zhyang-dev/openfoam
1
0
Fork 0
mirror of https://develop.openfoam.com/Development/openfoam.git synced 2025-11-28 03:28:01 +00:00
Code Issues Actions Packages Projects Releases Wiki Activity

Merge branch 'master' of /home/noisy3/OpenFOAM/OpenFOAM-dev

Browse Source
This commit is contained in:
mattijs
2009-06-30 22:21:21 +01:00
parent 3852087d1a e77c7a9bb6
commit 55a9be9cea
237 changed files with 5947 additions and 3446 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/finiteVolume/Make/files
View File

@ -109,7 +109,6 @@ $(derivedFvPatchFields)/directMappedFixedValue/directMappedFixedValueFvPatchFiel
$(derivedFvPatchFields)/directMappedVelocityFluxFixedValue/directMappedVelocityFluxFixedValueFvPatchField.C
$(derivedFvPatchFields)/fan/fanFvPatchFields.C
$(derivedFvPatchFields)/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
$(derivedFvPatchFields)/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
$(derivedFvPatchFields)/fixedFluxPressure/fixedFluxPressureFvPatchScalarField.C
$(derivedFvPatchFields)/fixedInternalValueFvPatchField/fixedInternalValueFvPatchFields.C
$(derivedFvPatchFields)/fixedNormalSlip/fixedNormalSlipFvPatchFields.C
@ -148,6 +147,7 @@ $(derivedFvPatchFields)/turbulentInlet/turbulentInletFvPatchFields.C
$(derivedFvPatchFields)/turbulentIntensityKineticEnergyInlet/turbulentIntensityKineticEnergyInletFvPatchScalarField.C
$(derivedFvPatchFields)/uniformFixedValue/uniformFixedValueFvPatchFields.C
$(derivedFvPatchFields)/waveTransmissive/waveTransmissiveFvPatchFields.C
$(derivedFvPatchFields)/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C
fvsPatchFields = fields/fvsPatchFields
$(fvsPatchFields)/fvsPatchField/fvsPatchFields.C

149
src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
View File

@ -1,149 +0,0 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 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 "fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H"
#include "addToRunTimeSelectionTable.H"
#include "fvPatchFieldMapper.H"
#include "volFields.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF
)
:
fixedGradientFvPatchScalarField(p, iF)
{}
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& ptf,
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const fvPatchFieldMapper& mapper
)
:
fixedGradientFvPatchScalarField(ptf, p, iF, mapper)
{}
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const dictionary&
)
:
fixedGradientFvPatchScalarField(p, iF)
{
fvPatchField<scalar>::operator=(patchInternalField());
gradient() = 0.0;
}
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& wbppsf
)
:
fixedGradientFvPatchScalarField(wbppsf)
{}
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& wbppsf,
const DimensionedField<scalar, volMesh>& iF
)
:
fixedGradientFvPatchScalarField(wbppsf, iF)
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
void fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::updateCoeffs()
{
if (updated())
{
return;
}
const dictionary& environmentalProperties
= db().lookupObject<IOdictionary>("environmentalProperties");
dimensionedVector g(environmentalProperties.lookup("g"));
const dictionary& transportProperties
= db().lookupObject<IOdictionary>("transportProperties");
dimensionedScalar beta(transportProperties.lookup("beta"));
const fvPatchField<scalar>& T =
patch().lookupPatchField<volScalarField, scalar>("T");
gradient() = beta.value()*T.snGrad()*(g.value() & patch().Cf());
fixedGradientFvPatchScalarField::updateCoeffs();
}
void fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::write
(
Ostream& os
) const
{
fixedGradientFvPatchScalarField::write(os);
writeEntry("value", os);
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
makePatchTypeField
(
fvPatchScalarField,
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
);
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //

50
src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
View File

@ -43,10 +43,27 @@ fixedFluxBuoyantPressureFvPatchScalarField
const DimensionedField<scalar, volMesh>& iF
)
:
fixedGradientFvPatchScalarField(p, iF)
fixedGradientFvPatchScalarField(p, iF),
rhoName_("rho")
{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const dictionary& dict
)
:
fixedGradientFvPatchScalarField(p, iF),
rhoName_(dict.lookupOrDefault<word>("rho", "rho"))
{
fvPatchField<scalar>::operator=(patchInternalField());
gradient() = 0.0;
}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
@ -56,43 +73,31 @@ fixedFluxBuoyantPressureFvPatchScalarField
const fvPatchFieldMapper& mapper
)
:
fixedGradientFvPatchScalarField(ptf, p, iF, mapper)
fixedGradientFvPatchScalarField(ptf, p, iF, mapper),
rhoName_(ptf.rhoName_)
{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const dictionary&
const fixedFluxBuoyantPressureFvPatchScalarField& ptf
)
:
fixedGradientFvPatchScalarField(p, iF)
{
fvPatchField<scalar>::operator=(patchInternalField());
gradient() = 0.0;
}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
const fixedFluxBuoyantPressureFvPatchScalarField& wbppsf
)
:
fixedGradientFvPatchScalarField(wbppsf)
fixedGradientFvPatchScalarField(ptf),
rhoName_(ptf.rhoName_)
{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
const fixedFluxBuoyantPressureFvPatchScalarField& wbppsf,
const fixedFluxBuoyantPressureFvPatchScalarField& ptf,
const DimensionedField<scalar, volMesh>& iF
)
:
fixedGradientFvPatchScalarField(wbppsf, iF)
fixedGradientFvPatchScalarField(ptf, iF),
rhoName_(ptf.rhoName_)
{}
@ -111,7 +116,7 @@ void fixedFluxBuoyantPressureFvPatchScalarField::updateCoeffs()
dimensionedVector g(environmentalProperties.lookup("g"));
const fvPatchField<scalar>& rho =
patch().lookupPatchField<volScalarField, scalar>("rho");
patch().lookupPatchField<volScalarField, scalar>(rhoName_);
// If the variable name is "pd" assume it is p - rho*g.h
// and set the gradient appropriately.
@ -132,6 +137,7 @@ void fixedFluxBuoyantPressureFvPatchScalarField::updateCoeffs()
void fixedFluxBuoyantPressureFvPatchScalarField::write(Ostream& os) const
{
fixedGradientFvPatchScalarField::write(os);
os.writeKeyword("rho") << rhoName_ << token::END_STATEMENT << nl;
writeEntry("value", os);
}

5
src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.H
View File

@ -55,6 +55,11 @@ class fixedFluxBuoyantPressureFvPatchScalarField
:
public fixedGradientFvPatchScalarField
{
// Private data
//- Name of the density field used to calculate the buoyancy force
word rhoName_;
public:

1
src/finiteVolume/fields/fvPatchFields/derived/totalPressure/totalPressureFvPatchScalarField.C
View File

@ -30,7 +30,6 @@ License
#include "volFields.H"
#include "surfaceFields.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //

168
src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C Normal file
View File

@ -0,0 +1,168 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 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 "uniformDensityHydrostaticPressureFvPatchScalarField.H"
#include "addToRunTimeSelectionTable.H"
#include "fvPatchFieldMapper.H"
#include "volFields.H"
#include "surfaceFields.H"
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF
)
:
fixedValueFvPatchScalarField(p, iF),
rho_(0.0),
pRefValue_(0.0),
pRefPoint_(vector::zero)
{}
Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const dictionary& dict
)
:
fixedValueFvPatchScalarField(p, iF),
rho_(readScalar(dict.lookup("rho"))),
pRefValue_(readScalar(dict.lookup("pRefValue"))),
pRefPoint_(dict.lookup("pRefPoint"))
{
if (dict.found("value"))
{
fvPatchField<scalar>::operator=
(
scalarField("value", dict, p.size())
);
}
else
{
evaluate();
}
}
Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
uniformDensityHydrostaticPressureFvPatchScalarField
(
const uniformDensityHydrostaticPressureFvPatchScalarField& ptf,
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
const fvPatchFieldMapper& mapper
)
:
fixedValueFvPatchScalarField(ptf, p, iF, mapper),
rho_(ptf.rho_),
pRefValue_(ptf.pRefValue_),
pRefPoint_(ptf.pRefPoint_)
{}
Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
uniformDensityHydrostaticPressureFvPatchScalarField
(
const uniformDensityHydrostaticPressureFvPatchScalarField& ptf
)
:
fixedValueFvPatchScalarField(ptf),
rho_(ptf.rho_),
pRefValue_(ptf.pRefValue_),
pRefPoint_(ptf.pRefPoint_)
{}
Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
uniformDensityHydrostaticPressureFvPatchScalarField
(
const uniformDensityHydrostaticPressureFvPatchScalarField& ptf,
const DimensionedField<scalar, volMesh>& iF
)
:
fixedValueFvPatchScalarField(ptf, iF),
rho_(ptf.rho_),
pRefValue_(ptf.pRefValue_),
pRefPoint_(ptf.pRefPoint_)
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
void Foam::uniformDensityHydrostaticPressureFvPatchScalarField::updateCoeffs()
{
if (updated())
{
return;
}
const dictionary& environmentalProperties
= db().lookupObject<IOdictionary>("environmentalProperties");
dimensionedVector g(environmentalProperties.lookup("g"));
operator==
(
pRefValue_
+ rho_*((g.value() & patch().Cf()) - (g.value() & pRefPoint_))
);
fixedValueFvPatchScalarField::updateCoeffs();
}
void Foam::uniformDensityHydrostaticPressureFvPatchScalarField::write
(
Ostream& os
) const
{
fvPatchScalarField::write(os);
os.writeKeyword("rho") << rho_ << token::END_STATEMENT << nl;
os.writeKeyword("pRefValue") << pRefValue_ << token::END_STATEMENT << nl;
os.writeKeyword("pRefPoint") << pRefPoint_ << token::END_STATEMENT << nl;
writeEntry("value", os);
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
makePatchTypeField
(
fvPatchScalarField,
uniformDensityHydrostaticPressureFvPatchScalarField
);
}
// ************************************************************************* //

110
src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H → src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.H
View File

@ -23,23 +23,24 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
Foam::fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
Foam::uniformDensityHydrostaticPressureFvPatchScalarField
Description
Boundary condition on pressure for use with buoyant solvers employing the
Boussinesq approximation to balance the flux generated by the temperature
gradient.
Hydrostatic pressure boundary condition calculated as
pRefValue + rho*g.(x - pRefPoint)
where rho is provided and assumed uniform.
SourceFiles
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
uniformDensityHydrostaticPressureFvPatchScalarField.C
\*---------------------------------------------------------------------------*/
#ifndef fixedFluxBoussinesqBuoyantPressureFvPatchScalarFields_H
#define fixedFluxBoussinesqBuoyantPressureFvPatchScalarFields_H
#ifndef uniformDensityHydrostaticPressureFvPatchScalarField_H
#define uniformDensityHydrostaticPressureFvPatchScalarField_H
#include "fvPatchFields.H"
#include "fixedGradientFvPatchFields.H"
#include "fixedValueFvPatchFields.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -47,30 +48,42 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class fixedFluxBoussinesqBuoyantPressureFvPatchScalarField Declaration
Class uniformDensityHydrostaticPressureFvPatch Declaration
\*---------------------------------------------------------------------------*/
class fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
class uniformDensityHydrostaticPressureFvPatchScalarField
:
public fixedGradientFvPatchScalarField
public fixedValueFvPatchScalarField
{
// Private data
//- Constant density in the far-field
scalar rho_;
//- Reference pressure
scalar pRefValue_;
//- Reference pressure location
vector pRefPoint_;
public:
//- Runtime type information
TypeName("fixedFluxBoussinesqBuoyantPressure");
TypeName("uniformDensityHydrostaticPressure");
// Constructors
//- Construct from patch and internal field
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch&,
const DimensionedField<scalar, volMesh>&
);
//- Construct from patch, internal field and dictionary
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch&,
const DimensionedField<scalar, volMesh>&,
@ -78,20 +91,19 @@ public:
);
//- Construct by mapping given
// fixedFluxBoussinesqBuoyantPressureFvPatchScalarField onto a new
// patch
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
// uniformDensityHydrostaticPressureFvPatchScalarField onto a new patch
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&,
const uniformDensityHydrostaticPressureFvPatchScalarField&,
const fvPatch&,
const DimensionedField<scalar, volMesh>&,
const fvPatchFieldMapper&
);
//- Construct as copy
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&
const uniformDensityHydrostaticPressureFvPatchScalarField&
);
//- Construct and return a clone
@ -99,14 +111,14 @@ public:
{
return tmp<fvPatchScalarField>
(
new fixedFluxBoussinesqBuoyantPressureFvPatchScalarField(*this)
new uniformDensityHydrostaticPressureFvPatchScalarField(*this)
);
}
//- Construct as copy setting internal field reference
fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
uniformDensityHydrostaticPressureFvPatchScalarField
(
const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&,
const uniformDensityHydrostaticPressureFvPatchScalarField&,
const DimensionedField<scalar, volMesh>&
);
@ -118,7 +130,7 @@ public:
{
return tmp<fvPatchScalarField>
(
new fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
new uniformDensityHydrostaticPressureFvPatchScalarField
(
*this,
iF
@ -129,8 +141,52 @@ public:
// Member functions
//- Update the coefficients associated with the patch field
virtual void updateCoeffs();
// Access
//- Return the constant density in the far-field
scalar rho() const
{
return rho_;
}
//- Return reference to the constant density in the far-field
// to allow adjustment
scalar& rho()
{
return rho_;
}
//- Return the reference pressure
scalar pRefValue() const
{
return pRefValue_;
}
//- Return reference to the reference pressure to allow adjustment
scalar& pRefValue()
{
return pRefValue_;
}
//- Return the pressure reference location
const vector& pRefPoint() const
{
return pRefPoint_;
}
//- Return reference to the pressure reference location
// to allow adjustment
vector& pRefPoint()
{
return pRefPoint_;
}
// Evaluation functions
//- Update the coefficients associated with the patch field
virtual void updateCoeffs();
//- Write
virtual void write(Ostream&) const;

10
src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
View File

@ -152,26 +152,26 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#define makeBinaryCollisionModel(CloudType) \
#define makeBinaryCollisionModel(CloudType) \
\
defineNamedTemplateTypeNameAndDebug \
( \
BinaryCollisionModel<CloudType>, \
BinaryCollisionModel<CloudType>, \
0 \
); \
\
defineTemplateRunTimeSelectionTable \
( \
BinaryCollisionModel<CloudType>, \
BinaryCollisionModel<CloudType>, \
dictionary \
);
#define makeBinaryCollisionModelType(SS, CloudType, ParcelType) \
#define makeBinaryCollisionModelType(SS, CloudType, ParcelType) \
\
defineNamedTemplateTypeNameAndDebug(SS<CloudType<ParcelType> >, 0); \
\
BinaryCollisionModel<CloudType<ParcelType> >:: \
BinaryCollisionModel<CloudType<ParcelType> >:: \
adddictionaryConstructorToTable<SS<CloudType<ParcelType> > > \
add##SS##CloudType##ParcelType##ConstructorToTable_;

15
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -126,6 +126,7 @@ void Foam::bufferedAccumulator<Type>::setSizes
}
}
template<class Type>
Foam::label Foam::bufferedAccumulator<Type>::addToBuffers
(
@ -184,11 +185,10 @@ Foam::Field<Type> Foam::bufferedAccumulator<Type>::averaged() const
WarningIn
(
"bufferedAccumulator<Type>::averagedbufferedAccumulator() const"
)
<< "Averaged correlation function requested but averagesTaken = "
<< averagesTaken_
<< ". Returning empty field."
<< endl;
) << "Averaged correlation function requested but averagesTaken = "
<< averagesTaken_
<< ". Returning empty field."
<< endl;
return Field<Type>(bufferLength(), pTraits<Type>::zero);
}
@ -218,8 +218,7 @@ void Foam::bufferedAccumulator<Type>::operator=
FatalErrorIn
(
"bufferedAccumulator<Type>::operator=(const bufferedAccumulator&)"
)
<< "Attempted assignment to self"
) << "Attempted assignment to self"
<< abort(FatalError);
}

2
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

8
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -34,9 +34,9 @@ Foam::Ostream&
Foam::operator<<(Ostream& os, const bufferedAccumulator<Type>& bA)
{
os<< bA.averagesTaken_
<< static_cast<const List< Field<Type> >&>(bA)
<< bA.bufferOffsets();
os << bA.averagesTaken_
<< static_cast<const List< Field<Type> >&>(bA)
<< bA.bufferOffsets();
// Check state of Ostream
os.check

6
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -138,7 +138,7 @@ void Foam::correlationFunction<Type>::calculateCorrelationFunction
FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
<< "Trying to supply a Field of length"
<< currentValues.size()
<<" to calculate the correlation function. "
<< " to calculate the correlation function. "
<< "Expecting a Field of length "
<< measurandFieldSize() << nl
<< abort(FatalError);
@ -205,7 +205,7 @@ Foam::scalar Foam::correlationFunction<Type>::integral() const
scalar cFIntegral = 0.0;
for(label v = 0; v < averageCF.size() - 1; v++)
for (label v = 0; v < averageCF.size() - 1; v++)
{
cFIntegral +=
0.5

7
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -155,7 +155,10 @@ public:
// IOstream Operators
friend Ostream& operator<< <Type>
(Ostream&, const correlationFunction<Type>&);
(
Ostream&,
const correlationFunction<Type>&
);
};

2
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

22
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -34,10 +34,10 @@ bool Foam::correlationFunction<Type>::writeAveraged(Ostream& os) const
forAll(averageCF, v)
{
os<< v*sampleInterval()
<< token::SPACE
<< averageCF[v]
<< nl;
os << v*sampleInterval()
<< token::SPACE
<< averageCF[v]
<< nl;
}
return os.good();
@ -51,12 +51,12 @@ Foam::Ostream& Foam::operator<<
const correlationFunction<Type>& cF
)
{
os<< cF.duration()
<< nl << cF.sampleInterval()
<< nl << cF.averagingInterval()
<< nl << cF.sampleSteps()
<< nl << cF.tZeroBuffers()
<< nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
os << cF.duration()
<< nl << cF.sampleInterval()
<< nl << cF.averagingInterval()
<< nl << cF.sampleSteps()
<< nl << cF.tZeroBuffers()
<< nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
// Check state of Ostream
os.check

16
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -75,7 +75,7 @@ label distribution::totalEntries() const
<< "sumOfEntries = " << sumOfEntries
<< ". This is most likely to be because too many samples "
<< "have been added to the bins and the label has 'rolled "
<< "round'. Try distribution::approxTotalEntries which "
<< "round'. Try distribution::approxTotalEntries which "
<< "returns a scalar." << endl;
sumOfEntries = -1;
@ -336,8 +336,8 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
*(oldDist[u].second() - oldDist[u-1].second())
+
(
oldDist[u-1].second() * oldDist[u].first()
- oldDist[u].second() * oldDist[u-1].first()
oldDist[u-1].second()*oldDist[u].first()
- oldDist[u].second()*oldDist[u-1].first()
)
/binWidth_;
}
@ -348,7 +348,7 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
{
newDist[u].second() =
(0.5 + scalar(newKey))*-oldDist[u].second()
+ oldDist[u].second() * (oldDist[u].first() + binWidth_)
+ oldDist[u].second()*(oldDist[u].first() + binWidth_)
/binWidth_;
}
else
@ -358,8 +358,8 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
*(oldDist[u+1].second() - oldDist[u].second())
+
(
oldDist[u].second() * oldDist[u+1].first()
- oldDist[u+1].second() * oldDist[u].first()
oldDist[u].second()*oldDist[u+1].first()
- oldDist[u+1].second()*oldDist[u].first()
)
/binWidth_;
}
@ -395,7 +395,7 @@ List<Pair<scalar> > distribution::raw()
{
label key = keys[k];
rawDist[k].first() = (0.5 + scalar(key)) * binWidth_;
rawDist[k].first() = (0.5 + scalar(key))*binWidth_;
rawDist[k].second() = scalar((*this)[key]);
}

5
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -30,7 +30,6 @@ Description
SourceFiles
distributionI.H
distribution.C
distributionIO.C
\*---------------------------------------------------------------------------*/
@ -46,7 +45,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class distribution Declaration
Class distribution Declaration
\*---------------------------------------------------------------------------*/
class distribution

2
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

35
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
View File

@ -1,35 +0,0 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 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 "distribution.H"
#include "IOstreams.H"
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
// construct from Istream
// ************************************************************************* //

99
src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -79,8 +79,12 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellI],
cellJ) == -1
findIndex
(
directInteractionList[cellI],
cellJ
)
== -1
)
{
directInteractionList[cellI].append(cellJ);
@ -91,8 +95,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellJ],
cellI) == -1
findIndex
(
directInteractionList[cellJ],
cellI
)
==
-1
)
{
directInteractionList[cellJ].append(cellI);
@ -109,18 +118,16 @@ void Foam::directInteractionList::buildDirectInteractionList
Info<< tab << "Point-Face, Edge-Edge direct interaction list build."
<< endl;
forAll (mesh.points(), p)
forAll(mesh.points(), p)
{
forAll(mesh.faces(), f)
{
if(il_.testPointFaceDistance(p, f))
if (il_.testPointFaceDistance(p, f))
{
const labelList& pCells(mesh.pointCells()[p]);
const label cellO(mesh.faceOwner()[f]);
const label cellN(mesh.faceNeighbour()[f]);
forAll(pCells, pC)
{
const label cellI(pCells[pC]);
@ -131,8 +138,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellI],
cellO) == -1
findIndex
(
directInteractionList[cellI],
cellO
)
==
-1
)
{
directInteractionList[cellI].append(cellO);
@ -143,8 +155,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellO],
cellI) == -1
findIndex
(
directInteractionList[cellO],
cellI
)
==
-1
)
{
directInteractionList[cellO].append(cellI);
@ -156,12 +173,19 @@ void Foam::directInteractionList::buildDirectInteractionList
// boundary faces will not have neighbour
// information
const label cellN(mesh.faceNeighbour()[f]);
if (cellN > cellI)
{
if
(
findIndex(directInteractionList[cellI],
cellN) == -1
findIndex
(
directInteractionList[cellI],
cellN
)
==
-1
)
{
directInteractionList[cellI].append(cellN);
@ -172,8 +196,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellN],
cellI) == -1
findIndex
(
directInteractionList[cellN],
cellI
)
==
-1
)
{
directInteractionList[cellN].append(cellI);
@ -187,7 +216,7 @@ void Foam::directInteractionList::buildDirectInteractionList
label edgeJIndex;
forAll (mesh.edges(), edgeIIndex)
forAll(mesh.edges(), edgeIIndex)
{
const edge& eI(mesh.edges()[edgeIIndex]);
@ -218,8 +247,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellI],
cellJ) == -1
findIndex
(
directInteractionList[cellI],
cellJ
)
==
-1
)
{
directInteractionList[cellI].append(cellJ);
@ -230,8 +264,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
findIndex(directInteractionList[cellJ],
cellI) == -1
findIndex
(
directInteractionList[cellJ],
cellI
)
==
-1
)
{
directInteractionList[cellJ].append(cellI);
@ -272,11 +311,11 @@ Foam::directInteractionList::directInteractionList
labelListList(il.mesh().nCells()),
il_(il)
{
if((*this).size() > 1)
if ((*this).size() > 1)
{
buildDirectInteractionList(pointPointListBuild);
}
else if((*this).size() == 1)
else if ((*this).size() == 1)
{
Info<< nl
<< "Single cell mesh, no direct interaction lists required."
@ -305,16 +344,4 @@ Foam::directInteractionList::~directInteractionList()
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Friend Functions * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
// ************************************************************************* //

11
src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -59,6 +59,7 @@ class directInteractionList
const interactionLists& il_;
// Private Member Functions
void buildDirectInteractionList
@ -72,6 +73,7 @@ class directInteractionList
//- Disallow default bitwise assignment
void operator=(const directInteractionList&);
public:
// Constructors
@ -89,6 +91,7 @@ public:
const interactionLists& il
);
// Destructor
~directInteractionList();
@ -100,12 +103,6 @@ public:
inline const interactionLists& il() const;
// Check
// Edit
// Write
// IOstream Operators

7
src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::interactionLists& Foam::directInteractionList::il() const
@ -34,7 +32,4 @@ inline const Foam::interactionLists& Foam::directInteractionList::il() const
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

3
src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -342,6 +342,7 @@ bool Foam::interactionLists::testPointFaceDistance
);
}
bool Foam::interactionLists::testPointFaceDistance
(
const vector& p,

9
src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -52,7 +52,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class interactionLists Declaration
Class interactionLists Declaration
\*---------------------------------------------------------------------------*/
class interactionLists
@ -71,6 +71,7 @@ class interactionLists
List<receivingReferralList> cellReceivingReferralLists_;
// Private Member Functions
//- Build referralLists which define how to send information
@ -83,6 +84,7 @@ class interactionLists
//- Disallow default bitwise assignment
void operator=(const interactionLists&);
public:
// Static data members
@ -90,6 +92,7 @@ public:
//- Tolerance for checking that faces on a patch segment
static scalar transTol;
// Constructors
//- Construct and create all information from the mesh
@ -103,6 +106,7 @@ public:
//- Construct from file
interactionLists(const polyMesh& mesh);
// Destructor
~interactionLists();
@ -177,6 +181,7 @@ public:
const labelList& segmentPoints
) const;
// Access
inline const polyMesh& mesh() const;

2
src/lagrangian/molecularDynamics/molecule/interactionLists/interactionListsI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

8
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -143,7 +143,7 @@ bool operator==
Foam::Istream& Foam::operator>>(Istream& is, receivingReferralList& rRL)
{
is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
is.check
(
@ -160,7 +160,7 @@ Foam::Ostream& Foam::operator<<
const receivingReferralList& rRL
)
{
os << rRL.sourceProc() << token::SPACE
os << rRL.sourceProc() << token::SPACE
<< static_cast< const labelListList& >(rRL);
os.check
@ -171,7 +171,5 @@ Foam::Ostream& Foam::operator<<
return os;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

2
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

7
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::receivingReferralList::sourceProc() const
@ -46,7 +44,4 @@ inline bool operator!=
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

8
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -145,7 +145,7 @@ Foam::Istream& Foam::operator>>
sendingReferralList& sRL
)
{
is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
is.check("Istream& operator<<(Istream& f, const sendingReferralList& sRL");
@ -159,7 +159,7 @@ Foam::Ostream& Foam::operator<<
const sendingReferralList& rL
)
{
os << rL.destinationProc() << token::SPACE
os << rL.destinationProc() << token::SPACE
<< static_cast< const labelList& >(rL);
os.check("Ostream& operator<<(Ostream& f, const sendingReferralList& rL");
@ -168,6 +168,4 @@ Foam::Ostream& Foam::operator<<
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

2
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

6
src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::sendingReferralList::destinationProc() const
@ -46,6 +44,4 @@ inline bool operator!=
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

22
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -38,7 +38,7 @@ void referredCell::setConstructionData
const label sourceCell
)
{
// * * * * * * * * * * * Points * * * * * * * * * * *
// Points
const labelList& points = mesh.cellPoints()[sourceCell];
@ -51,7 +51,8 @@ void referredCell::setConstructionData
vertexPositions_ = referPositions(sourceCellVertices);
// * * * * * * * * * * * Edges * * * * * * * * * * *
// Edges
const labelList& edges = mesh.cellEdges()[sourceCell];
@ -64,7 +65,8 @@ void referredCell::setConstructionData
locallyMapEdgeList(points, sourceCellEdges);
// * * * * * * * * * * * Faces * * * * * * * * * * *
// Faces
labelList faces(mesh.cells()[sourceCell]);
@ -383,8 +385,8 @@ bool referredCell::duplicate(const referredCell& refCellDupl) const
return
(
sourceProc_ == refCellDupl.sourceProc()
&& sourceCell_ == refCellDupl.sourceCell()
&& mag(offset_ - refCellDupl.offset()) < interactionLists::transTol
&& sourceCell_ == refCellDupl.sourceCell()
&& mag(offset_ - refCellDupl.offset()) < interactionLists::transTol
);
}
@ -394,8 +396,8 @@ bool referredCell::duplicate(const label procNo,const label nCells) const
return
(
sourceProc_ == procNo
&& sourceCell_ < nCells
&& mag(offset_) < interactionLists::transTol
&& sourceCell_ < nCells
&& mag(offset_) < interactionLists::transTol
);
}
@ -405,7 +407,7 @@ bool referredCell::duplicate(const label procNo,const label nCells) const
Istream& operator>>(Istream& is, referredCell& rC)
{
is >> rC.sourceProc_
is >> rC.sourceProc_
>> rC.sourceCell_
>> rC.vertexPositions_
>> rC.edges_
@ -424,7 +426,7 @@ Istream& operator>>(Istream& is, referredCell& rC)
Ostream& operator<<(Ostream& os, const referredCell& rC)
{
os << rC.sourceProc()
os << rC.sourceProc()
<< token::SPACE << rC.sourceCell()
<< token::SPACE << rC.vertexPositions()
<< token::SPACE << rC.edges()

4
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -53,7 +53,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class referredCell Declaration
Class referredCell Declaration
\*---------------------------------------------------------------------------*/
class referredCell

2
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCellI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

129
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -357,7 +357,7 @@ void Foam::referredCellList::buildReferredCellList
label iterationNo = 0;
while(cellsReferredThisIteration)
while (cellsReferredThisIteration)
{
label refIntListStartSize = referredInteractionList.size();
@ -499,7 +499,10 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
) == -1)
)
==
-1
)
{
meshPointsOnThisSegment.append(facePoint);
}
@ -610,18 +613,20 @@ void Foam::referredCellList::buildReferredCellList
forAll(referredCellsFoundInRange,cFIR)
{
referredCell& existingRefCell = referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredCell& existingRefCell =
referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredCell cellToReRefer = existingRefCell.reRefer
(
patch.faceCentres()[0],
patch.faceCentres()[patch.size()/2],
patch.faceNormals()[0],
patch.faceNormals()[patch.size()/2]
);
referredCell cellToReRefer =
existingRefCell.reRefer
(
patch.faceCentres()[0],
patch.faceCentres()[patch.size()/2],
patch.faceNormals()[0],
patch.faceNormals()[patch.size()/2]
);
// Test all existing referred and real cells to check
// duplicates are not being made or cells aren't being
@ -705,7 +710,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshEdgesOnThisSegment,
faceEdge
) == -1
)
==
-1
)
{
meshEdgesOnThisSegment.append(faceEdge);
@ -724,7 +731,10 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
) == -1)
)
==
-1
)
{
meshPointsOnThisSegment.append(facePoint);
}
@ -823,28 +833,30 @@ void Foam::referredCellList::buildReferredCellList
referredInteractionList.shrink();
referredCellsFoundInRange =
il_.referredCellsInRangeOfSegment
(
referredInteractionList,
meshFacesOnThisSegment,
meshEdgesOnThisSegment,
meshPointsOnThisSegment
);
il_.referredCellsInRangeOfSegment
(
referredInteractionList,
meshFacesOnThisSegment,
meshEdgesOnThisSegment,
meshPointsOnThisSegment
);
forAll(referredCellsFoundInRange,cFIR)
{
referredCell& existingRefCell = referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredCell& existingRefCell =
referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredCell cellToReRefer = existingRefCell.reRefer
(
patch.faceCentres()[patch.size()/2],
patch.faceCentres()[0],
patch.faceNormals()[patch.size()/2],
patch.faceNormals()[0]
);
referredCell cellToReRefer =
existingRefCell.reRefer
(
patch.faceCentres()[patch.size()/2],
patch.faceCentres()[0],
patch.faceNormals()[patch.size()/2],
patch.faceNormals()[0]
);
// Test all existing referred and real cells to check
// duplicates are not being made or cells aren't being
@ -901,15 +913,15 @@ void Foam::referredCellList::buildReferredCellList
forAll(procPatches,pP)
{
const processorPolyPatch& patch =
refCast<const processorPolyPatch>
(
mesh.boundaryMesh()[procPatches[pP]]
);
refCast<const processorPolyPatch>
(
mesh.boundaryMesh()[procPatches[pP]]
);
DynamicList<referredCell> referredCellsToTransfer;
const vectorList& neighbFaceCentres =
allNeighbourFaceCentres[pP];
allNeighbourFaceCentres[pP];
const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
@ -971,7 +983,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshEdgesOnThisSegment,
faceEdge
) == -1
)
==
-1
)
{
meshEdgesOnThisSegment.append(faceEdge);
@ -990,7 +1004,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
) == -1
)
==
-1
)
{
meshPointsOnThisSegment.append(facePoint);
@ -1032,7 +1048,7 @@ void Foam::referredCellList::buildReferredCellList
forAll(realCellsFoundInRange,cFIR)
{
const label realCell =
realCellsFoundInRange[cFIR];
realCellsFoundInRange[cFIR];
referredCell cellToRefer
(
@ -1074,19 +1090,20 @@ void Foam::referredCellList::buildReferredCellList
forAll(referredCellsFoundInRange,cFIR)
{
referredCell& existingRefCell =
referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredInteractionList
[
referredCellsFoundInRange[cFIR]
];
referredCell cellToReRefer = existingRefCell.reRefer
(
patch.faceCentres()[faceT],
neighbFaceCentres[faceT],
patch.faceNormals()[faceT],
neighbFaceAreas[faceT]
/(mag(neighbFaceAreas[faceT]) + VSMALL)
);
referredCell cellToReRefer =
existingRefCell.reRefer
(
patch.faceCentres()[faceT],
neighbFaceCentres[faceT],
patch.faceNormals()[faceT],
neighbFaceAreas[faceT]
/(mag(neighbFaceAreas[faceT]) + VSMALL)
);
referredCellsToTransfer.append(cellToReRefer);
}
@ -1409,6 +1426,7 @@ void Foam::referredCellList::buildReferredCellList
}
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::referredCellList::referredCellList
@ -1557,7 +1575,4 @@ void Foam::referredCellList::referMolecules
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

7
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -48,7 +48,7 @@ namespace Foam
class interactionLists;
/*---------------------------------------------------------------------------*\
Class referredCellList Declaration
Class referredCellList Declaration
\*---------------------------------------------------------------------------*/
class referredCellList
@ -59,7 +59,8 @@ class referredCellList
const interactionLists& il_;
// Private Member Functions
// Private Member Functions
void buildReferredCellList
(

2
src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellListI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

4
src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -83,6 +83,4 @@ Foam::Ostream& Foam::operator<<
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

4
src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,7 +45,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class referredMolecule Declaration
Class referredMolecule Declaration
\*---------------------------------------------------------------------------*/
class referredMolecule

5
src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,6 +45,7 @@ Foam::referredMolecule::sitePositions() const
return sitePositions_;
}
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
inline bool Foam::operator==
@ -71,6 +72,4 @@ inline bool Foam::operator!=
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

100
src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
View File

@ -5,68 +5,68 @@ if (runTime.outputTime())
\*-----------------------------------------------------------------------*/
scalarField totalRhoN_sum(mesh.nCells(), 0.0);
forAll (allSpeciesRhoN, rN)
{
allSpeciesRhoN[rN].internalField() =
allSpeciesN_RU[rN]
/mesh.cellVolumes()
/nAveragingSteps;
totalRhoN_sum += allSpeciesRhoN[rN].internalField();
}
totalRhoN.internalField() = totalRhoN_sum;
/*-----------------------------------------------------------------------*\
Mass density
\*-----------------------------------------------------------------------*/
scalarField totalRhoM_sum(mesh.nCells(), 0.0);
forAll (allSpeciesRhoM, rM)
{
allSpeciesRhoM[rM].internalField() =
allSpeciesM_RU[rM]
/mesh.cellVolumes()
/nAveragingSteps;
totalRhoM_sum += allSpeciesRhoM[rM].internalField();
}
totalRhoM.internalField() = totalRhoM_sum;
/*-----------------------------------------------------------------------*\
Bulk velocity
\*-----------------------------------------------------------------------*/
vectorField totalMomentum_sum(mesh.nCells(), vector::zero);
scalarField totalMass_sum(mesh.nCells(), 0.0);
forAll (allSpeciesVelocity, v)
{
// A check for 1/0 molecules is required.
vectorField& singleSpeciesVelocity
(
allSpeciesVelocity[v].internalField()
);
forAll(singleSpeciesVelocity, sSV)
{
if(allSpeciesN_RU[v][sSV])
if (allSpeciesN_RU[v][sSV])
{
singleSpeciesVelocity[sSV] =
singleSpeciesVelocity[sSV] =
allSpeciesVelocitySum_RU[v][sSV]
/allSpeciesN_RU[v][sSV];
totalMomentum_sum[sSV] +=
allSpeciesM_RU[v][sSV]
/allSpeciesN_RU[v][sSV]
*allSpeciesVelocitySum_RU[v][sSV];
totalMass_sum[sSV] += allSpeciesM_RU[v][sSV];
}
else
@ -75,10 +75,10 @@ if (runTime.outputTime())
}
}
}
forAll(totalVelocity.internalField(), tV)
{
if(totalMass_sum[tV] > VSMALL)
if (totalMass_sum[tV] > VSMALL)
{
totalVelocity.internalField()[tV] =
totalMomentum_sum[tV]
@ -90,34 +90,33 @@ if (runTime.outputTime())
vector::zero;
}
}
/*-----------------------------------------------------------------------*\
Kinetic temperature
\*-----------------------------------------------------------------------*/
scalarField totalTemperatureVTerms_sum(mesh.nCells(), 0.0);
scalarField totalN_sum(mesh.nCells(), 0.0);
forAll (allSpeciesTemperature, t)
{
// A check for 1/0 molecules is required.
scalarField& singleSpeciesTemp
(
allSpeciesTemperature[t].internalField()
);
forAll(singleSpeciesTemp, sST)
{
if(allSpeciesN_RU[t][sST])
if (allSpeciesN_RU[t][sST])
{
singleSpeciesTemp[sST] =
singleSpeciesTemp[sST] =
allSpeciesM_RU[t][sST]
/allSpeciesN_RU[t][sST]
/(3.0 * moleculeCloud::kb * allSpeciesN_RU[t][sST])
*
(
*(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
-
(
@ -127,14 +126,13 @@ if (runTime.outputTime())
)
/allSpeciesN_RU[t][sST]
);
totalTemperatureVTerms_sum[sST] +=
allSpeciesM_RU[t][sST]
/allSpeciesN_RU[t][sST]
*
(
/allSpeciesN_RU[t][sST]
*(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
-
-
(
allSpeciesVelocitySum_RU[t][sST]
&
@ -142,7 +140,7 @@ if (runTime.outputTime())
)
/allSpeciesN_RU[t][sST]
);
totalN_sum[sST] += allSpeciesN_RU[t][sST];
}
else
@ -151,7 +149,7 @@ if (runTime.outputTime())
}
}
}
forAll(totalTemperature.internalField(), tT)
{
if(totalN_sum[tT] > 0)
@ -165,41 +163,39 @@ if (runTime.outputTime())
totalTemperature.internalField()[tT] = 0.0;
}
}
/*-----------------------------------------------------------------------*\
Mean kinetic energy
\*-----------------------------------------------------------------------*/
scalarField totalKE_sum(mesh.nCells(), 0.0);
forAll (allSpeciesMeanKE, mKE)
{
// A check for 1/0 molecules is required.
scalarField& singleSpeciesMeanKE
(
allSpeciesMeanKE[mKE].internalField()
);
forAll(singleSpeciesMeanKE, sSMKE)
{
if(allSpeciesN_RU[mKE][sSMKE])
{
singleSpeciesMeanKE[sSMKE] =
singleSpeciesMeanKE[sSMKE] =
allSpeciesM_RU[mKE][sSMKE]
/allSpeciesN_RU[mKE][sSMKE]
/(2.0 * allSpeciesN_RU[mKE][sSMKE])
*
(
/allSpeciesN_RU[mKE][sSMKE]
/(2.0*allSpeciesN_RU[mKE][sSMKE])
*(
allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
);
totalKE_sum[sSMKE] +=
allSpeciesM_RU[mKE][sSMKE]
/allSpeciesN_RU[mKE][sSMKE]
/2.0
*
(
*(
allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
);
}
@ -209,7 +205,7 @@ if (runTime.outputTime())
}
}
}
forAll(totalMeanKE.internalField(), tMKE)
{
if(totalN_sum[tMKE] > 0)

21
src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -60,18 +60,15 @@ if (mesh.time().timeIndex() % pacf.sampleSteps() == 0)
{
p.x() +=
mol().mass() * mol().U().y() * mol().U().z()
+
0.5 * mol().rf().yz();
+ 0.5*mol().rf().yz();
p.y() +=
mol().mass() * mol().U().z() * mol().U().x()
+
0.5 * mol().rf().zx();
+ 0.5*mol().rf().zx();
p.z() +=
mol().mass() * mol().U().x() * mol().U().y()
+
0.5 * mol().rf().xy();
+ 0.5*mol().rf().xy();
}
pacf.calculateCorrelationFunction(p);
@ -93,12 +90,10 @@ if (mesh.time().timeIndex() % hfacf.sampleSteps() == 0)
{
s +=
(
0.5 * mol().mass() * magSqr(mol().U())
+
mol().potentialEnergy()
) * mol().U()
+
0.5 * ( mol().rf() & mol().U() );
0.5*mol().mass()*magSqr(mol().U())
+ mol().potentialEnergy()
)*mol().U()
+ 0.5*(mol().rf() & mol().U());
}
hfacf.calculateCorrelationFunction(s);

10
src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -37,7 +37,7 @@ if (writeVacf)
}
}
Info << "Diffusion coefficient = "
Info<< "Diffusion coefficient = "
<< vacf.integral() << endl;
if (writePacf)
@ -57,13 +57,13 @@ Info<< "Viscosity = "
<< pacf.integral()/averageTemperature/moleculeCloud::kb/meshVolume
<< endl;
if(writeHFacf)
if (writeHFacf)
{
OFstream hfacfFile
(
runTime.path()/ + "hfacf"
);
if (!hfacf.writeAveraged(hfacfFile))
{
FatalErrorIn(args.executable())
@ -73,7 +73,7 @@ if(writeHFacf)
}
}
Info << "Thermal conductivity = "
Info<< "Thermal conductivity = "
<< hfacf.integral()
/averageTemperature
/averageTemperature

2
src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

12
src/lagrangian/molecularDynamics/molecule/mdTools/md.H
View File

@ -1,11 +1,9 @@
#ifndef md_H
#define md_H
# include "potential.H"
# include "moleculeCloud.H"
# include "correlationFunction.H"
# include "distribution.H"
# include "reducedUnits.H"
#include "potential.H"
#include "moleculeCloud.H"
#include "correlationFunction.H"
#include "distribution.H"
#include "reducedUnits.H"
#endif

47
src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -52,6 +52,8 @@ scalar singleStepTotalrDotf = 0.0;
label singleStepNMols = molecules.size();
label singleStepDOFs = 0;
{
IDLList<molecule>::iterator mol(molecules.begin());
@ -85,9 +87,11 @@ label singleStepNMols = molecules.size();
{
label molId = mol().id();
scalar molMass(molecules.constProps(molId).mass());
const molecule::constantProperties cP(molecules.constProps(molId));
const diagTensor& molMoI(molecules.constProps(molId).momentOfInertia());
scalar molMass(cP.mass());
const diagTensor& molMoI(cP.momentOfInertia());
const vector& molV(mol().v());
@ -112,6 +116,8 @@ label singleStepNMols = molecules.size();
singleStepTotalPE += mol().potentialEnergy();
singleStepTotalrDotf += tr(mol().rf());
singleStepDOFs += cP.degreesOfFreedom();
}
}
@ -134,50 +140,53 @@ if (Pstream::parRun())
reduce(singleStepTotalrDotf, sumOp<scalar>());
reduce(singleStepNMols, sumOp<label>());
reduce(singleStepDOFs, sumOp<label>());
}
if (singleStepNMols)
{
Info<< "Number of mols in system = "
Info<< "Number of molecules in system = "
<< singleStepNMols << nl
<< "Overall number density = "
<< singleStepNMols/meshVolume << nl
<< "Overall mass density = "
<< singleStepTotalMass/meshVolume << nl
<< "Average linear momentum per mol = "
<< "Average linear momentum per molecule = "
<< singleStepTotalLinearMomentum/singleStepNMols << ' '
<< mag(singleStepTotalLinearMomentum)/singleStepNMols << nl
<< "Average angular momentum per mol = "
<< "Average angular momentum per molecule = "
<< singleStepTotalAngularMomentum << ' '
<< mag(singleStepTotalAngularMomentum)/singleStepNMols << nl
<< "Maximum |velocity| = "
<< singleStepMaxVelocityMag << nl
<< "Average linear KE per mol = "
<< "Average linear KE per molecule = "
<< singleStepTotalLinearKE/singleStepNMols << nl
<< "Average angular KE per mol = "
<< "Average angular KE per molecule = "
<< singleStepTotalAngularKE/singleStepNMols << nl
<< "Average PE per mol = "
<< "Average PE per molecule = "
<< singleStepTotalPE/singleStepNMols << nl
<< "Average TE per mol = "
<< "Average TE per molecule = "
<<
(
singleStepTotalLinearKE
+ singleStepTotalAngularKE
+ singleStepTotalPE
+ singleStepTotalAngularKE
+ singleStepTotalPE
)
/singleStepNMols
<< endl;
// Info << singleStepNMols << " "
// // << singleStepTotalMomentum/singleStepTotalMass << " "
// << singleStepMaxVelocityMag << " "
// << singleStepTotalKE/singleStepNMols << " "
// << singleStepTotalPE/singleStepNMols << " "
// << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << endl;
// Info << singleStepNMols << " "
// << singleStepTotalMomentum/singleStepTotalMass << " "
// << singleStepMaxVelocityMag << " "
// << singleStepTotalKE/singleStepNMols << " "
// << singleStepTotalPE/singleStepNMols << " "
// << (singleStepTotalKE + singleStepTotalPE)
// /singleStepNMols << endl;
}
else
{
Info << "No molecules in system" << endl;
Info<< "No molecules in system" << endl;
}

8
src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
View File

@ -3,24 +3,24 @@ if (runTime.outputTime())
allSpeciesN_RU = List< scalarField >
(
molecules.potential().nIds(),
scalarField (mesh.nCells(), 0.0)
scalarField(mesh.nCells(), 0.0)
);
allSpeciesM_RU = List< scalarField >
(
molecules.potential().nIds(),
scalarField (mesh.nCells(), 0.0)
scalarField(mesh.nCells(), 0.0)
);
allSpeciesVelocitySum_RU = List< vectorField >
(
molecules.potential().nIds(),
vectorField (mesh.nCells(), vector::zero)
vectorField(mesh.nCells(), vector::zero)
);
allSpeciesVelocityMagSquaredSum_RU = List< scalarField >
(
molecules.potential().nIds(),
scalarField (mesh.nCells(), 0.0)
scalarField(mesh.nCells(), 0.0)
);
}

26
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -47,17 +47,17 @@ accumulatedTotalrDotfSum += singleStepTotalrDotf;
accumulatedNMols += singleStepNMols;
accumulatedDOFs += singleStepDOFs;
if (runTime.outputTime())
{
// calculate averages
if (accumulatedNMols)
{
Info << "calculating averages" << endl;
averageTemperature =
(
2.0/(6.0 * moleculeCloud::kb * accumulatedNMols)
2.0/(moleculeCloud::kb * accumulatedDOFs)
*
(
accumulatedTotalLinearKE + accumulatedTotalAngularKE
@ -79,27 +79,20 @@ if (runTime.outputTime())
meshVolume
);
// output values
Info << "----------------------------------------" << nl
<< "Averaged properties" << nl
<< "Average |velocity| = "
<< mag(accumulatedTotalLinearMomentum)/accumulatedTotalMass
<< " m/s" << nl
<< "Average temperature = "
<< averageTemperature << " K" << nl
<< "Average pressure = "
<< averagePressure << " N/m^2" << nl
<< mag(accumulatedTotalLinearMomentum)/accumulatedTotalMass << nl
<< "Average temperature = " << averageTemperature << nl
<< "Average pressure = " << averagePressure << nl
<< "----------------------------------------" << endl;
}
else
{
Info << "Not averaging temperature and pressure: "
Info<< "Not averaging temperature and pressure: "
<< "no molecules in system" << endl;
}
// reset counters
accumulatedTotalLinearMomentum = vector::zero;
accumulatedTotalMass = 0.0;
@ -113,6 +106,9 @@ if (runTime.outputTime())
accumulatedTotalrDotfSum = 0.0;
accumulatedNMols = 0;
accumulatedDOFs = 0;
}
// ************************************************************************* //

4
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -44,6 +44,8 @@ scalar accumulatedTotalrDotfSum = 0.0;
label accumulatedNMols = 0;
label accumulatedDOFs = 0;
scalar averageTemperature = 0.0;
scalar averagePressure = 0.0;

2
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
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) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

11
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) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -82,6 +82,8 @@ public:
Field<vector> siteReferencePositions_;
List<scalar> siteMasses_;
List<scalar> siteCharges_;
List<label> siteIds_;
@ -106,6 +108,7 @@ public:
bool linearMoleculeTest() const;
public:
inline constantProperties();
@ -117,6 +120,8 @@ public:
inline const Field<vector>& siteReferencePositions() const;
inline const List<scalar>& siteMasses() const;
inline const List<scalar>& siteCharges() const;
inline const List<label>& siteIds() const;
@ -137,6 +142,8 @@ public:
inline bool pointMolecule() const;
inline label degreesOfFreedom() const;
inline scalar mass() const;
inline label nSites() const;
@ -208,6 +215,7 @@ private:
List<vector> sitePositions_;
// Private Member Functions
tensor rotationTensorX(scalar deltaT) const;
@ -216,6 +224,7 @@ private:
tensor rotationTensorZ(scalar deltaT) const;
public:
friend class Cloud<molecule>;

67
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) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -29,6 +29,7 @@ License
inline Foam::molecule::constantProperties::constantProperties()
:
siteReferencePositions_(Field<vector>(0)),
siteMasses_(List<scalar>(0)),
siteCharges_(List<scalar>(0)),
siteIds_(List<label>(0)),
pairPotentialSites_(List<bool>(false)),
@ -44,6 +45,7 @@ inline Foam::molecule::constantProperties::constantProperties
)
:
siteReferencePositions_(dict.lookup("siteReferencePositions")),
siteMasses_(dict.lookup("siteMasses")),
siteCharges_(dict.lookup("siteCharges")),
siteIds_(List<word>(dict.lookup("siteIds")).size(), -1),
pairPotentialSites_(),
@ -59,9 +61,7 @@ inline Foam::molecule::constantProperties::constantProperties
List<word>(dict.lookup("pairPotentialSiteIds"))
);
scalarList siteMasses(dict.lookup("siteMasses"));
mass_ = sum(siteMasses);
mass_ = sum(siteMasses_);
vector centreOfMass(vector::zero);
@ -70,7 +70,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
centreOfMass += siteReferencePositions_[i]*siteMasses[i];
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@ -106,7 +106,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
centreOfMass += siteReferencePositions_[i]*siteMasses[i];
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@ -119,10 +119,8 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
momOfInertia += siteMasses[i]*diagTensor
(
0, p.x()*p.x(), p.x()*p.x()
);
momOfInertia +=
siteMasses_[i]*diagTensor(0, p.x()*p.x(), p.x()*p.x());
}
momentOfInertia_ = diagTensor
@ -144,7 +142,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
momOfInertia += siteMasses[i]*tensor
momOfInertia += siteMasses_[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
@ -156,8 +154,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
FatalErrorIn("molecule::constantProperties::constantProperties")
<< "An eigenvalue of the inertia tensor is zero, the molecule "
<< dict.name()
<< " is not a valid 6DOF shape."
<< dict.name() << " is not a valid 6DOF shape."
<< nl << abort(FatalError);
}
@ -172,7 +169,7 @@ inline Foam::molecule::constantProperties::constantProperties
// global axes
tensor Q =
vector(1,0,0)*e.x() + vector(0,1,0)*e.y() + vector(0,0,1)*e.z();
vector(1,0,0)*e.x() + vector(0,1,0)*e.y() + vector(0,0,1)*e.z();
// Transform the site positions
@ -187,7 +184,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
centreOfMass += siteReferencePositions_[i]*siteMasses[i];
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@ -203,7 +200,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
momOfInertia += siteMasses[i]*tensor
momOfInertia += siteMasses_[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
@ -337,6 +334,13 @@ Foam::molecule::constantProperties::siteReferencePositions() const
}
inline const Foam::List<Foam::scalar>&
Foam::molecule::constantProperties::siteMasses() const
{
return siteMasses_;
}
inline const Foam::List<Foam::scalar>&
Foam::molecule::constantProperties::siteCharges() const
{
@ -372,7 +376,7 @@ inline bool Foam::molecule::constantProperties::pairPotentialSite
{
label s = findIndex(siteIds_, sId);
if(s == -1)
if (s == -1)
{
FatalErrorIn("moleculeI.H") << nl
<< sId << " site not found."
@ -396,10 +400,12 @@ inline bool Foam::molecule::constantProperties::electrostaticSite
{
label s = findIndex(siteIds_, sId);
if(s == -1)
if (s == -1)
{
FatalErrorIn("moleculeI.H") << nl
<< sId << " site not found."
FatalErrorIn
(
"molecule::constantProperties::electrostaticSite(label)"
) << sId << " site not found."
<< nl << abort(FatalError);
}
@ -416,7 +422,7 @@ Foam::molecule::constantProperties::momentOfInertia() const
inline bool Foam::molecule::constantProperties::linearMolecule() const
{
return (momentOfInertia_.xx() < 0);
return ((momentOfInertia_.xx() < 0) && (momentOfInertia_.yy() > 0));
}
@ -426,6 +432,23 @@ inline bool Foam::molecule::constantProperties::pointMolecule() const
}
inline Foam::label Foam::molecule::constantProperties::degreesOfFreedom() const
{
if (linearMolecule())
{
return 5;
}
else if (pointMolecule())
{
return 3;
}
else
{
return 6;
}
}
inline Foam::scalar Foam::molecule::constantProperties::mass() const
{
return mass_;
@ -592,6 +615,4 @@ inline Foam::label Foam::molecule::id() const
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

112
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) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -55,16 +55,16 @@ Foam::molecule::molecule
{
if (is.format() == IOstream::ASCII)
{
is >> Q_;
is >> v_;
is >> a_;
is >> pi_;
is >> tau_;
is >> siteForces_;
is >> sitePositions_;
is >> specialPosition_;
is >> Q_;
is >> v_;
is >> a_;
is >> pi_;
is >> tau_;
is >> siteForces_;
is >> sitePositions_;
is >> specialPosition_;
potentialEnergy_ = readScalar(is);
is >> rf_;
is >> rf_;
special_ = readLabel(is);
id_ = readLabel(is);
}
@ -74,18 +74,18 @@ Foam::molecule::molecule
(
reinterpret_cast<char*>(&Q_),
sizeof(Q_)
+ sizeof(v_)
+ sizeof(a_)
+ sizeof(pi_)
+ sizeof(tau_)
+ sizeof(specialPosition_)
+ sizeof(potentialEnergy_)
+ sizeof(rf_)
+ sizeof(special_)
+ sizeof(id_)
+ sizeof(v_)
+ sizeof(a_)
+ sizeof(pi_)
+ sizeof(tau_)
+ sizeof(specialPosition_)
+ sizeof(potentialEnergy_)
+ sizeof(rf_)
+ sizeof(special_)
+ sizeof(id_)
);
is >> siteForces_ >> sitePositions_;
is >> siteForces_ >> sitePositions_;
}
}
@ -169,6 +169,38 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
IOField<label> special(mC.fieldIOobject("special", IOobject::NO_READ), np);
IOField<label> id(mC.fieldIOobject("id", IOobject::NO_READ), np);
// Post processing fields
IOField<vector> piGlobal
(
mC.fieldIOobject("piGlobal", IOobject::NO_READ),
np
);
IOField<vector> tauGlobal
(
mC.fieldIOobject("tauGlobal", IOobject::NO_READ),
np
);
IOField<vector> orientation1
(
mC.fieldIOobject("orientation1", IOobject::NO_READ),
np
);
IOField<vector> orientation2
(
mC.fieldIOobject("orientation2", IOobject::NO_READ),
np
);
IOField<vector> orientation3
(
mC.fieldIOobject("orientation3", IOobject::NO_READ),
np
);
label i = 0;
forAllConstIter(moleculeCloud, mC, iter)
{
@ -182,6 +214,14 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
specialPosition[i] = mol.specialPosition_;
special[i] = mol.special_;
id[i] = mol.id_;
piGlobal[i] = mol.Q_ & mol.pi_;
tauGlobal[i] = mol.Q_ & mol.tau_;
orientation1[i] = mol.Q_ & vector(1,0,0);
orientation2[i] = mol.Q_ & vector(0,1,0);
orientation3[i] = mol.Q_ & vector(0,0,1);
i++;
}
@ -193,6 +233,18 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
specialPosition.write();
special.write();
id.write();
piGlobal.write();
tauGlobal.write();
orientation1.write();
orientation2.write();
orientation3.write();
mC.writeXYZ
(
mC.mesh().time().timePath() + "/lagrangian" + "/moleculeCloud.xmol"
);
}
@ -225,17 +277,17 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
(
reinterpret_cast<const char*>(&mol.Q_),
sizeof(mol.Q_)
+ sizeof(mol.v_)
+ sizeof(mol.a_)
+ sizeof(mol.pi_)
+ sizeof(mol.tau_)
+ sizeof(mol.specialPosition_)
+ sizeof(mol.potentialEnergy_)
+ sizeof(mol.rf_)
+ sizeof(mol.special_)
+ sizeof(mol.id_)
+ sizeof(mol.v_)
+ sizeof(mol.a_)
+ sizeof(mol.pi_)
+ sizeof(mol.tau_)
+ sizeof(mol.specialPosition_)
+ sizeof(mol.potentialEnergy_)
+ sizeof(mol.rf_)
+ sizeof(mol.special_)
+ sizeof(mol.id_)
);
os << mol.siteForces_ << mol.sitePositions_;
os << mol.siteForces_ << mol.sitePositions_;
}
// Check state of Ostream

44
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) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -928,7 +928,6 @@ void Foam::moleculeCloud::initialiseMolecules
n++;
}
}
}
}
@ -1025,6 +1024,21 @@ void Foam::moleculeCloud::createMolecule
}
Foam::label Foam::moleculeCloud::nSites() const
{
label n = 0;
const_iterator mol(this->begin());
for (mol = this->begin(); mol != this->end(); ++mol)
{
n += constProps(mol().id()).nSites();
}
return n;
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::moleculeCloud::moleculeCloud
@ -1158,4 +1172,30 @@ void Foam::moleculeCloud::writeFields() const
}
void Foam::moleculeCloud::writeXYZ(const fileName& fName) const
{
OFstream str(fName);
str << nSites() << nl << "moleculeCloud site positions in angstroms" << nl;
const_iterator mol(this->begin());
for (mol = this->begin(); mol != this->end(); ++mol)
{
const molecule::constantProperties& cP = constProps(mol().id());
forAll(mol().sitePositions(), i)
{
const point& sP = mol().sitePositions()[i];
str << pot_.siteIdList()[cP.siteIds()[i]]
<< ' ' << sP.x()*1e10
<< ' ' << sP.y()*1e10
<< ' ' << sP.z()*1e10
<< nl;
}
}
}
// ************************************************************************* //

19
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -44,6 +44,7 @@ SourceFiles
#include "interactionLists.H"
#include "labelVector.H"
#include "Random.H"
#include "fileName.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -51,7 +52,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class moleculeCloud Declaration
Class moleculeCloud Declaration
\*---------------------------------------------------------------------------*/
class moleculeCloud
@ -75,6 +76,7 @@ private:
Random rndGen_;
// Private Member Functions
void buildConstProps();
@ -131,6 +133,8 @@ private:
const vector& bulkVelocity
);
label nSites() const;
inline vector equipartitionLinearVelocity
(
scalar temperature,
@ -160,6 +164,7 @@ public:
static scalar vacuumPermittivity;
// Constructors
//- Construct given mesh and potential references
@ -177,8 +182,8 @@ public:
const IOdictionary& mdInitialiseDict
);
// Member Functions
// Member Functions
//- Evolve the molecules (move, calculate forces, control state etc)
void evolve();
@ -191,6 +196,7 @@ public:
const scalar measuredTemperature
);
// Access
inline const polyMesh& mesh() const;
@ -204,15 +210,18 @@ public:
inline const List<molecule::constantProperties> constProps() const;
inline const molecule::constantProperties&
constProps(label id) const;
constProps(label id) const;
inline Random& rndGen();
// Member Operators
//- Write fields
void writeFields() const;
void writeFields() const;
//- Write molecule sites in XYZ format
void writeXYZ(const fileName& fName) const;
};

163
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -32,9 +32,9 @@ inline void Foam::moleculeCloud::evaluatePair
molecule* molJ
)
{
const pairPotentialList& pairPot(pot_.pairPotentials());
const pairPotentialList& pairPot = pot_.pairPotentials();
const electrostaticPotential& electrostatic(pot_.electrostatic());
const pairPotential& electrostatic = pairPot.electrostatic();
label idI = molI->id();
@ -67,7 +67,7 @@ inline void Foam::moleculeCloud::evaluatePair
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
{
vector rsIsJ =
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
@ -75,8 +75,9 @@ inline void Foam::moleculeCloud::evaluatePair
{
scalar rsIsJMag = mag(rsIsJ);
vector fsIsJ = (rsIsJ/rsIsJMag)
*pairPot.force(idsI, idsJ, rsIsJMag);
vector fsIsJ =
(rsIsJ/rsIsJMag)
*pairPot.force(idsI, idsJ, rsIsJMag);
molI->siteForces()[sI] += fsIsJ;
@ -91,9 +92,18 @@ inline void Foam::moleculeCloud::evaluatePair
molJ->potentialEnergy() += 0.5*potentialEnergy;
molI->rf() += rsIsJ * fsIsJ;
vector rIJ = molI->position() - molJ->position();
molJ->rf() += rsIsJ * fsIsJ;
tensor virialContribution =
(rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
molI->rf() += virialContribution;
molJ->rf() += virialContribution;
// molI->rf() += rsIsJ * fsIsJ;
// molJ->rf() += rsIsJ * fsIsJ;
}
}
@ -104,7 +114,7 @@ inline void Foam::moleculeCloud::evaluatePair
scalar rsIsJMagSq = magSqr(rsIsJ);
if(pairPot.rCutMaxSqr(rsIsJMagSq))
if(rsIsJMagSq <= electrostatic.rCutSqr())
{
scalar rsIsJMag = mag(rsIsJ);
@ -112,38 +122,50 @@ inline void Foam::moleculeCloud::evaluatePair
scalar chargeJ = constPropJ.siteCharges()[sJ];
vector fsIsJ = (rsIsJ/rsIsJMag)
*chargeI*chargeJ*electrostatic.force(rsIsJMag);
vector fsIsJ =
(rsIsJ/rsIsJMag)
*chargeI*chargeJ*electrostatic.force(rsIsJMag);
molI->siteForces()[sI] += fsIsJ;
molJ->siteForces()[sJ] += -fsIsJ;
scalar potentialEnergy = chargeI*chargeJ
*electrostatic.energy(rsIsJMag);
scalar potentialEnergy =
chargeI*chargeJ
*electrostatic.energy(rsIsJMag);
molI->potentialEnergy() += 0.5*potentialEnergy;
molJ->potentialEnergy() += 0.5*potentialEnergy;
molI->rf() += rsIsJ * fsIsJ;
vector rIJ = molI->position() - molJ->position();
molJ->rf() += rsIsJ * fsIsJ;
tensor virialContribution =
(rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
molI->rf() += virialContribution;
molJ->rf() += virialContribution;
// molI->rf() += rsIsJ * fsIsJ;
// molJ->rf() += rsIsJ * fsIsJ;
}
}
}
}
}
inline void Foam::moleculeCloud::evaluatePair
(
molecule* molReal,
referredMolecule* molRef
)
{
const pairPotentialList& pairPot(pot_.pairPotentials());
const pairPotentialList& pairPot = pot_.pairPotentials();
const electrostaticPotential& electrostatic(pot_.electrostatic());
const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@ -176,16 +198,18 @@ inline void Foam::moleculeCloud::evaluatePair
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
{
vector rsRealsRef =
molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
molReal->sitePositions()[sReal]
- molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
if(pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
vector fsRealsRef = (rsRealsRef/rsRealsRefMag)
*pairPot.force(idsReal, idsRef, rsRealsRefMag);
vector fsRealsRef =
(rsRealsRef/rsRealsRefMag)
*pairPot.force(idsReal, idsRef, rsRealsRefMag);
molReal->siteForces()[sReal] += fsRealsRef;
@ -196,7 +220,14 @@ inline void Foam::moleculeCloud::evaluatePair
molReal->potentialEnergy() += 0.5*potentialEnergy;
molReal->rf() += rsRealsRef * fsRealsRef;
vector rRealRef = molReal->position() - molRef->position();
molReal->rf() +=
(rsRealsRef*fsRealsRef)
*(rsRealsRef & rRealRef)
/rsRealsRefMagSq;
// molReal->rf() += rsRealsRef * fsRealsRef;
}
}
@ -204,11 +235,12 @@ inline void Foam::moleculeCloud::evaluatePair
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
{
vector rsRealsRef =
molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
molReal->sitePositions()[sReal]
- molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
if(pairPot.rCutMaxSqr(rsRealsRefMagSq))
if (rsRealsRefMagSq <= electrostatic.rCutSqr())
{
scalar rsRealsRefMag = mag(rsRealsRef);
@ -216,18 +248,27 @@ inline void Foam::moleculeCloud::evaluatePair
scalar chargeRef = constPropRef.siteCharges()[sRef];
vector fsRealsRef = (rsRealsRef/rsRealsRefMag)
*chargeReal*chargeRef
*electrostatic.force(rsRealsRefMag);
vector fsRealsRef =
(rsRealsRef/rsRealsRefMag)
*chargeReal*chargeRef
*electrostatic.force(rsRealsRefMag);
molReal->siteForces()[sReal] += fsRealsRef;
scalar potentialEnergy = chargeReal*chargeRef
*electrostatic.energy(rsRealsRefMag);
scalar potentialEnergy =
chargeReal*chargeRef
*electrostatic.energy(rsRealsRefMag);
molReal->potentialEnergy() += 0.5*potentialEnergy;
molReal->rf() += rsRealsRef * fsRealsRef;
vector rRealRef = molReal->position() - molRef->position();
molReal->rf() +=
(rsRealsRef*fsRealsRef)
*(rsRealsRef & rRealRef)
/rsRealsRefMagSq;
// molReal->rf() += rsRealsRef * fsRealsRef;
}
}
}
@ -241,9 +282,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
molecule* molJ
) const
{
const pairPotentialList& pairPot(pot_.pairPotentials());
const pairPotentialList& pairPot = pot_.pairPotentials();
const electrostaticPotential& electrostatic(pot_.electrostatic());
const pairPotential& electrostatic = pairPot.electrostatic();
label idI = molI->id();
@ -276,11 +317,11 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
{
vector rsIsJ =
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
if(pairPot.rCutSqr(idsI, idsJ, rsIsJMagSq))
if (pairPot.rCutSqr(idsI, idsJ, rsIsJMagSq))
{
scalar rsIsJMag = mag(rsIsJ);
@ -291,7 +332,7 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
<< "Molecule site pair closer than "
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
@ -325,11 +366,11 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
{
vector rsIsJ =
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
if(pairPot.rCutMaxSqr(rsIsJMagSq))
if (pairPot.rCutMaxSqr(rsIsJMagSq))
{
scalar rsIsJMag = mag(rsIsJ);
@ -340,18 +381,23 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
<< "Molecule site pair closer than "
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
<< " other by a rounding error in molConfig in"
<< " parallel or a block filled with molecules "
<< " other by a rounding error in mdInitialise in"
<< " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
return true;
}
if (rsIsJMag < electrostatic.rMin())
{
return true;
}
scalar chargeI = constPropI.siteCharges()[sI];
scalar chargeJ = constPropJ.siteCharges()[sJ];
@ -379,9 +425,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
referredMolecule* molRef
) const
{
const pairPotentialList& pairPot(pot_.pairPotentials());
const pairPotentialList& pairPot = pot_.pairPotentials();
const electrostaticPotential& electrostatic(pot_.electrostatic());
const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@ -414,11 +460,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
{
vector rsRealsRef =
molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
molReal->sitePositions()[sReal]
- molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
if(pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
@ -429,12 +476,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsRealsRefMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
<< "Molecule site pair closer than "
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsRealsRefMag
<< ". These may have been placed on top of each"
<< " other by a rounding error in molConfig in"
<< " parallel or a block filled with molecules "
<< " other by a rounding error in mdInitialise in"
<< " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
@ -464,11 +511,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
{
vector rsRealsRef =
molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
molReal->sitePositions()[sReal]
- molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
if(pairPot.rCutMaxSqr(rsRealsRefMagSq))
if (pairPot.rCutMaxSqr(rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
@ -479,18 +527,23 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsRealsRefMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
<< "Molecule site pair closer than "
<< "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsRealsRefMag
<< ". These may have been placed on top of each"
<< " other by a rounding error in molConfig in"
<< " parallel or a block filled with molecules "
<< " other by a rounding error in mdInitialise in"
<< " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
return true;
}
if (rsRealsRefMag < electrostatic.rMin())
{
return true;
}
scalar chargeReal = constPropReal.siteCharges()[sReal];
scalar chargeRef = constPropRef.siteCharges()[sRef];
@ -499,8 +552,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
(
mag
(
chargeReal*chargeRef
*electrostatic.energy(rsRealsRefMag)
chargeReal
*chargeRef
*electrostatic.energy(rsRealsRefMag)
)
> pot_.potentialEnergyLimit()
)
@ -559,6 +613,7 @@ inline Foam::vector Foam::moleculeCloud::equipartitionAngularMomentum
}
}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::polyMesh& Foam::moleculeCloud::mesh() const

2
src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

4
src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class reducedUnits Declaration
Class reducedUnits Declaration
\*---------------------------------------------------------------------------*/
class reducedUnits

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

3
src/lagrangian/molecularDynamics/potential/Make/files
View File

@ -15,6 +15,7 @@ $(pairPotential)/derived/maitlandSmith/maitlandSmith.C
$(pairPotential)/derived/azizChen/azizChen.C
$(pairPotential)/derived/exponentialRepulsion/exponentialRepulsion.C
$(pairPotential)/derived/coulomb/coulomb.C
$(pairPotential)/derived/dampedCoulomb/dampedCoulomb.C
$(pairPotential)/derived/noInteraction/noInteraction.C
energyScalingFunction = energyScalingFunction
@ -43,4 +44,4 @@ electrostaticPotential = electrostaticPotential
$(electrostaticPotential)/electrostaticPotential.C
LIB = $(FOAM_LIBBIN)/libpotential
LIB = $(FOAM_LIBBIN)/libpotential

4
src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -27,8 +27,6 @@ License
#include "electrostaticPotential.H"
#include "mathematicalConstants.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::electrostaticPotential::electrostaticPotential()

4
src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -44,7 +44,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class electrostaticPotential Declaration
Class electrostaticPotential Declaration
\*---------------------------------------------------------------------------*/
class electrostaticPotential

5
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -36,8 +36,6 @@ namespace Foam
defineTypeNameAndDebug(energyScalingFunction, 0);
defineRunTimeSelectionTable(energyScalingFunction, dictionary);
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::energyScalingFunction::energyScalingFunction
@ -66,6 +64,7 @@ bool Foam::energyScalingFunction::read
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam

6
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -48,7 +48,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class energyScalingFunction Declaration
Class energyScalingFunction Declaration
\*---------------------------------------------------------------------------*/
class energyScalingFunction
@ -144,8 +144,6 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

6
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -58,8 +58,8 @@ autoPtr<energyScalingFunction> energyScalingFunction::New
(
"energyScalingFunction::New()"
) << "Unknown energyScalingFunction type "
<< energyScalingFunctionTypeName << endl << endl
<< "Valid energyScalingFunctions are : " << endl
<< energyScalingFunctionTypeName << nl << nl
<< "Valid energyScalingFunctions are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}

15
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -57,6 +57,7 @@ scalar doubleSigmoid::sigmoidScale
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
doubleSigmoid::doubleSigmoid
@ -67,13 +68,17 @@ doubleSigmoid::doubleSigmoid
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
doubleSigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
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
@ -81,17 +86,19 @@ 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_ =
energyScalingFunctionProperties.subDict(typeName + "Coeffs");
doubleSigmoidCoeffs_.lookup("shift1") >> shift1_;
doubleSigmoidCoeffs_.lookup("scale1") >> scale1_;
doubleSigmoidCoeffs_.lookup("shift2") >> shift2_;
doubleSigmoidCoeffs_.lookup("scale2") >> scale2_;
return true;
}

7
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class doubleSigmoid Declaration
Class doubleSigmoid Declaration
\*---------------------------------------------------------------------------*/
class doubleSigmoid
@ -62,6 +62,7 @@ class doubleSigmoid
scalar shift2_;
scalar scale2_;
// Private Member Functions
scalar sigmoidScale
@ -98,7 +99,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};

8
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -60,15 +58,17 @@ noScaling::noScaling
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;
}

4
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -80,7 +80,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};

8
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -61,6 +59,7 @@ shifted::shifted
e_at_rCut_(pairPot.unscaledEnergy(pairPot.rCut()))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void shifted::scaleEnergy(scalar& e, const scalar r) const
@ -68,10 +67,11 @@ void shifted::scaleEnergy(scalar& e, const scalar r) const
e -= e_at_rCut_;
}
bool shifted::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
return true;
}

6
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -57,6 +57,7 @@ class shifted
scalar e_at_rCut_;
public:
//- Runtime type information
@ -79,11 +80,12 @@ public:
~shifted()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};

8
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -63,6 +61,7 @@ shiftedForce::shiftedForce
de_dr_at_rCut_(pairPot.energyDerivative(rCut_, false))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void shiftedForce::scaleEnergy(scalar& e, const scalar r) const
@ -70,10 +69,11 @@ 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;
}

6
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
Class shiftedForce Declaration
Class shiftedForce Declaration
\*---------------------------------------------------------------------------*/
class shiftedForce
@ -89,7 +89,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};

16
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,6 +45,7 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
scalar sigmoid::sigmoidScale
@ -57,6 +58,7 @@ scalar sigmoid::sigmoidScale
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
sigmoid::sigmoid
@ -67,11 +69,15 @@ sigmoid::sigmoid
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
sigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
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
@ -79,15 +85,17 @@ 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_ =
energyScalingFunctionProperties.subDict(typeName + "Coeffs");
sigmoidCoeffs_.lookup("shift") >> shift_;
sigmoidCoeffs_.lookup("scale") >> shift_;
return true;
}

4
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -98,7 +98,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};

6
src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -54,8 +54,8 @@ autoPtr<pairPotential> pairPotential::New
(
"pairPotential::New()"
) << "Unknown pairPotential type "
<< pairPotentialTypeName << endl << endl
<< "Valid pairPotentials are : " << endl
<< pairPotentialTypeName << nl << nl
<< "Valid pairPotentials are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}

10
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -93,7 +93,7 @@ void Foam::pairPotential::setLookupTables()
}
Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
Foam::scalar Foam::pairPotential::force(const scalar r) const
{
scalar k_rIJ = (r - rMin_)/dr_;
@ -102,7 +102,7 @@ Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
<< "r less than rMin" << nl
<< "r less than rMin in pair potential " << name_ << nl
<< abort(FatalError);
}
@ -130,7 +130,7 @@ Foam::pairPotential::forceTable() const
}
Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
Foam::scalar Foam::pairPotential::energy(const scalar r) const
{
scalar k_rIJ = (r - rMin_)/dr_;
@ -139,7 +139,7 @@ Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
<< "r less than rMin" << nl
<< "r less than rMin in pair potential " << name_ << nl
<< abort(FatalError);
}

13
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -54,7 +54,7 @@ namespace Foam
class energyScalingFunction;
/*---------------------------------------------------------------------------*\
Class pairPotential Declaration
Class pairPotential Declaration
\*---------------------------------------------------------------------------*/
class pairPotential
@ -80,6 +80,7 @@ protected:
bool writeTables_;
// Private Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
@ -94,7 +95,7 @@ protected:
public:
//- Runtime type information
TypeName("pairPotential");
TypeName("pairPotential");
// Declare run-time constructor selection table
@ -150,9 +151,9 @@ public:
inline scalar rCutSqr() const;
scalar energyLookup (const scalar r) const;
scalar energy (const scalar r) const;
scalar forceLookup (const scalar r) const;
scalar force (const scalar r) const;
List<Pair<scalar> > energyTable() const;
@ -160,7 +161,7 @@ public:
inline bool writeTables() const;
virtual scalar unscaledEnergy (const scalar r) const = 0;
virtual scalar unscaledEnergy(const scalar r) const = 0;
scalar scaledEnergy(const scalar r) const;

2
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License

14
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -38,12 +38,12 @@ bool Foam::pairPotential::writeEnergyAndForceTables(Ostream& os) const
forAll(eTab, e)
{
os<< eTab[e].first()
<< token::SPACE
<< eTab[e].second()
<< token::SPACE
<< fTab[e].second()
<< nl;
os << eTab[e].first()
<< token::SPACE
<< eTab[e].second()
<< token::SPACE
<< fTab[e].second()
<< nl;
}
return os.good();

26
src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -71,6 +69,7 @@ azizChen::azizChen
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar azizChen::unscaledEnergy(const scalar r) const
@ -84,15 +83,16 @@ scalar azizChen::unscaledEnergy(const scalar r) const
F = exp(-pow(((D_ / x) - 1.0),2));
}
return epsilon_ *
(
A_ * Foam::pow(x, gamma_) * exp(-alpha_ * x)
- (
(C6_/ Foam::pow(x, 6))
+ (C8_/ Foam::pow(x, 8))
+ (C10_/ Foam::pow(x, 10))
)
* F
return
epsilon_
*(
A_ * Foam::pow(x, gamma_)*exp(-alpha_*x)
- (
(C6_/ Foam::pow(x, 6))
+ (C8_/ Foam::pow(x, 8))
+ (C10_/ Foam::pow(x, 10))
)
*F
);
}
@ -112,7 +112,7 @@ bool azizChen::read(const dictionary& azizChen)
azizChenCoeffs_.lookup("C10") >> C10_;
azizChenCoeffs_.lookup("D") >> D_;
azizChenCoeffs_.lookup("gamma") >> gamma_;
return true;
}

5
src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -85,6 +85,7 @@ class azizChen
scalar D_;
scalar gamma_;
public:
//- Runtime type information
@ -111,7 +112,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

9
src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -25,6 +25,7 @@ License
\*---------------------------------------------------------------------------*/
#include "coulomb.H"
#include "mathematicalConstants.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -45,7 +46,8 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
scalar coulomb::oneOverFourPiEps0 =
1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -61,11 +63,12 @@ coulomb::coulomb
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar coulomb::unscaledEnergy(const scalar r) const
{
return 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12 * r);
return oneOverFourPiEps0/r;
}

11
src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
Foam::pairPotentials::coulomb
Foam::pairPotentials::electrostatic
Description
@ -53,13 +53,16 @@ class coulomb
:
public pairPotential
{
public:
//- Runtime type information
TypeName("coulomb");
// Static data members
static scalar oneOverFourPiEps0;
// Constructors
//- Construct from components
@ -80,7 +83,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

98
src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C Normal file
View File

@ -0,0 +1,98 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2009 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 "dampedCoulomb.H"
#include "mathematicalConstants.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace pairPotentials
{
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
defineTypeNameAndDebug(dampedCoulomb, 0);
addToRunTimeSelectionTable
(
pairPotential,
dampedCoulomb,
dictionary
);
scalar dampedCoulomb::oneOverFourPiEps0 =
1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
dampedCoulomb::dampedCoulomb
(
const word& name,
const dictionary& pairPotentialProperties
)
:
pairPotential(name, pairPotentialProperties),
dampedCoulombCoeffs_
(
pairPotentialProperties.subDict(typeName + "Coeffs")
),
alpha_(readScalar(dampedCoulombCoeffs_.lookup("alpha")))
{
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar dampedCoulomb::unscaledEnergy(const scalar r) const
{
return oneOverFourPiEps0*erfc(alpha_*r)/r;
}
bool dampedCoulomb::read(const dictionary& pairPotentialProperties)
{
pairPotential::read(pairPotentialProperties);
dampedCoulombCoeffs_ =
pairPotentialProperties.subDict(typeName + "Coeffs");
dampedCoulombCoeffs_.lookup("alpha") >> alpha_;
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace pairPotentials
} // End namespace Foam
// ************************************************************************* //

108
src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H Normal file
View File

@ -0,0 +1,108 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2008-2009 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::pairPotentials::electrostatic
Description
SourceFiles
dampedCoulomb.C
\*---------------------------------------------------------------------------*/
#ifndef dampedCoulomb_H
#define dampedCoulomb_H
#include "pairPotential.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
Class dampedCoulomb Declaration
\*---------------------------------------------------------------------------*/
class dampedCoulomb
:
public pairPotential
{
// Private data
dictionary dampedCoulombCoeffs_;
scalar alpha_;
public:
//- Runtime type information
TypeName("dampedCoulomb");
// Static data members
static scalar oneOverFourPiEps0;
// Constructors
//- Construct from components
dampedCoulomb
(
const word& name,
const dictionary& pairPotentialProperties
);
// Destructor
~dampedCoulomb()
{}
// Member Functions
scalar unscaledEnergy(const scalar r) const;
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace pairPotentials
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

13
src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -57,13 +55,17 @@ exponentialRepulsion::exponentialRepulsion
)
:
pairPotential(name, exponentialRepulsion),
exponentialRepulsionCoeffs_(exponentialRepulsion.subDict(typeName + "Coeffs")),
exponentialRepulsionCoeffs_
(
exponentialRepulsion.subDict(typeName + "Coeffs")
),
rm_(readScalar(exponentialRepulsionCoeffs_.lookup("rm"))),
epsilon_(readScalar(exponentialRepulsionCoeffs_.lookup("epsilon")))
{
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar exponentialRepulsion::unscaledEnergy(const scalar r) const
@ -76,7 +78,8 @@ bool exponentialRepulsion::read(const dictionary& exponentialRepulsion)
{
pairPotential::read(exponentialRepulsion);
exponentialRepulsionCoeffs_ = exponentialRepulsion.subDict(typeName + "Coeffs");
exponentialRepulsionCoeffs_ =
exponentialRepulsion.subDict(typeName + "Coeffs");
exponentialRepulsionCoeffs_.lookup("rm") >> rm_;
exponentialRepulsionCoeffs_.lookup("epsilon") >> epsilon_;

7
src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
Class exponentialRepulsion Declaration
Class exponentialRepulsion Declaration
\*---------------------------------------------------------------------------*/
class exponentialRepulsion
@ -60,6 +60,7 @@ class exponentialRepulsion
scalar rm_;
scalar epsilon_;
public:
//- Runtime type information
@ -86,7 +87,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

5
src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -64,6 +62,7 @@ lennardJones::lennardJones
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar lennardJones::unscaledEnergy(const scalar r) const

7
src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
Class lennardJones Declaration
Class lennardJones Declaration
\*---------------------------------------------------------------------------*/
class lennardJones
@ -60,6 +60,7 @@ class lennardJones
scalar sigma_;
scalar epsilon_;
public:
//- Runtime type information
@ -86,7 +87,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

7
src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -66,6 +64,7 @@ maitlandSmith::maitlandSmith
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar maitlandSmith::unscaledEnergy(const scalar r) const
@ -90,7 +89,7 @@ bool maitlandSmith::read(const dictionary& maitlandSmith)
maitlandSmithCoeffs_.lookup("gamma") >> gamma_;
maitlandSmithCoeffs_.lookup("rm") >> rm_;
maitlandSmithCoeffs_.lookup("epsilon") >> epsilon_;
return true;
}

7
src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -72,7 +72,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
Class maitlandSmith Declaration
Class maitlandSmith Declaration
\*---------------------------------------------------------------------------*/
class maitlandSmith
@ -88,6 +88,7 @@ class maitlandSmith
scalar rm_;
scalar epsilon_;
public:
//- Runtime type information
@ -114,7 +115,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

5
src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@ -61,6 +59,7 @@ noInteraction::noInteraction
setLookupTables();
}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar noInteraction::unscaledEnergy(const scalar r) const

6
src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
Class noInteraction Declaration
Class noInteraction Declaration
\*---------------------------------------------------------------------------*/
class noInteraction
@ -80,7 +80,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
//- Read transportProperties dictionary
//- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};

76
src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -60,9 +60,9 @@ void Foam::pairPotentialList::readPairPotentialDict
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " not found"
<< nl << abort(FatalError);
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " not found"
<< nl << abort(FatalError);
}
}
else
@ -80,10 +80,10 @@ void Foam::pairPotentialList::readPairPotentialDict
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " or "
<< idB << "-" << idA << " not found"
<< nl << abort(FatalError);
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " or "
<< idB << "-" << idA << " not found"
<< nl << abort(FatalError);
}
if
@ -93,10 +93,10 @@ void Foam::pairPotentialList::readPairPotentialDict
)
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " and "
<< idB << "-" << idA << " found multiple definition"
<< nl << abort(FatalError);
<< "Pair pairPotential specification subDict "
<< idA << "-" << idB << " and "
<< idB << "-" << idA << " found multiple definition"
<< nl << abort(FatalError);
}
}
@ -136,9 +136,41 @@ void Foam::pairPotentialList::readPairPotentialDict
}
}
if (!pairPotentialDict.found("electrostatic"))
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict electrostatic"
<< nl << abort(FatalError);
}
electrostaticPotential_ = pairPotential::New
(
"electrostatic",
pairPotentialDict.subDict("electrostatic")
);
if (electrostaticPotential_->rCut() > rCutMax_)
{
rCutMax_ = electrostaticPotential_->rCut();
}
if (electrostaticPotential_->writeTables())
{
OFstream ppTabFile(mesh.time().path()/"electrostatic");
if(!electrostaticPotential_->writeEnergyAndForceTables(ppTabFile))
{
FatalErrorIn("pairPotentialList::readPairPotentialDict")
<< "Failed writing to "
<< ppTabFile.name() << nl
<< abort(FatalError);
}
}
rCutMaxSqr_ = rCutMax_*rCutMax_;
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::pairPotentialList::pairPotentialList()
@ -146,6 +178,7 @@ Foam::pairPotentialList::pairPotentialList()
PtrList<pairPotential>()
{}
Foam::pairPotentialList::pairPotentialList
(
const List<word>& idList,
@ -188,13 +221,13 @@ const Foam::pairPotential& Foam::pairPotentialList::pairPotentialFunction
const label b
) const
{
return (*this)[pairPotentialIndex (a, b)];
return (*this)[pairPotentialIndex(a, b)];
}
bool Foam::pairPotentialList::rCutMaxSqr(const scalar rIJMagSqr) const
{
if (rIJMagSqr <= rCutMaxSqr_)
if (rIJMagSqr < rCutMaxSqr_)
{
return true;
}
@ -212,7 +245,7 @@ bool Foam::pairPotentialList::rCutSqr
const scalar rIJMagSqr
) const
{
if (rIJMagSqr <= rCutSqr (a, b))
if (rIJMagSqr < rCutSqr(a, b))
{
return true;
}
@ -229,7 +262,7 @@ Foam::scalar Foam::pairPotentialList::rMin
const label b
) const
{
return (*this)[pairPotentialIndex (a, b)].rMin();
return (*this)[pairPotentialIndex(a, b)].rMin();
}
@ -239,7 +272,7 @@ Foam::scalar Foam::pairPotentialList::dr
const label b
) const
{
return (*this)[pairPotentialIndex (a, b)].dr();
return (*this)[pairPotentialIndex(a, b)].dr();
}
@ -249,7 +282,7 @@ Foam::scalar Foam::pairPotentialList::rCutSqr
const label b
) const
{
return (*this)[pairPotentialIndex (a, b)].rCutSqr();
return (*this)[pairPotentialIndex(a, b)].rCutSqr();
}
@ -259,7 +292,7 @@ Foam::scalar Foam::pairPotentialList::rCut
const label b
) const
{
return (*this)[pairPotentialIndex (a, b)].rCut();
return (*this)[pairPotentialIndex(a, b)].rCut();
}
@ -270,7 +303,7 @@ Foam::scalar Foam::pairPotentialList::force
const scalar rIJMag
) const
{
scalar f = (*this)[pairPotentialIndex (a, b)].forceLookup(rIJMag);
scalar f = (*this)[pairPotentialIndex(a, b)].force(rIJMag);
return f;
}
@ -283,11 +316,10 @@ Foam::scalar Foam::pairPotentialList::energy
const scalar rIJMag
) const
{
scalar e = (*this)[pairPotentialIndex (a, b)].energyLookup(rIJMag);
scalar e = (*this)[pairPotentialIndex(a, b)].energy(rIJMag);
return e;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //

21
src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -47,7 +47,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
Class pairPotentialList Declaration
Class pairPotentialList Declaration
\*---------------------------------------------------------------------------*/
class pairPotentialList
@ -62,6 +62,9 @@ class pairPotentialList
scalar rCutMaxSqr_;
autoPtr<pairPotential> electrostaticPotential_;
// Private Member Functions
inline label pairPotentialIndex
@ -83,6 +86,7 @@ class pairPotentialList
//- Disallow default bitwise copy construct
pairPotentialList(const pairPotentialList&);
public:
// Constructors
@ -97,10 +101,12 @@ public:
const polyMesh& mesh
);
// Destructor
~pairPotentialList();
// Member Functions
void buildPotentials
@ -110,6 +116,7 @@ public:
const polyMesh& mesh
);
// Access
inline scalar rCutMax() const;
@ -132,13 +139,13 @@ public:
const scalar rIJMagSqr
) const;
scalar rMin (const label a, const label b) const;
scalar rMin(const label a, const label b) const;
scalar dr (const label a, const label b) const;
scalar dr(const label a, const label b) const;
scalar rCutSqr (const label a, const label b) const;
scalar rCutSqr(const label a, const label b) const;
scalar rCut (const label a, const label b) const;
scalar rCut(const label a, const label b) const;
scalar force
(
@ -153,6 +160,8 @@ public:
const label b,
const scalar rIJMag
) const;
inline const pairPotential& electrostatic() const;
};

9
src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
\\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -56,6 +56,7 @@ inline Foam::label Foam::pairPotentialList::pairPotentialIndex
return index;
}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::scalar Foam::pairPotentialList::rCutMax() const
@ -70,4 +71,10 @@ inline Foam::scalar Foam::pairPotentialList::rCutMaxSqr() const
}
inline const Foam::pairPotential& Foam::pairPotentialList::electrostatic() const
{
return electrostaticPotential_;
}
// ************************************************************************* //

Some files were not shown because too many files have changed in this diff Show More