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molecularDynamics: Consolidated into a single library

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This simplifies the directory structure and resolves some name clashes
with other parts of OpenFOAM.
This commit is contained in:
Will Bainbridge
2024-06-11 11:20:51 +01:00
parent e1e0e258c8
commit b57e83304b
51 changed files with 92 additions and 817 deletions
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10
applications/legacy/lagrangian/mdEquilibrationFoam/Make/options
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@ -1,15 +1,11 @@
EXE_INC = \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude
-I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
EXE_LIBS = \
-lmeshTools \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
-lmolecularDynamics

4
applications/legacy/lagrangian/mdEquilibrationFoam/mdEquilibrationFoam.C
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@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -30,7 +30,7 @@ Description
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "md.H"
#include "moleculeCloud.H"
using namespace Foam;

10
applications/legacy/lagrangian/mdFoam/Make/options
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@ -1,15 +1,11 @@
EXE_INC = \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude
-I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
EXE_LIBS = \
-lmeshTools \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
-lmolecularDynamics

4
applications/legacy/lagrangian/mdFoam/mdFoam.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -31,7 +31,7 @@ Description
#include "argList.H"
#include "timeSelector.H"
#include "md.H"
#include "moleculeCloud.H"
using namespace Foam;

11
applications/utilities/preProcessing/mdInitialise/Make/options
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@ -1,18 +1,13 @@
EXE_INC = \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/polyTopoChange/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude
-I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
EXE_LIBS = \
-lmeshTools \
-lpolyTopoChange \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
-lmolecularDynamics

4
applications/utilities/preProcessing/mdInitialise/mdInitialise.C
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@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -27,7 +27,7 @@ Description
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "md.H"
#include "moleculeCloud.H"
using namespace Foam;

4
src/lagrangian/Allwmake
View File

@ -8,9 +8,7 @@ wmake $targetType basic
wmake $targetType solidParticle
wmake $targetType parcel
wmake $targetType DSMC
molecularDynamics/Allwmake $targetType $*
wmake $targetType molecularDynamics
wmake $targetType functionObjects
#------------------------------------------------------------------------------

11
src/lagrangian/molecularDynamics/Allwmake
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@ -1,11 +0,0 @@
#!/bin/sh
cd ${0%/*} || exit 1 # Run from this directory
# Parse arguments for library compilation
. $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
wmake $targetType potential
wmake $targetType molecularMeasurements
wmake $targetType molecule
#------------------------------------------------------------------------------

45
src/lagrangian/molecularDynamics/Make/files Normal file
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@ -0,0 +1,45 @@
reducedUnits/reducedUnits.C
reducedUnits/reducedUnitsIO.C
molecule/molecule.C
molecule/moleculeIO.C
moleculeCloud/moleculeCloud.C
potential/potential/potential.C
potential/pairPotential/pairPotentialList/pairPotentialList.C
potential/pairPotential/basic/pairPotential.C
potential/pairPotential/basic/pairPotentialIO.C
potential/pairPotential/basic/pairPotentialNew.C
potential/pairPotential/derived/lennardJones/lennardJones.C
potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
potential/pairPotential/derived/azizChen/azizChen.C
potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
potential/pairPotential/derived/coulomb/coulomb.C
potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
potential/pairPotential/derived/noInteraction/noInteraction.C
potential/energyScalingFunction/basic/energyScalingFunction.C
potential/energyScalingFunction/basic/energyScalingFunctionNew.C
potential/energyScalingFunction/derived/shifted/shifted.C
potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
potential/energyScalingFunction/derived/noScaling/noScaling.C
potential/energyScalingFunction/derived/sigmoid/sigmoid.C
potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
potential/tetherPotential/basic/tetherPotential.C
potential/tetherPotential/basic/tetherPotentialNew.C
potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
potential/tetherPotential/derived/pitchForkRing/pitchForkRing.C
potential/electrostaticPotential/electrostaticPotential.C
LIB = $(FOAM_LIBBIN)/libmolecularDynamics

9
src/lagrangian/molecularDynamics/Make/options Normal file
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@ -0,0 +1,9 @@
EXE_INC = \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude
LIB_LIBS = \
-lfiniteVolume \
-lmeshTools \
-llagrangian

2
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C → src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulator.C
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@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2020 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C → src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulatorIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C → src/lagrangian/molecularDynamics/correlationFunction/correlationFunction.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2020 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C → src/lagrangian/molecularDynamics/correlationFunction/correlationFunctionIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

0
src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H → src/lagrangian/molecularDynamics/mdTools/averageMDFields.H
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2
src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H → src/lagrangian/molecularDynamics/mdTools/calculateAutoCorrelationFunctions.H
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@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

2
src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H → src/lagrangian/molecularDynamics/mdTools/calculateTransportProperties.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

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

2
src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H → src/lagrangian/molecularDynamics/mdTools/meanMomentumEnergyAndNMols.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

0
src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H → src/lagrangian/molecularDynamics/mdTools/resetMDFields.H
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2
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H → src/lagrangian/molecularDynamics/mdTools/temperatureAndPressure.H
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@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H → src/lagrangian/molecularDynamics/mdTools/temperatureAndPressureVariables.H
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

3
src/lagrangian/molecularDynamics/molecularMeasurements/Make/files
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@ -1,3 +0,0 @@
distribution/distribution.C
LIB = $(FOAM_LIBBIN)/libmolecularMeasurements

0
src/lagrangian/molecularDynamics/molecularMeasurements/Make/options
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478
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
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@ -1,478 +0,0 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
OpenFOAM is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
\*---------------------------------------------------------------------------*/
#include "distribution.H"
#include "OFstream.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
defineTypeNameAndDebug(distribution, 0);
}
// * * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * //
void Foam::distribution::write
(
const fileName& file,
const List<Pair<scalar>>& pairs
)
{
OFstream os(file);
forAll(pairs, i)
{
os << pairs[i].first() << ' ' << pairs[i].second() << nl;
}
}
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::distribution::distribution()
:
Map<label>(),
binWidth_(1)
{}
Foam::distribution::distribution(const scalar binWidth)
:
Map<label>(),
binWidth_(binWidth)
{}
Foam::distribution::distribution(const distribution& d)
:
Map<label>(static_cast<Map<label>>(d)),
binWidth_(d.binWidth())
{}
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
Foam::distribution::~distribution()
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
Foam::label Foam::distribution::totalEntries() const
{
label sumOfEntries = 0;
forAllConstIter(Map<label>, *this, iter)
{
sumOfEntries += iter();
if (sumOfEntries < 0)
{
WarningInFunction
<< "Accumulated distribution values total has become negative: "
<< "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 "
<< "returns a scalar." << endl;
sumOfEntries = -1;
break;
}
}
return sumOfEntries;
}
Foam::scalar Foam::distribution::approxTotalEntries() const
{
scalar sumOfEntries = 0;
forAllConstIter(Map<label>, *this, iter)
{
sumOfEntries += scalar(iter());
}
return sumOfEntries;
}
Foam::scalar Foam::distribution::mean() const
{
scalar runningSum = 0;
scalar totEnt = approxTotalEntries();
List<label> keys = toc();
forAll(keys,k)
{
label key = keys[k];
runningSum +=
(0.5 + scalar(key))
*binWidth_
*scalar((*this)[key])
/totEnt;
}
return runningSum;
}
Foam::scalar Foam::distribution::median()
{
// Reference:
// http://mathworld.wolfram.com/StatisticalMedian.html
// The statistical median is the value of the distribution variable
// where the cumulative distribution = 0.5.
scalar median = 0.0;
scalar runningSum = 0.0;
List<Pair<scalar>> normDist(normalised());
if (normDist.size())
{
if (normDist.size() == 1)
{
median = normDist[0].first();
}
else if
(
normDist.size() > 1
&& normDist[0].second()*binWidth_ > 0.5
)
{
scalar xk = normDist[1].first();
scalar xkm1 = normDist[0].first();
scalar Sk =
(normDist[0].second() + normDist[1].second())*binWidth_;
scalar Skm1 = normDist[0].second()*binWidth_;
median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
}
else
{
label lastNonZeroIndex = 0;
forAll(normDist,nD)
{
if (runningSum + (normDist[nD].second()*binWidth_) > 0.5)
{
scalar xk = normDist[nD].first();
scalar xkm1 = normDist[lastNonZeroIndex].first();
scalar Sk = runningSum + (normDist[nD].second()*binWidth_);
scalar Skm1 = runningSum;
median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
break;
}
else if (normDist[nD].second() > 0.0)
{
runningSum += normDist[nD].second()*binWidth_;
lastNonZeroIndex = nD;
}
}
}
}
return median;
}
void Foam::distribution::add(const scalar valueToAdd)
{
iterator iter(this->begin());
label n = label(valueToAdd/binWidth_) - label(neg(valueToAdd/binWidth_));
iter = find(n);
if (iter == this->end())
{
this->insert(n,1);
}
else
{
(*this)[n]++;
}
if ((*this)[n] < 0)
{
FatalErrorInFunction
<< "Accumulated distribution value has become negative: "
<< "bin = " << (0.5 + scalar(n)) * binWidth_
<< ", value = " << (*this)[n]
<< ". This is most likely to be because too many samples "
<< "have been added to a bin and the label has 'rolled round'"
<< abort(FatalError);
}
}
void Foam::distribution::add(const label valueToAdd)
{
add(scalar(valueToAdd));
}
void Foam::distribution::insertMissingKeys()
{
iterator iter(this->begin());
List<label> keys = toc();
sort(keys);
if (keys.size())
{
for (label k = keys[0]; k < keys.last(); k++)
{
iter = find(k);
if (iter == this->end())
{
this->insert(k,0);
}
}
}
}
Foam::List<Foam::Pair<Foam::scalar>> Foam::distribution::normalised()
{
scalar totEnt = approxTotalEntries();
insertMissingKeys();
List<label> keys = toc();
sort(keys);
List<Pair<scalar>> normDist(size());
forAll(keys,k)
{
label key = keys[k];
normDist[k].first() = (0.5 + scalar(key))*binWidth_;
normDist[k].second() = scalar((*this)[key])/totEnt/binWidth_;
}
if (debug)
{
Info<< "totEnt: " << totEnt << endl;
}
return normDist;
}
Foam::List<Foam::Pair<Foam::scalar>> Foam::distribution::normalisedMinusMean()
{
return normalisedShifted(mean());
}
Foam::List<Foam::Pair<Foam::scalar>> Foam::distribution::normalisedShifted
(
scalar shiftValue
)
{
List<Pair<scalar>> oldDist(normalised());
List<Pair<scalar>> newDist(oldDist.size());
forAll(oldDist,u)
{
oldDist[u].first() -= shiftValue;
}
scalar lowestOldBin = oldDist[0].first()/binWidth_ - 0.5;
label lowestNewKey = label
(
lowestOldBin + 0.5*sign(lowestOldBin)
);
scalar interpolationStartDirection =
sign(scalar(lowestNewKey) - lowestOldBin);
label newKey = lowestNewKey;
if (debug)
{
Info<< shiftValue
<< nl << lowestOldBin
<< nl << lowestNewKey
<< nl << interpolationStartDirection
<< endl;
scalar checkNormalisation = 0;
forAll(oldDist, oD)
{
checkNormalisation += oldDist[oD].second()*binWidth_;
}
Info<< "Initial normalisation = " << checkNormalisation << endl;
}
forAll(oldDist,u)
{
newDist[u].first() = (0.5 + scalar(newKey)) * binWidth_;
if (interpolationStartDirection < 0)
{
if (u == 0)
{
newDist[u].second() =
(0.5 + scalar(newKey))*oldDist[u].second()
- oldDist[u].second()
*(oldDist[u].first() - binWidth_)/ binWidth_;
}
else
{
newDist[u].second() =
(0.5 + scalar(newKey))
*(oldDist[u].second() - oldDist[u-1].second())
+
(
oldDist[u-1].second()*oldDist[u].first()
- oldDist[u].second()*oldDist[u-1].first()
)
/binWidth_;
}
}
else
{
if (u == oldDist.size() - 1)
{
newDist[u].second() =
(0.5 + scalar(newKey))*-oldDist[u].second()
+ oldDist[u].second()*(oldDist[u].first() + binWidth_)
/binWidth_;
}
else
{
newDist[u].second() =
(0.5 + scalar(newKey))
*(oldDist[u+1].second() - oldDist[u].second())
+
(
oldDist[u].second()*oldDist[u+1].first()
- oldDist[u+1].second()*oldDist[u].first()
)
/binWidth_;
}
}
newKey++;
}
if (debug)
{
scalar checkNormalisation = 0;
forAll(newDist, nD)
{
checkNormalisation += newDist[nD].second()*binWidth_;
}
Info<< "Shifted normalisation = " << checkNormalisation << endl;
}
return newDist;
}
Foam::List<Foam::Pair<Foam::scalar>> Foam::distribution::raw()
{
insertMissingKeys();
List<label> keys = toc();
sort(keys);
List<Pair<scalar>> rawDist(size());
forAll(keys,k)
{
label key = keys[k];
rawDist[k].first() = (0.5 + scalar(key))*binWidth_;
rawDist[k].second() = scalar((*this)[key]);
}
return rawDist;
}
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
void Foam::distribution::operator=(const distribution& rhs)
{
// Check for assignment to self
if (this == &rhs)
{
FatalErrorInFunction
<< "Attempted assignment to self"
<< abort(FatalError);
}
Map<label>::operator=(rhs);
binWidth_ = rhs.binWidth();
}
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
Foam::Ostream& Foam::operator<<(Ostream& os, const distribution& d)
{
os << d.binWidth_
<< static_cast<const Map<label>&>(d);
// Check state of Ostream
os.check
(
"Ostream& operator<<(Ostream&, "
"const distribution&)"
);
return os;
}
// ************************************************************************* //

155
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
View File

@ -1,155 +0,0 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
OpenFOAM is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
Class
Foam::distribution
Description
Accumulating histogram of values. Specified bin resolution
automatic generation of bins.
SourceFiles
distributionI.H
distribution.C
\*---------------------------------------------------------------------------*/
#ifndef distribution_H
#define distribution_H
#include "Map.H"
#include "Pair.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// Forward declaration of friend functions and operators
class distribution;
Ostream& operator<<(Ostream&, const distribution&);
/*---------------------------------------------------------------------------*\
Class distribution Declaration
\*---------------------------------------------------------------------------*/
class distribution
:
public Map<label>
{
// Private Data
scalar binWidth_;
public:
//- Runtime type information
TypeName("distribution");
// Static functions
//- Write to file
static void write
(
const fileName& file,
const List<Pair<scalar>>& pairs
);
// Constructors
//- Construct null
distribution();
//- Construct from binWidth
distribution(const scalar binWidth);
//- Copy constructor
distribution(const distribution&);
//- Destructor
virtual ~distribution();
// Member Functions
label totalEntries() const;
scalar approxTotalEntries() const;
scalar mean() const;
scalar median();
//- Add a value to the appropriate bin of the distribution.
void add(const scalar valueToAdd);
void add(const label valueToAdd);
void insertMissingKeys();
List<Pair<scalar>> normalised();
List<Pair<scalar>> normalisedMinusMean();
List<Pair<scalar>> normalisedShifted(scalar shiftValue);
List<Pair<scalar>> raw();
// Access
inline scalar binWidth() const;
// Member Operators
void operator=(const distribution&);
// IOstream Operators
friend Ostream& operator<<(Ostream&, const distribution&);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#include "distributionI.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

34
src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H
View File

@ -1,34 +0,0 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
OpenFOAM is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
\*---------------------------------------------------------------------------*/
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::scalar Foam::distribution::binWidth() const
{
return binWidth_;
}
// ************************************************************************* //

9
src/lagrangian/molecularDynamics/molecule/Make/files
View File

@ -1,9 +0,0 @@
reducedUnits/reducedUnits.C
reducedUnits/reducedUnitsIO.C
molecule/molecule.C
molecule/moleculeIO.C
moleculeCloud/moleculeCloud.C
LIB = $(FOAM_LIBBIN)/libmolecule

13
src/lagrangian/molecularDynamics/molecule/Make/options
View File

@ -1,13 +0,0 @@
EXE_INC = \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude
LIB_LIBS = \
-lfiniteVolume \
-lmeshTools \
-llagrangian \
-lpotential \
-lmolecularMeasurements

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

@ -1,8 +0,0 @@
#ifndef md_H
#define md_H
#include "potential.H"
#include "moleculeCloud.H"
#include "correlationFunction.H"
#include "distribution.H"
#include "reducedUnits.H"
#endif

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

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2023 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

2
src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C → src/lagrangian/molecularDynamics/molecule/moleculeIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2022 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

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

0
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H → src/lagrangian/molecularDynamics/moleculeCloud/moleculeCloudI.H
View File

47
src/lagrangian/molecularDynamics/potential/Make/files
View File

@ -1,47 +0,0 @@
potential = potential
$(potential)/potential.C
pairPotential = pairPotential
$(pairPotential)/pairPotentialList/pairPotentialList.C
$(pairPotential)/basic/pairPotential.C
$(pairPotential)/basic/pairPotentialIO.C
$(pairPotential)/basic/pairPotentialNew.C
$(pairPotential)/derived/lennardJones/lennardJones.C
$(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
$(energyScalingFunction)/basic/energyScalingFunction.C
$(energyScalingFunction)/basic/energyScalingFunctionNew.C
$(energyScalingFunction)/derived/shifted/shifted.C
$(energyScalingFunction)/derived/shiftedForce/shiftedForce.C
$(energyScalingFunction)/derived/noScaling/noScaling.C
$(energyScalingFunction)/derived/sigmoid/sigmoid.C
$(energyScalingFunction)/derived/doubleSigmoid/doubleSigmoid.C
tetherPotential = tetherPotential
$(tetherPotential)/tetherPotentialList/tetherPotentialList.C
$(tetherPotential)/basic/tetherPotential.C
$(tetherPotential)/basic/tetherPotentialNew.C
$(tetherPotential)/derived/harmonicSpring/harmonicSpring.C
$(tetherPotential)/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
$(tetherPotential)/derived/pitchForkRing/pitchForkRing.C
electrostaticPotential = electrostaticPotential
$(electrostaticPotential)/electrostaticPotential.C
LIB = $(FOAM_LIBBIN)/libpotential

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

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

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2020 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License

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

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2024 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License