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ENH: Running and improvements.

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This commit is contained in:
graham
2011-07-01 19:55:48 +01:00
parent 8a93505589
commit 0c51d2628a
14 changed files with 269 additions and 29 deletions
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2
applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C
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@ -49,6 +49,8 @@ int main(int argc, char *argv[])
molecules.evolve();
runTime.write();
Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;

0
applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/files → applications/solvers/discreteMethods/molecularDynamics/old/mdEquilibrationFoam/Make/files
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0
applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/options → applications/solvers/discreteMethods/molecularDynamics/old/mdEquilibrationFoam/Make/options
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0
applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C → applications/solvers/discreteMethods/molecularDynamics/old/mdEquilibrationFoam/mdEquilibrationFoam.C
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0
applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H → applications/solvers/discreteMethods/molecularDynamics/old/mdEquilibrationFoam/readmdEquilibrationDict.H
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8
applications/utilities/preProcessing/mdInitialise/mdInitialise.C
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@ -26,8 +26,8 @@ Description
\*---------------------------------------------------------------------------*/
#include "md.H"
#include "fvCFD.H"
#include "polyatomicCloud.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -64,7 +64,9 @@ int main(int argc, char *argv[])
potential pot(mesh, mdInitialiseDict, idListDict);
moleculeCloud molecules(mesh, pot, mdInitialiseDict);
polyatomicCloud molecules(mesh, pot, mdInitialiseDict);
Info<< "Cloud is called " << molecules.name() << endl;
label totalMolecules = molecules.size();
@ -81,7 +83,7 @@ int main(int argc, char *argv[])
if (!mesh.write())
{
FatalErrorIn(args.executable())
<< "Failed writing moleculeCloud."
<< "Failed writing polyatomicCloud."
<< nl << exit(FatalError);
}

45
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSite.C
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@ -71,6 +71,49 @@ Foam::constPropSite::~constPropSite()
{}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * IOstream Operators * * * * * * * * * * * * //
Foam::Istream& Foam::operator>>(Istream& is, constPropSite& cPS)
{
is >> cPS.siteReferencePosition_
>> cPS.siteMass_
>> cPS.siteCharge_
>> cPS.siteId_
>> cPS.name_
>> cPS.pairPotentialSite_
>> cPS.electrostaticSite_;
// Check state of Istream
is.check
(
"Foam::Istream& Foam::operator>>"
"(Foam::Istream&, Foam::constPropSite&)"
);
return is;
}
Foam::Ostream& Foam::operator<<(Ostream& os, const constPropSite& cPS)
{
os << token::SPACE << cPS.siteReferencePosition()
<< token::SPACE << cPS.siteMass()
<< token::SPACE << cPS.siteCharge()
<< token::SPACE << cPS.siteId()
<< token::SPACE << cPS.name()
<< token::SPACE << cPS.pairPotentialSite()
<< token::SPACE << cPS.electrostaticSite();
// Check state of Ostream
os.check
(
"Foam::Ostream& Foam::operator<<(Foam::Ostream&, "
"const Foam::constPropSite&)"
);
return os;
}
// ************************************************************************* //

25
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSite.H
View File

@ -35,14 +35,23 @@ SourceFiles
#define constPropSite_H
#include "vector.H"
#include "IFstream.H"
#include "OFstream.H"
#include "IOstreams.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// Forward declaration of classes
class Istream;
class Ostream;
// Forward declaration of friend functions and operators
class constPropSite;
Istream& operator>>(Istream&, constPropSite&);
Ostream& operator<<(Ostream&, const constPropSite&);
/*---------------------------------------------------------------------------*\
Class constPropSite Declaration
\*---------------------------------------------------------------------------*/
@ -144,6 +153,18 @@ public:
//-
inline bool& electrostaticSite();
// Member Operators
inline bool operator==(const constPropSite&) const;
inline bool operator!=(const constPropSite&) const;
// IOstream Operators
friend Istream& operator>>(Istream&, constPropSite&);
friend Ostream& operator<<(Ostream&, const constPropSite&);
};

27
src/lagrangian/molecularDynamics/molecule/constPropSite/constPropSiteI.H
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@ -114,4 +114,31 @@ inline bool& Foam::constPropSite::electrostaticSite()
}
// * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * * //
bool Foam::constPropSite::operator==
(
const constPropSite& rhs
) const
{
return
siteReferencePosition_ == rhs.siteReferencePosition_
&& siteMass_ == rhs.siteMass_
&& siteCharge_ == rhs.siteCharge_
&& siteId_ == rhs.siteId_
&& name_ == rhs.name_
&& pairPotentialSite_ == rhs.pairPotentialSite_
&& electrostaticSite_ == rhs.electrostaticSite_;
}
bool Foam::constPropSite::operator!=
(
const constPropSite& rhs
) const
{
return !(*this == rhs);
}
// ************************************************************************* //

18
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomicI.H
View File

@ -57,11 +57,12 @@ inline Foam::polyatomic::constantProperties::constantProperties
List<word> pairPotentialIds(dict.lookup("pairPotentialSiteIds"));
sites_.setSize(siteReferencePositions.size());
if
(
( siteIdNames.size() != sites_.size() )
|| ( siteReferencePositions.size() != sites_.size() )
|| ( siteCharges.size() != sites_.size() )
(siteIdNames.size() != sites_.size())
|| (siteCharges.size() != sites_.size())
)
{
FatalErrorIn
@ -72,12 +73,13 @@ inline Foam::polyatomic::constantProperties::constantProperties
")"
)
<< "Sizes of site id, charge and "
<< "referencePositions are not the same: " << sites_.size()
<< nl << abort(FatalError);
<< "referencePositions are not the same: " << nl
<< siteIdNames << nl
<< siteReferencePositions << nl
<< siteCharges << nl
<< abort(FatalError);
}
sites_.setSize(siteIdNames.size());
electrostaticSites_.setSize(sites_.size(), -1);
pairPotSites_.setSize(sites_.size(), -1);
@ -107,7 +109,7 @@ inline Foam::polyatomic::constantProperties::constantProperties
electrostaticSites_[electrostaticI++] = sI;
}
if (sites_[sI].pairPotentialSite() && !sites_[sI].electrostaticSite())
if (!sites_[sI].pairPotentialSite() && !sites_[sI].electrostaticSite())
{
WarningIn
(

148
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloud.C
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@ -40,7 +40,7 @@ namespace Foam
void Foam::polyatomicCloud::buildConstProps()
{
Info<< nl << "Reading polyatomicProperties dictionary." << endl;
Info<< nl << "Reading mdProperties dictionary." << endl;
const List<word>& idList(pot_.idList());
@ -48,11 +48,11 @@ void Foam::polyatomicCloud::buildConstProps()
const List<word>& siteIdList(pot_.siteIdList());
IOdictionary polyatomicPropertiesDict
IOdictionary mdPropertiesDict
(
IOobject
(
"polyatomicProperties",
"mdProperties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
@ -65,7 +65,7 @@ void Foam::polyatomicCloud::buildConstProps()
{
const word& id = idList[i];
const dictionary& molDict(polyatomicPropertiesDict.subDict(id));
const dictionary& molDict(mdPropertiesDict.subDict(id));
List<word> siteIdNames = molDict.lookup("siteIds");
@ -1183,6 +1183,8 @@ void Foam::polyatomicCloud::evolve()
polyatomic::trackingData td3(*this, 3);
Cloud<polyatomic>::move(td3, mesh_.time().deltaTValue());
info();
}
@ -1237,6 +1239,144 @@ void Foam::polyatomicCloud::applyConstraintsAndThermostats
}
void Foam::polyatomicCloud::info() const
{
// Calculates and prints the mean momentum and energy in the system
// and the number of molecules.
vector totalLinearMomentum(vector::zero);
vector totalAngularMomentum(vector::zero);
scalar maxVelocityMag = 0.0;
scalar totalMass = 0.0;
scalar totalLinearKE = 0.0;
scalar totalAngularKE = 0.0;
scalar totalPE = 0.0;
scalar totalrDotf = 0.0;
//vector CentreOfMass(vector::zero);
label nMols = this->size();
label dofs = 0;
{
forAllConstIter(polyatomicCloud, *this, mol)
{
const label molId = mol().id();
scalar molMass(this->constProps(molId).mass());
totalMass += molMass;
//CentreOfMass += mol().position()*molMass;
}
// if (nMols)
// {
// CentreOfMass /= totalMass;
// }
forAllConstIter(polyatomicCloud, *this, mol)
{
const label molId = mol().id();
const polyatomic::constantProperties cP(this->constProps(molId));
scalar molMass(cP.mass());
const diagTensor& molMoI(cP.momentOfInertia());
const vector& molV(mol().v());
const vector& molOmega(inv(molMoI) & mol().pi());
vector molPiGlobal = mol().Q() & mol().pi();
totalLinearMomentum += molV * molMass;
totalAngularMomentum += molPiGlobal;
//+((mol().position() - CentreOfMass) ^ (molV * molMass));
if (mag(molV) > maxVelocityMag)
{
maxVelocityMag = mag(molV);
}
totalLinearKE += 0.5*molMass*magSqr(molV);
totalAngularKE += 0.5*(molOmega & molMoI & molOmega);
totalPE += mol().potentialEnergy();
totalrDotf += tr(mol().rf());
dofs += cP.degreesOfFreedom();
}
}
scalar meshVolume = sum(mesh_.cellVolumes());
if (Pstream::parRun())
{
reduce(totalLinearMomentum, sumOp<vector>());
reduce(totalAngularMomentum, sumOp<vector>());
reduce(maxVelocityMag, maxOp<scalar>());
reduce(totalMass, sumOp<scalar>());
reduce(totalLinearKE, sumOp<scalar>());
reduce(totalAngularKE, sumOp<scalar>());
reduce(totalPE, sumOp<scalar>());
reduce(totalrDotf, sumOp<scalar>());
reduce(nMols, sumOp<label>());
reduce(dofs, sumOp<label>());
reduce(meshVolume, sumOp<scalar>());
}
if (nMols)
{
Info<< "Number of molecules in " << this->name() << " = "
<< nMols << nl
<< "Overall number density = "
<< nMols/meshVolume << nl
<< "Overall mass density = "
<< totalMass/meshVolume << nl
<< "Average linear momentum per molecule = "
<< totalLinearMomentum/nMols << ' '
<< mag(totalLinearMomentum)/nMols << nl
<< "Average angular momentum per molecule = "
<< totalAngularMomentum << ' '
<< mag(totalAngularMomentum)/nMols << nl
<< "maximum |velocity| = "
<< maxVelocityMag << nl
<< "Average linear KE per molecule = "
<< totalLinearKE/nMols << nl
<< "Average angular KE per molecule = "
<< totalAngularKE/nMols << nl
<< "Average PE per molecule = "
<< totalPE/nMols << nl
<< "Average TE per molecule = "
<<
(
totalLinearKE
+ totalAngularKE
+ totalPE
)
/nMols
<< endl;
}
else
{
Info<< "No molecules in " << this->name() << endl;
}
}
void Foam::polyatomicCloud::writeXYZ(const fileName& fName) const
{
OFstream os(fName);

3
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloud.H
View File

@ -178,6 +178,9 @@ public:
const scalar measuredTemperature
);
//- Print cloud information
void info() const;
// Access

20
src/lagrangian/molecularDynamics/potential/potential/potential.C
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@ -27,7 +27,7 @@ License
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::potential::setSiteIdList(const dictionary& moleculePropertiesDict)
void Foam::potential::setSiteIdList(const dictionary& mdPropertiesDict)
{
DynamicList<word> siteIdList;
DynamicList<word> pairPotentialSiteIdList;
@ -36,14 +36,14 @@ void Foam::potential::setSiteIdList(const dictionary& moleculePropertiesDict)
{
const word& id(idList_[i]);
if (!moleculePropertiesDict.found(id))
if (!mdPropertiesDict.found(id))
{
FatalErrorIn("potential::setSiteIdList(const dictionary&)")
<< id << " molecule subDict not found"
<< nl << abort(FatalError);
}
const dictionary& molDict(moleculePropertiesDict.subDict(id));
const dictionary& molDict(mdPropertiesDict.subDict(id));
List<word> siteIdNames = molDict.lookup("siteIds");
@ -117,7 +117,7 @@ void Foam::potential::potential::readPotentialDict()
(
IOobject
(
"moleculeProperties",
"mdProperties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
@ -247,11 +247,11 @@ void Foam::potential::potential::readMdInitialiseDict
IOdictionary& idListDict
)
{
IOdictionary moleculePropertiesDict
IOdictionary mdPropertiesDict
(
IOobject
(
"moleculeProperties",
"mdProperties",
mesh_.time().constant(),
mesh_,
IOobject::MUST_READ_IF_MODIFIED,
@ -280,7 +280,7 @@ void Foam::potential::potential::readMdInitialiseDict
{
const word& id = latticeIds[i];
if (!moleculePropertiesDict.found(id))
if (!mdPropertiesDict.found(id))
{
FatalErrorIn
(
@ -290,7 +290,7 @@ void Foam::potential::potential::readMdInitialiseDict
"IOdictionary&"
")"
) << "Molecule type " << id
<< " not found in moleculeProperties dictionary." << nl
<< " not found in mdProperties dictionary." << nl
<< abort(FatalError);
}
@ -322,7 +322,7 @@ void Foam::potential::potential::readMdInitialiseDict
List<word> siteIds
(
moleculePropertiesDict.subDict(id).lookup("siteIds")
mdPropertiesDict.subDict(id).lookup("siteIds")
);
if (findIndex(siteIds, tetherSiteId) != -1)
@ -359,7 +359,7 @@ void Foam::potential::potential::readMdInitialiseDict
idListDict.add("tetherSiteIdList", tetherSiteIdList);
setSiteIdList(moleculePropertiesDict);
setSiteIdList(mdPropertiesDict);
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //

2
src/lagrangian/molecularDynamics/potential/potential/potential.H
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@ -76,7 +76,7 @@ class potential
// Private Member Functions
void setSiteIdList(const dictionary& moleculePropertiesDict);
void setSiteIdList(const dictionary& mdPropertiesDict);
void readPotentialDict();