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ENH: Re-worked lagrangian/molecularDynamics

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This commit is contained in:
andy
2011-02-24 16:44:46 +00:00
parent f5da7edfe4
commit e8ea1f031d
5 changed files with 76 additions and 164 deletions
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76
src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2011 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -63,29 +63,14 @@ Foam::tensor Foam::molecule::rotationTensorZ(scalar phi) const
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::molecule::trackData::trackData
(
moleculeCloud& molCloud,
label part
)
:
Particle<molecule>::trackData(molCloud),
molCloud_(molCloud),
part_(part)
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
bool Foam::molecule::move(molecule::trackData& td, const scalar trackTime)
bool Foam::molecule::move(molecule::trackingData& td, const scalar trackTime)
{
td.switchProcessor = false;
td.keepParticle = true;
const constantProperties& constProps(td.molCloud().constProps(id_));
const constantProperties& constProps(td.cloud().constProps(id_));
if (td.part() == 0)
{
@ -195,9 +180,8 @@ bool Foam::molecule::move(molecule::trackData& td, const scalar trackTime)
}
else
{
FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
<< td.part()
<< " is an invalid part of the integration method."
FatalErrorIn("molecule::move(trackingData&, const scalar)") << nl
<< td.part() << " is an invalid part of the integration method."
<< abort(FatalError);
}
@ -207,7 +191,7 @@ bool Foam::molecule::move(molecule::trackData& td, const scalar trackTime)
void Foam::molecule::transformProperties(const tensor& T)
{
Particle<molecule>::transformProperties(T);
particle::transformProperties(T);
Q_ = T & Q_;
@ -229,7 +213,7 @@ void Foam::molecule::transformProperties(const tensor& T)
void Foam::molecule::transformProperties(const vector& separation)
{
Particle<molecule>::transformProperties(separation);
particle::transformProperties(separation);
if (special_ == SPECIAL_TETHERED)
{
@ -257,20 +241,7 @@ void Foam::molecule::setSiteSizes(label size)
bool Foam::molecule::hitPatch
(
const polyPatch&,
molecule::trackData&,
const label,
const scalar,
const tetIndices&
)
{
return false;
}
bool Foam::molecule::hitPatch
(
const polyPatch&,
int&,
trackingData&,
const label,
const scalar,
const tetIndices&
@ -283,25 +254,17 @@ bool Foam::molecule::hitPatch
void Foam::molecule::hitProcessorPatch
(
const processorPolyPatch&,
molecule::trackData& td
trackingData& td
)
{
td.switchProcessor = true;
}
void Foam::molecule::hitProcessorPatch
(
const processorPolyPatch&,
int&
)
{}
void Foam::molecule::hitWallPatch
(
const wallPolyPatch& wpp,
molecule::trackData& td,
trackingData& td,
const tetIndices& tetIs
)
{
@ -320,31 +283,14 @@ void Foam::molecule::hitWallPatch
}
void Foam::molecule::hitWallPatch
(
const wallPolyPatch&,
int&,
const tetIndices&
)
{}
void Foam::molecule::hitPatch
(
const polyPatch&,
molecule::trackData& td
trackingData& td
)
{
td.keepParticle = false;
}
void Foam::molecule::hitPatch
(
const polyPatch&,
int&
)
{}
// ************************************************************************* //

104
src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2011 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -37,7 +37,7 @@ SourceFiles
#ifndef molecule_H
#define molecule_H
#include "Particle.H"
#include "particle.H"
#include "IOstream.H"
#include "autoPtr.H"
#include "diagTensor.H"
@ -56,7 +56,7 @@ class moleculeCloud;
class molecule
:
public Particle<molecule>
public particle
{
public:
@ -76,7 +76,6 @@ public:
//- Class to hold molecule constant properties
class constantProperties
{
// Private data
Field<vector> siteReferencePositions_;
@ -95,6 +94,7 @@ public:
scalar mass_;
// Private Member Functions
void checkSiteListSizes() const;
@ -150,12 +150,10 @@ public:
//- Class used to pass tracking data to the trackToFace function
class trackData
class trackingData
:
public Particle<molecule>::trackData
public particle::TrackingData<moleculeCloud>
{
moleculeCloud& molCloud_;
// label specifying which part of the integration algorithm is taking
label part_;
@ -164,17 +162,18 @@ public:
// Constructors
trackData
(
moleculeCloud& molCloud,
label part
);
trackingData(moleculeCloud& cloud, label part)
:
particle::TrackingData<moleculeCloud>(cloud),
part_(part)
{}
// Member functions
inline moleculeCloud& molCloud();
inline label part() const;
inline label part() const
{
return part_;
}
};
@ -226,7 +225,7 @@ public:
//- Construct from components
inline molecule
(
const Cloud<molecule>& c,
const polyMesh& mesh,
const vector& position,
const label cellI,
const label tetFaceI,
@ -245,23 +244,42 @@ public:
//- Construct from Istream
molecule
(
const Cloud<molecule>& c,
const polyMesh& mesh,
Istream& is,
bool readFields = true
);
//- Construct and return a clone
autoPtr<Particle<molecule> > clone() const
autoPtr<particle> clone() const
{
return autoPtr<Particle<molecule> >(new molecule(*this));
return autoPtr<particle>(new molecule(*this));
}
//- Factory class to read-construct particles used for
// parallel transfer
class iNew
{
const polyMesh& mesh_;
public:
iNew(const polyMesh& mesh)
:
mesh_(mesh)
{}
autoPtr<molecule> operator()(Istream& is) const
{
return autoPtr<molecule>(new molecule(mesh_, is, true));
}
};
// Member Functions
// Tracking
bool move(trackData&, const scalar trackTime);
bool move(trackingData&, const scalar trackTime);
void transformProperties(const tensor& T);
@ -318,18 +336,7 @@ public:
bool hitPatch
(
const polyPatch&,
molecule::trackData& td,
const label patchI,
const scalar trackFraction,
const tetIndices& tetIs
);
//- Overridable function to handle the particle hitting a patch
// Executed before other patch-hitting functions without trackData
bool hitPatch
(
const polyPatch& p,
int& td,
trackingData& td,
const label patchI,
const scalar trackFraction,
const tetIndices& tetIs
@ -339,31 +346,14 @@ public:
void hitProcessorPatch
(
const processorPolyPatch&,
molecule::trackData& td
);
//- Overridable function to handle the particle hitting a processorPatch
// without trackData
void hitProcessorPatch
(
const processorPolyPatch&,
int&
trackingData& td
);
//- Overridable function to handle the particle hitting a wallPatch
void hitWallPatch
(
const wallPolyPatch&,
molecule::trackData& td,
const tetIndices&
);
//- Overridable function to handle the particle hitting a wallPatch
// without trackData
void hitWallPatch
(
const wallPolyPatch&,
int&,
trackingData& td,
const tetIndices&
);
@ -371,15 +361,7 @@ public:
void hitPatch
(
const polyPatch&,
molecule::trackData& td
);
//- Overridable function to handle the particle hitting a polyPatch
// without trackData
void hitPatch
(
const polyPatch&,
int&
trackingData& td
);

23
src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2011 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -219,7 +219,7 @@ inline Foam::molecule::constantProperties::constantProperties
inline Foam::molecule::molecule
(
const Cloud<molecule>& c,
const polyMesh& mesh,
const vector& position,
const label cellI,
const label tetFaceI,
@ -236,7 +236,7 @@ inline Foam::molecule::molecule
)
:
Particle<molecule>(c, position, cellI, tetFaceI, tetPtI),
particle(mesh, position, cellI, tetFaceI, tetPtI),
Q_(Q),
v_(v),
a_(a),
@ -254,8 +254,7 @@ inline Foam::molecule::molecule
}
// * * * constantProperties Private Member Functions * * * * * * * * * * * * //
// * * * * * * * constantProperties Private Member Functions * * * * * * * * //
inline void Foam::molecule::constantProperties::checkSiteListSizes() const
{
@ -394,6 +393,7 @@ Foam::molecule::constantProperties::electrostaticSites() const
return electrostaticSites_;
}
inline bool Foam::molecule::constantProperties::electrostaticSite
(
label sId
@ -462,19 +462,6 @@ inline Foam::label Foam::molecule::constantProperties::nSites() const
}
// * * * * * * * * * * * trackData Member Functions * * * * * * * * * * * * //
inline Foam::moleculeCloud& Foam::molecule::trackData::molCloud()
{
return molCloud_;
}
inline Foam::label Foam::molecule::trackData::part() const
{
return part_;
}
// * * * * * * * * * * * * molecule Member Functions * * * * * * * * * * * * //

14
src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2011 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -31,12 +31,12 @@ License
Foam::molecule::molecule
(
const Cloud<molecule>& cloud,
const polyMesh& mesh,
Istream& is,
bool readFields
)
:
Particle<molecule>(cloud, is, readFields),
particle(mesh, is, readFields),
Q_(tensor::zero),
v_(vector::zero),
a_(vector::zero),
@ -104,7 +104,7 @@ void Foam::molecule::readFields(Cloud<molecule>& mC)
return;
}
Particle<molecule>::readFields(mC);
particle::readFields(mC);
IOField<tensor> Q(mC.fieldIOobject("Q", IOobject::MUST_READ));
mC.checkFieldIOobject(mC, Q);
@ -153,7 +153,7 @@ void Foam::molecule::readFields(Cloud<molecule>& mC)
void Foam::molecule::writeFields(const Cloud<molecule>& mC)
{
Particle<molecule>::writeFields(mC);
particle::writeFields(mC);
label np = mC.size();
@ -262,7 +262,7 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
{
if (os.format() == IOstream::ASCII)
{
os << token::SPACE << static_cast<const Particle<molecule>&>(mol)
os << token::SPACE << static_cast<const particle&>(mol)
<< token::SPACE << mol.face()
<< token::SPACE << mol.stepFraction()
<< token::SPACE << mol.Q_
@ -280,7 +280,7 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
}
else
{
os << static_cast<const Particle<molecule>&>(mol);
os << static_cast<const particle&>(mol);
os.write
(
reinterpret_cast<const char*>(&mol.Q_),

23
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2011 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -33,7 +33,6 @@ using namespace Foam::constant::mathematical;
namespace Foam
{
defineParticleTypeNameAndDebug(molecule, 0);
defineTemplateTypeNameAndDebug(Cloud<molecule>, 0);
}
@ -746,7 +745,7 @@ void Foam::moleculeCloud::initialiseMolecules
label tetFace = -1;
label tetPt = -1;
findCellFacePt
mesh_.findCellFacePt
(
globalPosition,
cell,
@ -834,7 +833,7 @@ void Foam::moleculeCloud::initialiseMolecules
label tetFace = -1;
label tetPt = -1;
findCellFacePt
mesh_.findCellFacePt
(
globalPosition,
cell,
@ -913,7 +912,7 @@ void Foam::moleculeCloud::initialiseMolecules
label tetFace = -1;
label tetPt = -1;
findCellFacePt
mesh_.findCellFacePt
(
globalPosition,
cell,
@ -1000,11 +999,9 @@ void Foam::moleculeCloud::createMolecule
const vector& bulkVelocity
)
{
const Cloud<molecule>& cloud = *this;
if (cell == -1)
{
findCellFacePt(position, cell, tetFace, tetPt);
mesh_.findCellFacePt(position, cell, tetFace, tetPt);
}
if (cell == -1)
@ -1063,7 +1060,7 @@ void Foam::moleculeCloud::createMolecule
(
new molecule
(
cloud,
mesh_,
position,
cell,
tetFace,
@ -1159,18 +1156,18 @@ Foam::moleculeCloud::moleculeCloud
void Foam::moleculeCloud::evolve()
{
molecule::trackData td0(*this, 0);
molecule::trackingData td0(*this, 0);
Cloud<molecule>::move(td0, mesh_.time().deltaTValue());
molecule::trackData td1(*this, 1);
molecule::trackingData td1(*this, 1);
Cloud<molecule>::move(td1, mesh_.time().deltaTValue());
molecule::trackData td2(*this, 2);
molecule::trackingData td2(*this, 2);
Cloud<molecule>::move(td2, mesh_.time().deltaTValue());
calculateForce();
molecule::trackData td3(*this, 3);
molecule::trackingData td3(*this, 3);
Cloud<molecule>::move(td3, mesh_.time().deltaTValue());
}