molecularDynamics: Consolidated into a single library

This simplifies the directory structure and resolves some name clashes
with other parts of OpenFOAM.

applications/legacy/lagrangian/mdEquilibrationFoam/Make/options

@@ -1,15 +1,11 @@
 EXE_INC = \
-    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/meshTools/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$(LIB_SRC)/meshTools/lnInclude
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule \
+    -lmolecularDynamics
-    -lpotential \
-    -lmolecularMeasurements

applications/legacy/lagrangian/mdEquilibrationFoam/mdEquilibrationFoam.C

@@ -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;
 

applications/legacy/lagrangian/mdFoam/Make/options

@@ -1,15 +1,11 @@
 EXE_INC = \
-    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/meshTools/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$(LIB_SRC)/meshTools/lnInclude
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule \
+    -lmolecularDynamics
-    -lpotential \
-    -lmolecularMeasurements

applications/legacy/lagrangian/mdFoam/mdFoam.C

@@ -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;
 

applications/utilities/preProcessing/mdInitialise/Make/options

@@ -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)/finiteVolume/lnInclude \
-    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
-    -I$(LIB_SRC)/finiteVolume/lnInclude
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
     -lpolyTopoChange \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule \
+    -lmolecularDynamics
-    -lpotential \
-    -lmolecularMeasurements
-

applications/utilities/preProcessing/mdInitialise/mdInitialise.C

@@ -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;
 

src/lagrangian/Allwmake

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

src/lagrangian/molecularDynamics/Allwmake

@@ -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
-
-#------------------------------------------------------------------------------

src/lagrangian/molecularDynamics/Make/files

@@ -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

src/lagrangian/molecularDynamics/Make/options

@@ -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

src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulator.C

@@ -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

src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulator.H

@@ -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

src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulatorI.H

@@ -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

src/lagrangian/molecularDynamics/bufferedAccumulator/bufferedAccumulatorIO.C

@@ -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

src/lagrangian/molecularDynamics/correlationFunction/correlationFunction.C

@@ -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

src/lagrangian/molecularDynamics/correlationFunction/correlationFunction.H

@@ -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

src/lagrangian/molecularDynamics/correlationFunction/correlationFunctionI.H

@@ -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

src/lagrangian/molecularDynamics/correlationFunction/correlationFunctionIO.C

@@ -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

src/lagrangian/molecularDynamics/mdTools/calculateAutoCorrelationFunctions.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/calculateTransportProperties.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/createAutoCorrelationFunctions.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/meanMomentumEnergyAndNMols.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/temperatureAndPressure.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/temperatureAndPressureVariables.H

@@ -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

src/lagrangian/molecularDynamics/mdTools/temperatureEquilibration.H

@@ -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

src/lagrangian/molecularDynamics/molecularMeasurements/Make/files

@@ -1,3 +0,0 @@
-distribution/distribution.C
-
-LIB = $(FOAM_LIBBIN)/libmolecularMeasurements

src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C

@@ -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;
-}
-
-
-// ************************************************************************* //

src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H

@@ -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
-
-// ************************************************************************* //

src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H

@@ -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_;
-}
-
-
-// ************************************************************************* //

src/lagrangian/molecularDynamics/molecule/Make/files

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

src/lagrangian/molecularDynamics/molecule/Make/options

@@ -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

src/lagrangian/molecularDynamics/molecule/mdTools/md.H

@@ -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

src/lagrangian/molecularDynamics/molecule/molecule.H

@@ -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

src/lagrangian/molecularDynamics/molecule/moleculeI.H

@@ -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

src/lagrangian/molecularDynamics/molecule/moleculeIO.C

@@ -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

src/lagrangian/molecularDynamics/potential/Make/files

@@ -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

src/lagrangian/molecularDynamics/potential/Make/options

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

src/lagrangian/molecularDynamics/reducedUnits/reducedUnits.C

@@ -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

src/lagrangian/molecularDynamics/reducedUnits/reducedUnits.H

@@ -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

src/lagrangian/molecularDynamics/reducedUnits/reducedUnitsI.H

@@ -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

src/lagrangian/molecularDynamics/reducedUnits/reducedUnitsIO.C

@@ -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