCloud::removeHighEnergyOverlaps()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::removeHighEnergyOverlaps()
{
Info<< nl << "Removing high energy overlaps, limit = "
<< pot_.potentialEnergyLimit()
@ -274,11 +275,11 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
// Real-Real interaction
polyatomic* molI = NULL;
polyatomic* molJ = NULL;
MoleculeType* molI = NULL;
MoleculeType* molJ = NULL;
{
DynamicList<polyatomic*> molsToDelete;
DynamicList<MoleculeType*> molsToDelete;
const labelListList& dil(il_.dil());
@ -290,7 +291,7 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
forAll(dil[d], interactingCells)
{
List<polyatomic*> cellJ =
List<MoleculeType*> cellJ =
cellOccupancy_[dil[d][interactingCells]];
forAll(cellJ, cellJMols)
@ -376,19 +377,19 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
// Real-Referred interaction
{
DynamicList<polyatomic*> molsToDelete;
DynamicList<MoleculeType*> molsToDelete;
const labelListList& ril(il_.ril());
List<IDLList<polyatomic> >& referredMols = il_.referredParticles();
List<IDLList<MoleculeType> >& referredMols = il_.referredParticles();
forAll(ril, r)
{
IDLList<polyatomic>& refMols = referredMols[r];
IDLList<MoleculeType>& refMols = referredMols[r];
forAllIter
(
IDLList<polyatomic>,
typename IDLList<MoleculeType>,
refMols,
refMol
)
@ -401,7 +402,7 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
{
label cellI = realCells[rC];
List<polyatomic*> cellIMols = cellOccupancy_[cellI];
List<MoleculeType*> cellIMols = cellOccupancy_[cellI];
forAll(cellIMols, cIM)
{
@ -430,7 +431,7 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
== findIndex(pot_.removalOrder(), idJ)
)
{
// Remove one of the polyatomics
// Remove one of the molecules
// arbitrarily, assuring that a
// consistent decision is made for
// both real-referred pairs.
@ -470,17 +471,18 @@ void Foam::polyatomicCloud::removeHighEnergyOverlaps()
reduce(molsRemoved, sumOp<label>());
}
Info<< tab << molsRemoved << " polyatomics removed" << endl;
Info<< tab << molsRemoved << " molecules removed" << endl;
}
void Foam::polyatomicCloud::initialiseMolecules
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::initialiseMolecules
(
const IOdictionary& mdInitialiseDict
)
{
Info<< nl
<< "Initialising polyatomics in each zone specified in "
<< "Initialising molecules in each zone specified in "
<< mdInitialiseDict.name()
<< endl;
@ -488,7 +490,10 @@ void Foam::polyatomicCloud::initialiseMolecules
if (!cellZones.size())
{
FatalErrorIn("void Foam::polyatomicCloud::initialiseMolecules")
FatalErrorIn
(
"void Foam::MoleculeCloud<MoleculeType>::initialiseMolecules"
)
<< "No cellZones found in the mesh."
<< abort(FatalError);
}
@ -528,7 +533,10 @@ void Foam::polyatomicCloud::initialiseMolecules
if (latticeIds.size() != latticePositions.size())
{
FatalErrorIn("Foam::polyatomicCloud::initialiseMolecules")
FatalErrorIn
(
"Foam::MoleculeCloud<MoleculeType>::initialiseMolecules"
)
<< "latticeIds and latticePositions must be the same "
<< " size." << nl
<< abort(FatalError);
@ -550,7 +558,10 @@ void Foam::polyatomicCloud::initialiseMolecules
if (numberDensity < VSMALL)
{
WarningIn("polyatomicCloud::initialiseMolecules")
WarningIn
(
"MoleculeCloud<MoleculeType>::initialiseMolecules"
)
<< "numberDensity too small, not filling zone "
<< zone.name() << endl;
@ -571,7 +582,7 @@ void Foam::polyatomicCloud::initialiseMolecules
{
label id = findIndex(pot_.idList(), latticeIds[i]);
const polyatomic::constantProperties& cP
const typename MoleculeType::constantProperties& cP
(
constProps(id)
);
@ -586,7 +597,10 @@ void Foam::polyatomicCloud::initialiseMolecules
if (massDensity < VSMALL)
{
WarningIn("polyatomicCloud::initialiseMolecules")
WarningIn
(
"MoleculeCloud<MoleculeType>::initialiseMolecules"
)
<< "massDensity too small, not filling zone "
<< zone.name() << endl;
@ -602,7 +616,10 @@ void Foam::polyatomicCloud::initialiseMolecules
}
else
{
FatalErrorIn("Foam::polyatomicCloud::initialiseMolecules")
FatalErrorIn
(
"Foam::MoleculeCloud<MoleculeType>::initialiseMolecules"
)
<< "massDensity or numberDensity not specified " << nl
<< abort(FatalError);
}
@ -697,8 +714,8 @@ void Foam::polyatomicCloud::initialiseMolecules
anchor += (R & (latticeCellShape & latticeAnchor));
// Continue trying to place polyatomics as long as at
// least one polyatomic is placed in each iteration.
// Continue trying to place molecule as long as at
// least one molecule is placed in each iteration.
// The "|| totalZoneMols == 0" condition means that the
// algorithm will continue if the origin is outside the
// zone.
@ -719,10 +736,6 @@ void Foam::polyatomicCloud::initialiseMolecules
bool partOfLayerInBounds = false;
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// start of placement of polyatomics
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if (n == 0)
{
// Special treatment is required for the first position,
@ -959,10 +972,6 @@ void Foam::polyatomicCloud::initialiseMolecules
}
}
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// end of placement of polyatomics
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if
(
totalZoneMols == 0
@ -971,11 +980,12 @@ void Foam::polyatomicCloud::initialiseMolecules
{
WarningIn
(
"Foam::polyatomicCloud::initialiseMolecules()"
"Foam::MoleculeCloud<MoleculeType>::"
"initialiseMolecules()"
)
<< "A whole layer of unit cells was placed "
<< "outside the bounds of the mesh, but no "
<< "polyatomics have been placed in zone '"
<< "molecules have been placed in zone '"
<< zone.name()
<< "'. This is likely to be because the zone "
<< "has few cells ("
@ -1001,7 +1011,8 @@ void Foam::polyatomicCloud::initialiseMolecules
}
void Foam::polyatomicCloud::createMolecule
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::createMolecule
(
const point& position,
label cell,
@ -1020,7 +1031,7 @@ void Foam::polyatomicCloud::createMolecule
if (cell == -1)
{
FatalErrorIn("Foam::polyatomicCloud::createMolecule")
FatalErrorIn("Foam::MoleculeCloud<MoleculeType>::createMolecule")
<< "Position specified does not correspond to a mesh cell." << nl
<< abort(FatalError);
}
@ -1033,10 +1044,10 @@ void Foam::polyatomicCloud::createMolecule
{
specialPosition = position;
special = polyatomic::SPECIAL_TETHERED;
special = MoleculeType::SPECIAL_TETHERED;
}
const polyatomic::constantProperties& cP(constProps(id));
const typename MoleculeType::constantProperties& cP(constProps(id));
vector v = equipartitionLinearVelocity(temperature, cP.mass());
@ -1072,7 +1083,7 @@ void Foam::polyatomicCloud::createMolecule
addParticle
(
new polyatomic
new MoleculeType
(
mesh_,
position,
@ -1093,11 +1104,12 @@ void Foam::polyatomicCloud::createMolecule
}
Foam::label Foam::polyatomicCloud::nSites() const
template<class MoleculeType>
Foam::label Foam::MoleculeCloud<MoleculeType>::nSites() const
{
label n = 0;
forAllConstIter(polyatomicCloud, *this, mol)
forAllConstIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
n += constProps(mol().id()).nSites();
}
@ -1108,14 +1120,17 @@ Foam::label Foam::polyatomicCloud::nSites() const
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::polyatomicCloud::polyatomicCloud
template<class MoleculeType>
Foam::MoleculeCloud<MoleculeType>::MoleculeCloud
(
const word& cloudName,
const polyMesh& mesh,
const potential& pot,
bool readFields
)
:
Cloud<polyatomic>(mesh, "polyatomicCloud", false),
Cloud<MoleculeType>(mesh, cloudName, false),
moleculeCloud(),
mesh_(mesh),
pot_(pot),
cellOccupancy_(mesh_.nCells()),
@ -1125,7 +1140,7 @@ Foam::polyatomicCloud::polyatomicCloud
{
if (readFields)
{
polyatomic::readFields(*this);
MoleculeType::readFields(*this);
}
buildConstProps();
@ -1138,15 +1153,18 @@ Foam::polyatomicCloud::polyatomicCloud
}
Foam::polyatomicCloud::polyatomicCloud
template<class MoleculeType>
Foam::MoleculeCloud<MoleculeType>::MoleculeCloud
(
const word& cloudName,
const polyMesh& mesh,
const potential& pot,
const IOdictionary& mdInitialiseDict,
bool readFields
)
:
Cloud<polyatomic>(mesh, "polyatomicCloud", false),
Cloud<MoleculeType>(mesh, cloudName, false),
moleculeCloud(),
mesh_(mesh),
pot_(pot),
il_(mesh_, 0.0, false),
@ -1155,10 +1173,10 @@ Foam::polyatomicCloud::polyatomicCloud
{
if (readFields)
{
polyatomic::readFields(*this);
MoleculeType::readFields(*this);
}
clear();
this->clear();
buildConstProps();
@ -1168,32 +1186,34 @@ Foam::polyatomicCloud::polyatomicCloud
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
void Foam::polyatomicCloud::evolve()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::evolve()
{
polyatomic::trackingData td0(*this, 0);
Cloud<polyatomic>::move(td0, mesh_.time().deltaTValue());
typename MoleculeType::trackingData td0(*this, 0);
Cloud<MoleculeType>::move(td0, mesh_.time().deltaTValue());
polyatomic::trackingData td1(*this, 1);
Cloud<polyatomic>::move(td1, mesh_.time().deltaTValue());
typename MoleculeType::trackingData td1(*this, 1);
Cloud<MoleculeType>::move(td1, mesh_.time().deltaTValue());
polyatomic::trackingData td2(*this, 2);
Cloud<polyatomic>::move(td2, mesh_.time().deltaTValue());
typename MoleculeType::trackingData td2(*this, 2);
Cloud<MoleculeType>::move(td2, mesh_.time().deltaTValue());
calculateForce();
polyatomic::trackingData td3(*this, 3);
Cloud<polyatomic>::move(td3, mesh_.time().deltaTValue());
typename MoleculeType::trackingData td3(*this, 3);
Cloud<MoleculeType>::move(td3, mesh_.time().deltaTValue());
info();
}
void Foam::polyatomicCloud::calculateForce()
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::calculateForce()
{
buildCellOccupancy();
// Set accumulated quantities to zero
forAllIter(polyatomicCloud, *this, mol)
forAllIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
mol().siteForces() = vector::zero;
@ -1210,36 +1230,8 @@ void Foam::polyatomicCloud::calculateForce()
}
void Foam::polyatomicCloud::applyConstraintsAndThermostats
(
const scalar targetTemperature,
const scalar measuredTemperature
)
{
scalar temperatureCorrectionFactor =
sqrt(targetTemperature/max(VSMALL, measuredTemperature));
Info<< "----------------------------------------" << nl
<< "Temperature equilibration" << nl
<< "Target temperature = "
<< targetTemperature << nl
<< "Measured temperature = "
<< measuredTemperature << nl
<< "Temperature correction factor = "
<< temperatureCorrectionFactor << nl
<< "----------------------------------------"
<< endl;
forAllIter(polyatomicCloud, *this, mol)
{
mol().v() *= temperatureCorrectionFactor;
mol().pi() *= temperatureCorrectionFactor;
}
}
void Foam::polyatomicCloud::info() const
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::info() const
{
// Calculates and prints the mean momentum and energy in the system
// and the number of molecules.
@ -1267,7 +1259,7 @@ void Foam::polyatomicCloud::info() const
label dofs = 0;
{
forAllConstIter(polyatomicCloud, *this, mol)
forAllConstIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
const label molId = mol().id();
@ -1283,11 +1275,14 @@ void Foam::polyatomicCloud::info() const
// CentreOfMass /= totalMass;
// }
forAllConstIter(polyatomicCloud, *this, mol)
forAllConstIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
const label molId = mol().id();
const polyatomic::constantProperties cP(this->constProps(molId));
const typename MoleculeType::constantProperties cP
(
this->constProps(molId)
);
scalar molMass(cP.mass());
@ -1340,27 +1335,27 @@ void Foam::polyatomicCloud::info() const
if (nMols)
{
Info<< "Number of molecules in " << this->name() << " = "
Info<< nl << "Number of molecules in " << this->name() << " = "
<< nMols << nl
<< "Overall number density = "
<< " Overall number density = "
<< nMols/meshVolume << nl
<< "Overall mass density = "
<< " Overall mass density = "
<< totalMass/meshVolume << nl
<< "Average linear momentum per molecule = "
<< " Average linear momentum per molecule = "
<< totalLinearMomentum/nMols << ' '
<< mag(totalLinearMomentum)/nMols << nl
<< "Average angular momentum per molecule = "
<< " Average angular momentum per molecule = "
<< totalAngularMomentum << ' '
<< mag(totalAngularMomentum)/nMols << nl
<< "maximum |velocity| = "
<< " maximum |velocity| = "
<< maxVelocityMag << nl
<< "Average linear KE per molecule = "
<< " Average linear KE per molecule = "
<< totalLinearKE/nMols << nl
<< "Average angular KE per molecule = "
<< " Average angular KE per molecule = "
<< totalAngularKE/nMols << nl
<< "Average PE per molecule = "
<< " Average PE per molecule = "
<< totalPE/nMols << nl
<< "Average TE per molecule = "
<< " Average TE per molecule = "
<<
(
totalLinearKE
@ -1368,25 +1363,29 @@ void Foam::polyatomicCloud::info() const
+ totalPE
)
/nMols
<< endl;
<< nl << endl;
}
else
{
Info<< "No molecules in " << this->name() << endl;
Info<< nl << "No molecules in " << this->name() << nl << endl;
}
}
void Foam::polyatomicCloud::writeXYZ(const fileName& fName) const
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::writeXYZ(const fileName& fName) const
{
OFstream os(fName);
os << nSites() << nl
<< "polyatomicCloud site positions in angstroms" << nl;
<< "MoleculeCloud<MoleculeType> site positions in angstroms" << nl;
forAllConstIter(polyatomicCloud, *this, mol)
forAllConstIter(typename MoleculeCloud<MoleculeType>, *this, mol)
{
const polyatomic::constantProperties& cP = constProps(mol().id());
const typename MoleculeType::constantProperties& cP
(
constProps(mol().id())
);
forAll(mol().sitePositions(), i)
{

102
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloud.H → src/lagrangian/molecularDynamics/molecule/clouds/Templates/MoleculeCloud/MoleculeCloud.H
View File

@ -22,22 +22,22 @@ License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
Class
Foam::polyatomicCloud
Foam::MoleculeCloud
Description
SourceFiles
polyatomicCloudI.H
polyatomicCloud.C
MoleculeCloudI.H
MoleculeCloud.C
\*---------------------------------------------------------------------------*/
#ifndef polyatomicCloud_H
#define polyatomicCloud_H
#ifndef MoleculeCloud_H
#define MoleculeCloud_H
#include "Cloud.H"
#include "polyatomic.H"
#include "moleculeCloud.H"
#include "IOdictionary.H"
#include "potential.H"
#include "InteractionLists.H"
@ -51,65 +51,83 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class polyatomicCloud Declaration
Class MoleculeCloud Declaration
\*---------------------------------------------------------------------------*/
class polyatomicCloud
template<class MoleculeType>
class MoleculeCloud
:
public Cloud<polyatomic>
public Cloud<MoleculeType>,
public moleculeCloud
{
private:
// Private data
//-
const polyMesh& mesh_;
//-
const potential& pot_;
List<DynamicList<polyatomic*> > cellOccupancy_;
//-
List<DynamicList<MoleculeType*> > cellOccupancy_;
InteractionLists<polyatomic> il_;
//-
InteractionLists<MoleculeType> il_;
List<polyatomic::constantProperties> constPropList_;
//-
List<typename MoleculeType::constantProperties> constPropList_;
//-
Random rndGen_;
// Private Member Functions
//-
void buildConstProps();
//-
void setSiteSizesAndPositions();
//- Determine which polyatomics are in which cells
//- Determine which molecules are in which cells
void buildCellOccupancy();
//-
void calculatePairForce();
//-
inline void evaluatePair
(
polyatomic& molI,
polyatomic& molJ
MoleculeType& molI,
MoleculeType& molJ
);
//-
inline bool evaluatePotentialLimit
(
polyatomic& molI,
polyatomic& molJ
MoleculeType& molI,
MoleculeType& molJ
) const;
//-
void calculateTetherForce();
//-
void calculateExternalForce();
//-
void removeHighEnergyOverlaps();
//-
void initialiseMolecules
(
const IOdictionary& mdInitialiseDict
);
//-
void createMolecule
(
const point& position,
@ -122,25 +140,28 @@ private:
const vector& bulkVelocity
);
//-
label nSites() const;
//-
inline vector equipartitionLinearVelocity
(
scalar temperature,
scalar mass
);
//-
inline vector equipartitionAngularMomentum
(
scalar temperature,
const polyatomic::constantProperties& cP
const typename MoleculeType::constantProperties& cP
);
//- Disallow default bitwise copy construct
polyatomicCloud(const polyatomicCloud&);
MoleculeCloud(const MoleculeCloud&);
//- Disallow default bitwise assignment
void operator=(const polyatomicCloud&);
void operator=(const MoleculeCloud&);
public:
@ -148,16 +169,18 @@ public:
// Constructors
//- Construct given mesh and potential references
polyatomicCloud
MoleculeCloud
(
const word& cloudName,
const polyMesh& mesh,
const potential& pot,
bool readFields = true
);
//- Construct given mesh, potential and mdInitialiseDict
polyatomicCloud
MoleculeCloud
(
const word& cloudName,
const polyMesh& mesh,
const potential& pot,
const IOdictionary& mdInitialiseDict,
@ -167,43 +190,46 @@ public:
// Member Functions
//- Evolve the polyatomics (move, calculate forces, control state etc)
//- Evolve the molecules (move, calculate forces, control state etc)
void evolve();
//-
void calculateForce();
void applyConstraintsAndThermostats
(
const scalar targetTemperature,
const scalar measuredTemperature
);
//- Print cloud information
void info() const;
// Access
//-
inline const polyMesh& mesh() const;
//-
inline const potential& pot() const;
inline const List<DynamicList<polyatomic*> >& cellOccupancy() const;
//-
inline const List<DynamicList<MoleculeType*> >&
cellOccupancy() const;
inline const InteractionLists<polyatomic>& il() const;
//-
inline const InteractionLists<MoleculeType>& il() const;
inline const List<polyatomic::constantProperties>
//-
inline const List<typename MoleculeType::constantProperties>
constProps() const;
inline const polyatomic::constantProperties&
//-
inline const typename MoleculeType::constantProperties&
constProps(label id) const;
//-
inline Random& rndGen();
// Member Operators
//- Write polyatomic sites in XYZ format
//- Write molecule sites in XYZ format
void writeXYZ(const fileName& fName) const;
};
@ -214,7 +240,13 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#include "polyatomicCloudI.H"
#include "MoleculeCloudI.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#ifdef NoRepository
# include "MoleculeCloud.C"
#endif
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

93
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloudI.H → src/lagrangian/molecularDynamics/molecule/clouds/Templates/MoleculeCloud/MoleculeCloudI.H
View File

@ -29,10 +29,11 @@ using namespace Foam::constant;
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
inline void Foam::polyatomicCloud::evaluatePair
template<class MoleculeType>
void Foam::MoleculeCloud<MoleculeType>::evaluatePair
(
polyatomic& molI,
polyatomic& molJ
MoleculeType& molI,
MoleculeType& molJ
)
{
const pairPotentialList& pairPot = pot_.pairPotentials();
@ -43,9 +44,15 @@ inline void Foam::polyatomicCloud::evaluatePair
label idJ = molJ.id();
const polyatomic::constantProperties& constPropI(constProps(idI));
const typename MoleculeType::constantProperties& constPropI
(
constProps(idI)
);
const polyatomic::constantProperties& constPropJ(constProps(idJ));
const typename MoleculeType::constantProperties& constPropJ
(
constProps(idJ)
);
forAll(constPropI.pairPotSites(), pI)
{
@ -149,10 +156,11 @@ inline void Foam::polyatomicCloud::evaluatePair
}
inline bool Foam::polyatomicCloud::evaluatePotentialLimit
template<class MoleculeType>
bool Foam::MoleculeCloud<MoleculeType>::evaluatePotentialLimit
(
polyatomic& molI,
polyatomic& molJ
MoleculeType& molI,
MoleculeType& molJ
) const
{
const pairPotentialList& pairPot = pot_.pairPotentials();
@ -163,9 +171,15 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
label idJ = molJ.id();
const polyatomic::constantProperties& constPropI(constProps(idI));
const typename MoleculeType::constantProperties& constPropI
(
constProps(idI)
);
const polyatomic::constantProperties& constPropJ(constProps(idJ));
const typename MoleculeType::constantProperties& constPropJ
(
constProps(idJ)
);
forAll(constPropI.pairPotSites(), pI)
{
@ -194,14 +208,18 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("polyatomicCloud::removeHighEnergyOverlaps()")
WarningIn
(
"MoleculeCloud<MoleculeType>::"
"removeHighEnergyOverlaps()"
)
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
<< " other by a rounding error in mdInitialise in"
<< " parallel or a block filled with polyatomics"
<< " twice. Removing one of the polyatomics."
<< " parallel or a block filled with moleculess"
<< " twice. Removing one of the molecules."
<< endl;
return true;
@ -250,14 +268,18 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("polyatomicCloud::removeHighEnergyOverlaps()")
WarningIn
(
"MoleculeCloud<MoleculeType>::"
"removeHighEnergyOverlaps()"
)
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
<< " other by a rounding error in mdInitialise in"
<< " parallel or a block filled with polyatomics"
<< " twice. Removing one of the polyatomics."
<< " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
return true;
@ -288,7 +310,9 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
}
inline Foam::vector Foam::polyatomicCloud::equipartitionLinearVelocity
template<class MoleculeType>
Foam::vector
Foam::MoleculeCloud<MoleculeType>::equipartitionLinearVelocity
(
scalar temperature,
scalar mass
@ -303,10 +327,12 @@ inline Foam::vector Foam::polyatomicCloud::equipartitionLinearVelocity
}
inline Foam::vector Foam::polyatomicCloud::equipartitionAngularMomentum
template<class MoleculeType>
Foam::vector
Foam::MoleculeCloud<MoleculeType>::equipartitionAngularMomentum
(
scalar temperature,
const polyatomic::constantProperties& cP
const typename MoleculeType::constantProperties& cP
)
{
scalar sqrtKbT = sqrt(physicoChemical::k.value()*temperature);
@ -334,47 +360,54 @@ inline Foam::vector Foam::polyatomicCloud::equipartitionAngularMomentum
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::polyMesh& Foam::polyatomicCloud::mesh() const
template<class MoleculeType>
const Foam::polyMesh& Foam::MoleculeCloud<MoleculeType>::mesh() const
{
return mesh_;
}
inline const Foam::potential& Foam::polyatomicCloud::pot() const
template<class MoleculeType>
const Foam::potential& Foam::MoleculeCloud<MoleculeType>::pot() const
{
return pot_;
}
inline const Foam::List<Foam::DynamicList<Foam::polyatomic*> >&
Foam::polyatomicCloud::cellOccupancy() const
template<class MoleculeType>
const Foam::List<Foam::DynamicList<MoleculeType*> >&
Foam::MoleculeCloud<MoleculeType>::cellOccupancy() const
{
return cellOccupancy_;
}
inline const Foam::InteractionLists<Foam::polyatomic>&
Foam::polyatomicCloud::il() const
template<class MoleculeType>
const Foam::InteractionLists<MoleculeType>&
Foam::MoleculeCloud<MoleculeType>::il() const
{
return il_;
}
inline const Foam::List<Foam::polyatomic::constantProperties>
Foam::polyatomicCloud::constProps() const
template<class MoleculeType>
const Foam::List<typename MoleculeType::constantProperties>
Foam::MoleculeCloud<MoleculeType>::constProps() const
{
return constPropList_;
}
inline const Foam::polyatomic::constantProperties&
Foam::polyatomicCloud::constProps(label id) const
template<class MoleculeType>
const typename MoleculeType::constantProperties&
Foam::MoleculeCloud<MoleculeType>::constProps(label id) const
{
return constPropList_[id];
}
inline Foam::Random& Foam::polyatomicCloud::rndGen()
template<class MoleculeType>
Foam::Random& Foam::MoleculeCloud<MoleculeType>::rndGen()
{
return rndGen_;
}

48
src/lagrangian/molecularDynamics/molecule/clouds/baseClasses/moleculeCloud/moleculeCloud.C Normal file
View File

@ -0,0 +1,48 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2011 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 3 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, see <http://www.gnu.org/licenses/>.
\*---------------------------------------------------------------------------*/
#include "moleculeCloud.H"
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
namespace Foam
{
defineTypeNameAndDebug(moleculeCloud, 0);
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::moleculeCloud::moleculeCloud()
{}
// * * * * * * * * * * * * * * * * Destructors * * * * * * * * * * * * * * //
Foam::moleculeCloud::~moleculeCloud()
{}
// ************************************************************************* //

83
src/lagrangian/molecularDynamics/molecule/clouds/baseClasses/moleculeCloud/moleculeCloud.H Normal file
View File

@ -0,0 +1,83 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2011 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 3 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, see <http://www.gnu.org/licenses/>.
Class
Foam::moleculeCloud
Description
Virtual abstract base class for templated moleculeCloud
SourceFiles
moleculeCloud.C
\*---------------------------------------------------------------------------*/
#ifndef moleculeCloud_H
#define moleculeCloud_H
#include "volFields.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
/*---------------------------------------------------------------------------*\
Class moleculeCloud Declaration
\*---------------------------------------------------------------------------*/
class moleculeCloud
{
// Private Member Functions
//- Disallow default bitwise copy construct
moleculeCloud(const moleculeCloud&);
//- Disallow default bitwise assignment
void operator=(const moleculeCloud&);
public:
//- Runtime type information
TypeName("moleculeCloud");
// Constructors
//- Null constructor
moleculeCloud();
//- Destructor
virtual ~moleculeCloud();
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

52
src/lagrangian/molecularDynamics/molecule/clouds/derived/polyatomicCloud/polyatomicCloud.H Normal file
View File

@ -0,0 +1,52 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2011 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 3 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, see <http://www.gnu.org/licenses/>.
Class
Foam::polyatomicCloud
Description
Cloud class to simulate polyatomic molecules
SourceFiles
polyatomicCloud.C
\*---------------------------------------------------------------------------*/
#ifndef polyatomicCloud_H
#define polyatomicCloud_H
#include "MoleculeCloud.H"
#include "polyatomic.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
typedef MoleculeCloud<polyatomic> polyatomicCloud;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

0
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSite.C → src/lagrangian/molecularDynamics/molecule/molecules/constPropSite/constPropSite.C
View File

0
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSite.H → src/lagrangian/molecularDynamics/molecule/molecules/constPropSite/constPropSite.H
View File

0
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSiteI.H → src/lagrangian/molecularDynamics/molecule/molecules/constPropSite/constPropSiteI.H
View File

12
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomic.C → src/lagrangian/molecularDynamics/molecule/molecules/polyatomic/polyatomic.C
View File

@ -23,11 +23,19 @@ License
\*----------------------------------------------------------------------------*/
#include "polyatomicCloud.H"
#include "polyatomic.H"
#include "Random.H"
#include "Time.H"
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
namespace Foam
{
defineTypeNameAndDebug(polyatomic, 0);
defineTemplateTypeNameAndDebug(Cloud<polyatomic>, 0);
}
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
Foam::tensor Foam::polyatomic::rotationTensorX(scalar phi) const
@ -285,7 +293,7 @@ void Foam::polyatomic::hitWallPatch
)
{
// Use of the normal from tetIs is not required as
// hasWallImpactDistance for a polyatomicCloud is false.
// hasWallImpactDistance is false.
vector nw = normal();
nw /= mag(nw);

88
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomic.H → src/lagrangian/molecularDynamics/molecule/molecules/polyatomic/polyatomic.H
View File

@ -42,14 +42,15 @@ SourceFiles
#include "autoPtr.H"
#include "diagTensor.H"
#include "constPropSite.H"
#include "MoleculeCloud.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// Class forward declarations
class polyatomicCloud;
template<class ParcelType>
class DsmcParcel;
/*---------------------------------------------------------------------------*\
Class polyatomic Declaration
@ -91,22 +92,19 @@ public:
//- Moment of intertia (in principal axis configiration)
diagTensor momentOfInertia_;
//-
scalar mass_;
// Private Member Functions
void setInteracionSiteBools
(
const List<word>& siteIds,
const List<word>& pairPotSiteIds
);
//-
bool linearMoleculeTest() const;
public:
//-
inline constantProperties();
//- Construct from dictionary
@ -118,22 +116,31 @@ public:
// Member functions
//-
inline const List<constPropSite>& sites() const;
//-
inline const List<label>& pairPotSites() const;
//-
inline const List<label>& electrostaticSites() const;
//-
inline const diagTensor& momentOfInertia() const;
//-
inline bool linearMolecule() const;
//-
inline bool pointMolecule() const;
//-
inline label degreesOfFreedom() const;
//-
inline scalar mass() const;
//-
inline label nSites() const;
};
@ -141,7 +148,7 @@ public:
//- Class used to pass tracking data to the trackToFace function
class trackingData
:
public particle::TrackingData<polyatomicCloud>
public particle::TrackingData<MoleculeCloud<polyatomic> >
{
// label specifying which part of the integration algorithm is taking
label part_;
@ -151,9 +158,9 @@ public:
// Constructors
trackingData(polyatomicCloud& cloud, label part)
trackingData(MoleculeCloud<polyatomic>& cloud, label part)
:
particle::TrackingData<polyatomicCloud>(cloud),
particle::TrackingData<MoleculeCloud<polyatomic> >(cloud),
part_(part)
{}
@ -176,10 +183,10 @@ private:
// bodyLocalVector = Q_.T() & globalVector
tensor Q_;
// Linear velocity of polyatomic
//- Linear velocity of polyatomic
vector v_;
// Total linear acceleration of polyatomic
//- Total linear acceleration of polyatomic
vector a_;
//- Angular momentum of polyatomic, in body local reference frame
@ -188,8 +195,10 @@ private:
//- Total torque on polyatomic, in body local reference frame
vector tau_;
//-
vector specialPosition_;
//-
scalar potentialEnergy_;
// - r_ij f_ij, stress dyad
@ -198,31 +207,42 @@ private:
// // - r_ij outer product f_ij: virial contribution
// tensor rDotf_;
//-
label special_;
//-
label id_;
//-
List<vector> siteForces_;
//-
List<vector> sitePositions_;
// Private Member Functions
//-
tensor rotationTensorX(scalar deltaT) const;
//-
tensor rotationTensorY(scalar deltaT) const;
//-
tensor rotationTensorZ(scalar deltaT) const;
public:
//- Runtime type information
TypeName("polyatomic");
friend class Cloud<polyatomic>;
// Constructors
//- Construct from components
//- Construct from all components
inline polyatomic
(
const polyMesh& mesh,
@ -279,53 +299,91 @@ public:
// Tracking
//-
bool move(trackingData&, const scalar trackTime);
//-
virtual void transformProperties(const tensor& T);
//-
virtual void transformProperties(const vector& separation);
//-
void setSitePositions(const constantProperties& constProps);
//-
void setSiteSizes(label size);
// Access
//-
inline const tensor& Q() const;
//-
inline tensor& Q();
//-
inline const vector& v() const;
//-
inline vector& v();
//-
inline const vector& a() const;
//-
inline vector& a();
//-
inline const vector& pi() const;
//-
inline vector& pi();
//-
inline const vector& tau() const;
//-
inline vector& tau();
//-
inline const List<vector>& siteForces() const;
//-
inline List<vector>& siteForces();
//-
inline const List<vector>& sitePositions() const;
//-
inline List<vector>& sitePositions();
//-
inline const vector& specialPosition() const;
//-
inline vector& specialPosition();
//-
inline scalar potentialEnergy() const;
//-
inline scalar& potentialEnergy();
//-
inline const tensor& rf() const;
//-
inline tensor& rf();
//-
inline label special() const;
//-
inline bool tethered() const;
//-
inline label id() const;
@ -367,8 +425,10 @@ public:
// I-O
//- Read
static void readFields(Cloud<polyatomic>& mC);
//- Write
static void writeFields(const Cloud<polyatomic>& mC);

0
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomicI.H → src/lagrangian/molecularDynamics/molecule/molecules/polyatomic/polyatomicI.H
View File

25
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomicIO.C → src/lagrangian/molecularDynamics/molecule/molecules/polyatomic/polyatomicIO.C
View File

@ -25,7 +25,7 @@ License
#include "polyatomic.H"
#include "IOstreams.H"
#include "polyatomicCloud.H"
#include "Cloud.H"
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -92,7 +92,11 @@ Foam::polyatomic::polyatomic
is.check
(
"Foam::polyatomic::polyatomic"
"(const Cloud<polyatomic>& cloud, Foam::Istream&), bool"
"("
"const polyMesh& mesh,"
"Istream& is,"
"bool readFields"
")"
);
}
@ -134,7 +138,8 @@ void Foam::polyatomic::readFields(Cloud<polyatomic>& mC)
mC.checkFieldIOobject(mC, id);
label i = 0;
forAllIter(polyatomicCloud, mC, iter)
forAllIter(typename Cloud<polyatomic>, mC, iter)
{
polyatomic& mol = iter();
@ -203,7 +208,7 @@ void Foam::polyatomic::writeFields(const Cloud<polyatomic>& mC)
);
label i = 0;
forAllConstIter(polyatomicCloud, mC, iter)
forAllConstIter(typename Cloud<polyatomic>, mC, iter)
{
const polyatomic& mol = iter();
@ -241,18 +246,6 @@ void Foam::polyatomic::writeFields(const Cloud<polyatomic>& mC)
orientation1.write();
orientation2.write();
orientation3.write();
Info<< "writeFields " << mC.name() << endl;
if (isA<polyatomicCloud>(mC))
{
const polyatomicCloud& m = dynamic_cast<const polyatomicCloud&>(mC);
m.writeXYZ
(
m.mesh().time().timePath()/cloud::prefix/"polyatomicCloud.xmol"
);
}
}

88
src/lagrangian/molecularDynamics/potential/potential/potential.C
View File

@ -27,7 +27,7 @@ License
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::potential::setSiteIdList(const dictionary& mdPropertiesDict)
void Foam::potential::setSiteIdList(const dictionary& moleculePropertiesDict)
{
DynamicList<word> siteIdList;
DynamicList<word> pairPotentialSiteIdList;
@ -36,14 +36,14 @@ void Foam::potential::setSiteIdList(const dictionary& mdPropertiesDict)
{
const word& id(idList_[i]);
if (!mdPropertiesDict.found(id))
if (!moleculePropertiesDict.found(id))
{
FatalErrorIn("potential::setSiteIdList(const dictionary&)")
<< id << " molecule subDict not found"
<< nl << abort(FatalError);
}
const dictionary& molDict(mdPropertiesDict.subDict(id));
const dictionary& molDict(moleculePropertiesDict.subDict(id));
List<word> siteIdNames = molDict.lookup("siteIds");
@ -93,7 +93,10 @@ void Foam::potential::setSiteIdList(const dictionary& mdPropertiesDict)
}
void Foam::potential::potential::readPotentialDict()
void Foam::potential::potential::readPotentialDict
(
const dictionary& moleculePropertiesDict
)
{
Info<< nl << "Reading potential dictionary:" << endl;
@ -111,31 +114,28 @@ void Foam::potential::potential::readPotentialDict()
idList_ = List<word>(idListDict.lookup("idList"));
setSiteIdList
(
IOdictionary
(
IOobject
(
"mdProperties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE,
false
)
)
);
setSiteIdList(moleculePropertiesDict);
List<word> pairPotentialSiteIdList
(
SubList<word>(siteIdList_, nPairPotIds_)
);
Info<< nl << "Unique site ids found: " << siteIdList_
<< nl << "Site Ids requiring a pair potential: "
<< pairPotentialSiteIdList
<< endl;
Info<< nl << "Unique site ids found:";
forAll(siteIdList_, i)
{
Info<< " " << siteIdList_[i];
}
Info << nl << "Site Ids requiring a pair potential:";
forAll(pairPotentialSiteIdList, i)
{
Info<< " " << pairPotentialSiteIdList[i];
}
Info<< nl;
List<word> tetherSiteIdList(0);
@ -229,37 +229,25 @@ void Foam::potential::potential::readPotentialDict()
if (potentialDict.found("external"))
{
Info<< nl << "Reading external forces:" << endl;
Info<< nl << "Reading external forces: ";
const dictionary& externalDict = potentialDict.subDict("external");
// gravity
externalDict.readIfPresent("gravity", gravity_);
}
Info<< nl << tab << "gravity = " << gravity_ << endl;
Info<< "gravity = " << gravity_ << nl << endl;
}
}
void Foam::potential::potential::readMdInitialiseDict
(
const IOdictionary& mdInitialiseDict,
const dictionary& moleculePropertiesDict,
IOdictionary& idListDict
)
{
IOdictionary mdPropertiesDict
(
IOobject
(
"mdProperties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE,
false
)
);
DynamicList<word> idList;
DynamicList<word> tetherSiteIdList;
@ -280,7 +268,7 @@ void Foam::potential::potential::readMdInitialiseDict
{
const word& id = latticeIds[i];
if (!mdPropertiesDict.found(id))
if (!moleculePropertiesDict.found(id))
{
FatalErrorIn
(
@ -322,7 +310,7 @@ void Foam::potential::potential::readMdInitialiseDict
List<word> siteIds
(
mdPropertiesDict.subDict(id).lookup("siteIds")
moleculePropertiesDict.subDict(id).lookup("siteIds")
);
if (findIndex(siteIds, tetherSiteId) != -1)
@ -359,16 +347,20 @@ void Foam::potential::potential::readMdInitialiseDict
idListDict.add("tetherSiteIdList", tetherSiteIdList);
setSiteIdList(mdPropertiesDict);
setSiteIdList(moleculePropertiesDict);
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::potential::potential(const polyMesh& mesh)
Foam::potential::potential
(
const polyMesh& mesh,
const dictionary& moleculePropertiesDict
)
:
mesh_(mesh)
{
readPotentialDict();
readPotentialDict(moleculePropertiesDict);
}
@ -376,12 +368,18 @@ Foam::potential::potential
(
const polyMesh& mesh,
const IOdictionary& mdInitialiseDict,
const dictionary& moleculePropertiesDict,
IOdictionary& idListDict
)
:
mesh_(mesh)
{
readMdInitialiseDict(mdInitialiseDict, idListDict);
readMdInitialiseDict
(
mdInitialiseDict,
moleculePropertiesDict,
idListDict
);
}
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //

34
src/lagrangian/molecularDynamics/potential/potential/potential.H
View File

@ -55,34 +55,48 @@ class potential
{
// Private data
//-
const polyMesh& mesh_;
//-
List<word> idList_;
//-
List<word> siteIdList_;
//-
label nPairPotIds_;
//-
scalar potentialEnergyLimit_;
//-
labelList removalOrder_;
//-
pairPotentialList pairPotentials_;
//-
tetherPotentialList tetherPotentials_;
//-
vector gravity_;
// Private Member Functions
void setSiteIdList(const dictionary& mdPropertiesDict);
void readPotentialDict();
//-
void setSiteIdList(const dictionary& moleculePropertiesDict);
//-
void readPotentialDict(const dictionary& moleculePropertiesDict);
//-
void readMdInitialiseDict
(
const IOdictionary& mdInitialiseDict,
const dictionary& moleculePropertiesDict,
IOdictionary& idListDict
);
@ -98,13 +112,18 @@ public:
// Constructors
//- Construct from mesh reference
potential(const polyMesh& mesh);
potential
(
const polyMesh& mesh,
const dictionary& moleculePropertiesDict
);
//- Construct from mdInitialiseDict
potential
(
const polyMesh& mesh,
const IOdictionary& mdInitialiseDict,
const dictionary& moleculePropertiesDict,
IOdictionary& idListDict
);
@ -117,22 +136,31 @@ public:
// Access
//-
inline label nIds() const;
//-
inline const List<word>& idList() const;
//-
inline const List<word>& siteIdList() const;
//-
inline scalar potentialEnergyLimit() const;
//-
inline label nPairPotentials() const;
//-
inline const labelList& removalOrder() const;
//-
inline const pairPotentialList& pairPotentials() const;
//-
inline const tetherPotentialList& tetherPotentials() const;
//-
inline const vector& gravity() const;
};