From e77c7a9bb6da6afd768b693a0fc311fc1901441e Mon Sep 17 00:00:00 2001
From: andy <andy>
Date: Tue, 30 Jun 2009 09:53:10 +0100
Subject: [PATCH] code clean-up...
---
.../BinaryCollisionModel.H | 10 +-
.../bufferedAccumulator/bufferedAccumulator.C | 13 +-
.../bufferedAccumulatorIO.C | 6 +-
.../correlationFunction/correlationFunction.C | 4 +-
.../correlationFunction/correlationFunction.H | 5 +-
.../correlationFunctionIO.C | 20 +--
.../distribution/distribution.C | 14 +-
.../distribution/distribution.H | 3 +-
.../distribution/distributionIO.C | 35 -----
.../directInteractionList.C | 93 ++++++++-----
.../directInteractionList.H | 9 +-
.../directInteractionListI.H | 5 -
.../interactionLists/interactionLists.C | 1 +
.../interactionLists/interactionLists.H | 7 +-
.../referralLists/receivingReferralList.C | 6 +-
.../referralLists/receivingReferralListI.H | 5 -
.../referralLists/sendingReferralList.C | 6 +-
.../referralLists/sendingReferralListI.H | 4 -
.../referredCell/referredCell.C | 20 +--
.../referredCell/referredCell.H | 2 +-
.../referredCellList/referredCellList.C | 127 ++++++++++--------
.../referredCellList/referredCellList.H | 5 +-
.../referredMolecule/referredMolecule.C | 2 -
.../referredMolecule/referredMolecule.H | 2 +-
.../referredMolecule/referredMoleculeI.H | 3 +-
.../molecule/mdTools/averageMDFields.H | 26 ++--
.../calculateAutoCorrelationFunctions.H | 19 +--
.../mdTools/calculateTransportProperties.H | 8 +-
.../molecularDynamics/molecule/mdTools/md.H | 12 +-
.../mdTools/meanMomentumEnergyAndNMols.H | 2 +-
.../molecule/mdTools/resetMDFields.H | 8 +-
.../molecule/mdTools/temperatureAndPressure.H | 1 +
.../molecule/molecule/molecule.H | 3 +
.../molecule/molecule/moleculeI.H | 23 ++--
.../molecule/molecule/moleculeIO.C | 59 ++++----
.../molecule/moleculeCloud/moleculeCloud.C | 5 +-
.../molecule/moleculeCloud/moleculeCloud.H | 16 ++-
.../molecule/moleculeCloud/moleculeCloudI.H | 111 ++++++++-------
.../molecule/reducedUnits/reducedUnits.H | 2 +-
.../electrostaticPotential.C | 2 -
.../electrostaticPotential.H | 2 +-
.../basic/energyScalingFunction.C | 3 +-
.../basic/energyScalingFunction.H | 4 +-
.../basic/newEnergyScalingFunction.C | 4 +-
.../derived/doubleSigmoid/doubleSigmoid.C | 13 +-
.../derived/doubleSigmoid/doubleSigmoid.H | 3 +-
.../derived/noScaling/noScaling.C | 6 +-
.../derived/shifted/shifted.C | 6 +-
.../derived/shifted/shifted.H | 2 +
.../derived/shiftedForce/shiftedForce.C | 6 +-
.../derived/shiftedForce/shiftedForce.H | 2 +-
.../derived/sigmoid/sigmoid.C | 14 +-
.../pairPotential/basic/newPairPotential.C | 4 +-
.../pairPotential/basic/pairPotential.H | 5 +-
.../pairPotential/basic/pairPotentialIO.C | 12 +-
.../pairPotential/derived/azizChen/azizChen.C | 24 ++--
.../pairPotential/derived/azizChen/azizChen.H | 1 +
.../pairPotential/derived/coulomb/coulomb.C | 5 +-
.../pairPotential/derived/coulomb/coulomb.H | 3 +-
.../derived/dampedCoulomb/dampedCoulomb.C | 7 +-
.../derived/dampedCoulomb/dampedCoulomb.H | 7 +-
.../exponentialRepulsion.C | 11 +-
.../exponentialRepulsion.H | 3 +-
.../derived/lennardJones/lennardJones.C | 3 +-
.../derived/lennardJones/lennardJones.H | 3 +-
.../derived/maitlandSmith/maitlandSmith.C | 5 +-
.../derived/maitlandSmith/maitlandSmith.H | 3 +-
.../derived/noInteraction/noInteraction.C | 3 +-
.../derived/noInteraction/noInteraction.H | 2 +-
.../pairPotentialList/pairPotentialList.C | 3 +-
.../pairPotentialList/pairPotentialList.H | 15 ++-
.../pairPotentialList/pairPotentialListI.H | 1 +
.../potential/potential/potential.H | 4 +-
.../potential/potential/potentialI.H | 2 -
.../basic/newTetherPotential.C | 10 +-
.../tetherPotential/basic/tetherPotential.H | 2 +-
.../derived/harmonicSpring/harmonicSpring.H | 2 +-
.../derived/pitchForkRing/pitchForkRing.H | 2 +-
.../restrainedHarmonicSpring.C | 9 +-
.../restrainedHarmonicSpring.H | 2 +-
.../tetherPotentialList/tetherPotentialList.C | 1 -
.../tetherPotentialList/tetherPotentialList.H | 3 +
82 files changed, 481 insertions(+), 445 deletions(-)
delete mode 100644 src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
diff --git a/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H b/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
index 4b422bdd317..0dc8f02ea7d 100644
--- a/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
+++ b/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
@@ -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_;
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
index 80c930bb028..de7d31fcb52 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
@@ -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);
}
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
index 2de8ccfb119..ec1956a345d 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
index adad29b3f11..cce0d86a22c 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
index b751d044f75..fe2071aff37 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
@@ -155,7 +155,10 @@ public:
// IOstream Operators
friend Ostream& operator<< <Type>
- (Ostream&, const correlationFunction<Type>&);
+ (
+ Ostream&,
+ const correlationFunction<Type>&
+ );
};
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
index b1532271884..aa62cdcaf6e 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
index 8c666939e85..439ed64bdf0 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
@@ -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]);
}
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
index 363f68a6cfb..da1ce973bc7 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
deleted file mode 100644
index 7e5a0118f07..00000000000
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
+++ /dev/null
@@ -1,35 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / 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 "distribution.H"
-#include "IOstreams.H"
-
-// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
-
-// construct from Istream
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
index 6af4e7d5bf3..1556db83178 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
@@ -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);
@@ -109,11 +118,11 @@ 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]);
@@ -129,8 +138,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellI],
- cellO) == -1
+ findIndex
+ (
+ directInteractionList[cellI],
+ cellO
+ )
+ ==
+ -1
)
{
directInteractionList[cellI].append(cellO);
@@ -141,8 +155,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellO],
- cellI) == -1
+ findIndex
+ (
+ directInteractionList[cellO],
+ cellI
+ )
+ ==
+ -1
)
{
directInteractionList[cellO].append(cellI);
@@ -160,8 +179,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
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 * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
index 04a957170ce..8a85404ca04 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
index 26529babb6a..34c1d650806 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
@@ -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
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
index 10985a4cc27..f1036eaa0e9 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
@@ -342,6 +342,7 @@ bool Foam::interactionLists::testPointFaceDistance
);
}
+
bool Foam::interactionLists::testPointFaceDistance
(
const vector& p,
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
index a8eeb55ddfa..744b59b067a 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
@@ -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;
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
index e2db2ae6d72..2f646fcba5f 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
@@ -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;
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
index 56134aca58f..084863b01a0 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::receivingReferralList::sourceProc() const
@@ -46,7 +44,4 @@ inline bool operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
index e0a77379107..6235ddabfad 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
@@ -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<<
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
index c6479a14cf6..d34ffd35954 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::sendingReferralList::destinationProc() const
@@ -46,6 +44,4 @@ inline bool operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
index d2a0ecd475e..225ad5902a0 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
@@ -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()
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
index 7f2e5bdbe74..666b4f92682 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
@@ -53,7 +53,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class referredCell Declaration
+ Class referredCell Declaration
\*---------------------------------------------------------------------------*/
class referredCell
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
index 373385ae4dc..2ba95daa18e 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
@@ -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
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
index 54c137ed538..c8a77cb27f3 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
@@ -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
(
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
index 1b19d21d7f5..c1e2e487695 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
@@ -83,6 +83,4 @@ Foam::Ostream& Foam::operator<<
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
index 45d342d2edf..27c3c98ee39 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
@@ -45,7 +45,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class referredMolecule Declaration
+ Class referredMolecule Declaration
\*---------------------------------------------------------------------------*/
class referredMolecule
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
index 1b9666f20ea..1db2f9a923f 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
@@ -45,6 +45,7 @@ Foam::referredMolecule::sitePositions() const
return sitePositions_;
}
+
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
inline bool Foam::operator==
@@ -71,6 +72,4 @@ inline bool Foam::operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
index 7d038729506..9781c9d70f4 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
@@ -56,7 +56,7 @@ if (runTime.outputTime())
forAll(singleSpeciesVelocity, sSV)
{
- if(allSpeciesN_RU[v][sSV])
+ if (allSpeciesN_RU[v][sSV])
{
singleSpeciesVelocity[sSV] =
allSpeciesVelocitySum_RU[v][sSV]
@@ -78,7 +78,7 @@ if (runTime.outputTime())
forAll(totalVelocity.internalField(), tV)
{
- if(totalMass_sum[tV] > VSMALL)
+ if (totalMass_sum[tV] > VSMALL)
{
totalVelocity.internalField()[tV] =
totalMomentum_sum[tV]
@@ -110,14 +110,13 @@ if (runTime.outputTime())
forAll(singleSpeciesTemp, sST)
{
- if(allSpeciesN_RU[t][sST])
+ if (allSpeciesN_RU[t][sST])
{
singleSpeciesTemp[sST] =
allSpeciesM_RU[t][sST]
/allSpeciesN_RU[t][sST]
/(3.0 * moleculeCloud::kb * allSpeciesN_RU[t][sST])
- *
- (
+ *(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
-
(
@@ -130,11 +129,10 @@ if (runTime.outputTime())
totalTemperatureVTerms_sum[sST] +=
allSpeciesM_RU[t][sST]
- /allSpeciesN_RU[t][sST]
- *
- (
+ /allSpeciesN_RU[t][sST]
+ *(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
- -
+ -
(
allSpeciesVelocitySum_RU[t][sST]
&
@@ -187,10 +185,9 @@ if (runTime.outputTime())
{
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]
);
@@ -198,8 +195,7 @@ if (runTime.outputTime())
allSpeciesM_RU[mKE][sSMKE]
/allSpeciesN_RU[mKE][sSMKE]
/2.0
- *
- (
+ *(
allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
);
}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
index bc5848475d3..968cfa93cb8 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
@@ -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);
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
index 74f1db9da7f..0ee094ff149 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
index ae4ab081242..9a079764ae8 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
index 827ff3ffc26..fb5118bb5a4 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
@@ -186,7 +186,7 @@ if (singleStepNMols)
}
else
{
- Info << "No molecules in system" << endl;
+ Info<< "No molecules in system" << endl;
}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
index ff274a33366..af0197b5fe4 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
@@ -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)
);
}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
index cd02fcce08a..788763b163d 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
@@ -110,4 +110,5 @@ if (runTime.outputTime())
accumulatedDOFs = 0;
}
+
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
index 538d4f340cf..ef2de145c46 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
@@ -108,6 +108,7 @@ public:
bool linearMoleculeTest() const;
+
public:
inline constantProperties();
@@ -214,6 +215,7 @@ private:
List<vector> sitePositions_;
+
// Private Member Functions
tensor rotationTensorX(scalar deltaT) const;
@@ -222,6 +224,7 @@ private:
tensor rotationTensorZ(scalar deltaT) const;
+
public:
friend class Cloud<molecule>;
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
index 743d45b7f9b..447a04e4ea3 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
@@ -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
@@ -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
@@ -379,7 +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."
@@ -403,10 +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);
}
@@ -616,6 +615,4 @@ inline Foam::label Foam::molecule::id() const
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
index f43b4aac6e2..04ae825df59 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
@@ -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_;
}
}
@@ -176,6 +176,7 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
mC.fieldIOobject("piGlobal", IOobject::NO_READ),
np
);
+
IOField<vector> tauGlobal
(
mC.fieldIOobject("tauGlobal", IOobject::NO_READ),
@@ -276,17 +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
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
index e69f1dfa5d4..b747373e3a7 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
@@ -928,7 +928,6 @@ void Foam::moleculeCloud::initialiseMolecules
n++;
}
-
}
}
}
@@ -1177,7 +1176,7 @@ void Foam::moleculeCloud::writeXYZ(const fileName& fName) const
{
OFstream str(fName);
- str<< nSites() << nl << "moleculeCloud site positions in angstroms" << nl;
+ str << nSites() << nl << "moleculeCloud site positions in angstroms" << nl;
const_iterator mol(this->begin());
@@ -1189,7 +1188,7 @@ void Foam::moleculeCloud::writeXYZ(const fileName& fName) const
{
const point& sP = mol().sitePositions()[i];
- str<< pot_.siteIdList()[cP.siteIds()[i]]
+ str << pot_.siteIdList()[cP.siteIds()[i]]
<< ' ' << sP.x()*1e10
<< ' ' << sP.y()*1e10
<< ' ' << sP.z()*1e10
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
index 719605a89cc..6863227c12c 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
@@ -52,7 +52,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class moleculeCloud Declaration
+ Class moleculeCloud Declaration
\*---------------------------------------------------------------------------*/
class moleculeCloud
@@ -76,6 +76,7 @@ private:
Random rndGen_;
+
// Private Member Functions
void buildConstProps();
@@ -163,6 +164,7 @@ public:
static scalar vacuumPermittivity;
+
// Constructors
//- Construct given mesh and potential references
@@ -180,8 +182,8 @@ public:
const IOdictionary& mdInitialiseDict
);
- // Member Functions
+ // Member Functions
//- Evolve the molecules (move, calculate forces, control state etc)
void evolve();
@@ -194,6 +196,7 @@ public:
const scalar measuredTemperature
);
+
// Access
inline const polyMesh& mesh() const;
@@ -207,19 +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;
+ void writeXYZ(const fileName& fName) const;
};
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
index acc33480440..94c9f49286b 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
@@ -32,9 +32,9 @@ inline void Foam::moleculeCloud::evaluatePair
molecule* molJ
)
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const pairPotential& electrostatic(pairPot.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;
@@ -94,7 +95,7 @@ inline void Foam::moleculeCloud::evaluatePair
vector rIJ = molI->position() - molJ->position();
tensor virialContribution =
- (rsIsJ * fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
+ (rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
molI->rf() += virialContribution;
@@ -121,15 +122,17 @@ 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;
@@ -138,7 +141,7 @@ inline void Foam::moleculeCloud::evaluatePair
vector rIJ = molI->position() - molJ->position();
tensor virialContribution =
- (rsIsJ * fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
+ (rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
molI->rf() += virialContribution;
@@ -153,15 +156,16 @@ inline void Foam::moleculeCloud::evaluatePair
}
}
+
inline void Foam::moleculeCloud::evaluatePair
(
molecule* molReal,
referredMolecule* molRef
)
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const pairPotential& electrostatic(pairPot.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@@ -194,16 +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;
@@ -216,9 +222,10 @@ inline void Foam::moleculeCloud::evaluatePair
vector rRealRef = molReal->position() - molRef->position();
- molReal->rf() += (rsRealsRef * fsRealsRef)
- *(rsRealsRef & rRealRef)
- /rsRealsRefMagSq;
+ molReal->rf() +=
+ (rsRealsRef*fsRealsRef)
+ *(rsRealsRef & rRealRef)
+ /rsRealsRefMagSq;
// molReal->rf() += rsRealsRef * fsRealsRef;
@@ -228,11 +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(rsRealsRefMagSq <= electrostatic.rCutSqr())
+ if (rsRealsRefMagSq <= electrostatic.rCutSqr())
{
scalar rsRealsRefMag = mag(rsRealsRef);
@@ -240,22 +248,25 @@ 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;
vector rRealRef = molReal->position() - molRef->position();
- molReal->rf() += (rsRealsRef * fsRealsRef)
- *(rsRealsRef & rRealRef)
- /rsRealsRefMagSq;
+ molReal->rf() +=
+ (rsRealsRef*fsRealsRef)
+ *(rsRealsRef & rRealRef)
+ /rsRealsRefMagSq;
// molReal->rf() += rsRealsRef * fsRealsRef;
}
@@ -271,9 +282,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
molecule* molJ
) const
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const pairPotential& electrostatic(pairPot.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idI = molI->id();
@@ -306,11 +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);
@@ -321,7 +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"
@@ -355,11 +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);
@@ -370,7 +381,7 @@ 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"
@@ -414,9 +425,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
referredMolecule* molRef
) const
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const pairPotential& electrostatic(pairPot.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@@ -449,11 +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);
@@ -464,7 +476,7 @@ 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"
@@ -499,11 +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);
@@ -514,7 +527,7 @@ 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"
@@ -539,8 +552,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
(
mag
(
- chargeReal*chargeRef
- *electrostatic.energy(rsRealsRefMag)
+ chargeReal
+ *chargeRef
+ *electrostatic.energy(rsRealsRefMag)
)
> pot_.potentialEnergyLimit()
)
@@ -599,6 +613,7 @@ inline Foam::vector Foam::moleculeCloud::equipartitionAngularMomentum
}
}
+
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::polyMesh& Foam::moleculeCloud::mesh() const
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
index cce0c725f18..acefe4b8151 100644
--- a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
@@ -46,7 +46,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class reducedUnits Declaration
+ Class reducedUnits Declaration
\*---------------------------------------------------------------------------*/
class reducedUnits
diff --git a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
index bc0f50a9442..1dff432741c 100644
--- a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
@@ -27,8 +27,6 @@ License
#include "electrostaticPotential.H"
#include "mathematicalConstants.H"
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::electrostaticPotential::electrostaticPotential()
diff --git a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
index cee15d771bd..d2c4bb88b91 100644
--- a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
@@ -44,7 +44,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class electrostaticPotential Declaration
+ Class electrostaticPotential Declaration
\*---------------------------------------------------------------------------*/
class electrostaticPotential
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
index 2110ca84281..df247d84dea 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
index 5055db985f3..8815151bcf0 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
@@ -48,7 +48,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class energyScalingFunction Declaration
+ Class energyScalingFunction Declaration
\*---------------------------------------------------------------------------*/
class energyScalingFunction
@@ -144,8 +144,6 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
#endif
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
index e9c03e78c08..ccbdb8c92e7 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
@@ -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);
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
index 6c43a1d63e7..defeb779a06 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
index b2b9e189e96..27e75fb1901 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
index 4b89cb174e7..412f7538876 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
index 9b4c5a4b9ce..d6866cfc8f9 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
index 1177a35febc..01b0b413f34 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
@@ -57,6 +57,7 @@ class shifted
scalar e_at_rCut_;
+
public:
//- Runtime type information
@@ -79,6 +80,7 @@ public:
~shifted()
{}
+
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
index da2b2baaf04..72041de3e05 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
index 2ae26169ab5..f6d97d002b6 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
@@ -46,7 +46,7 @@ namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
- Class shiftedForce Declaration
+ Class shiftedForce Declaration
\*---------------------------------------------------------------------------*/
class shiftedForce
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
index 443fbb0ade9..c689608172a 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
index d9092c1a24f..2986a0e5394 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
@@ -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);
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
index e1ddc7b5448..9be12ebd0c8 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
@@ -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;
@@ -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;
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
index dffe4233b40..a07f21beceb 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
@@ -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();
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
index 2d990c110b9..2e44f617da3 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
index 5af682d87a6..53f93481281 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
@@ -85,6 +85,7 @@ class azizChen
scalar D_;
scalar gamma_;
+
public:
//- Runtime type information
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
index 21444b215f1..7dd02320322 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
@@ -47,9 +47,7 @@ addToRunTimeSelectionTable
);
scalar coulomb::oneOverFourPiEps0 =
-1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
-
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
+ 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -65,6 +63,7 @@ coulomb::coulomb
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar coulomb::unscaledEnergy(const scalar r) const
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
index cb3eada59e5..f1e06712bb7 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
@@ -56,7 +56,8 @@ class coulomb
public:
//- Runtime type information
- TypeName("coulomb");
+ TypeName("coulomb");
+
// Static data members
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
index 711c2a45112..fd771e1854e 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
@@ -47,9 +47,7 @@ addToRunTimeSelectionTable
);
scalar dampedCoulomb::oneOverFourPiEps0 =
-1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
-
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
+ 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -70,6 +68,7 @@ dampedCoulomb::dampedCoulomb
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar dampedCoulomb::unscaledEnergy(const scalar r) const
@@ -83,7 +82,7 @@ bool dampedCoulomb::read(const dictionary& pairPotentialProperties)
pairPotential::read(pairPotentialProperties);
dampedCoulombCoeffs_ =
- pairPotentialProperties.subDict(typeName + "Coeffs");
+ pairPotentialProperties.subDict(typeName + "Coeffs");
dampedCoulombCoeffs_.lookup("alpha") >> alpha_;
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
index eb44399dbe6..377b531824e 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
@@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class dampedCoulomb Declaration
+ Class dampedCoulomb Declaration
\*---------------------------------------------------------------------------*/
class dampedCoulomb
@@ -59,15 +59,18 @@ class dampedCoulomb
scalar alpha_;
+
public:
//- Runtime type information
- TypeName("dampedCoulomb");
+ TypeName("dampedCoulomb");
+
// Static data members
static scalar oneOverFourPiEps0;
+
// Constructors
//- Construct from components
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
index a303935b1e8..ae34ef4cdbc 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
@@ -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_;
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
index 148ea002cfd..8ce1ee4a0f9 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
index 4e3e6349305..d5a1deb88e6 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
index 92dc4b5f558..2ae3c036ae4 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
index 6ae3c92add6..7545573591b 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
@@ -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;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
index 37468b2daf5..cdeb01211b5 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
index d3c08871eb2..3326fd7fe1f 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
@@ -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
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
index 938f2a30a9c..5d3fd5742db 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
@@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class noInteraction Declaration
+ Class noInteraction Declaration
\*---------------------------------------------------------------------------*/
class noInteraction
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
index 0172cf94c07..2d77c4ce595 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
@@ -170,6 +170,7 @@ void Foam::pairPotentialList::readPairPotentialDict
rCutMaxSqr_ = rCutMax_*rCutMax_;
}
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::pairPotentialList::pairPotentialList()
@@ -177,6 +178,7 @@ Foam::pairPotentialList::pairPotentialList()
PtrList<pairPotential>()
{}
+
Foam::pairPotentialList::pairPotentialList
(
const List<word>& idList,
@@ -319,6 +321,5 @@ Foam::scalar Foam::pairPotentialList::energy
return e;
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
index 19e678eb229..b4193a46ae4 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
@@ -47,7 +47,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class pairPotentialList Declaration
+ Class pairPotentialList Declaration
\*---------------------------------------------------------------------------*/
class pairPotentialList
@@ -64,6 +64,7 @@ class pairPotentialList
autoPtr<pairPotential> electrostaticPotential_;
+
// Private Member Functions
inline label pairPotentialIndex
@@ -85,6 +86,7 @@ class pairPotentialList
//- Disallow default bitwise copy construct
pairPotentialList(const pairPotentialList&);
+
public:
// Constructors
@@ -99,10 +101,12 @@ public:
const polyMesh& mesh
);
+
// Destructor
~pairPotentialList();
+
// Member Functions
void buildPotentials
@@ -112,6 +116,7 @@ public:
const polyMesh& mesh
);
+
// Access
inline scalar rCutMax() const;
@@ -134,13 +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
(
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
index 0e296697f10..c14aa3695e1 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
@@ -56,6 +56,7 @@ inline Foam::label Foam::pairPotentialList::pairPotentialIndex
return index;
}
+
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::scalar Foam::pairPotentialList::rCutMax() const
diff --git a/src/lagrangian/molecularDynamics/potential/potential/potential.H b/src/lagrangian/molecularDynamics/potential/potential/potential.H
index 5c8569cb0cc..32f9b2a1d29 100644
--- a/src/lagrangian/molecularDynamics/potential/potential/potential.H
+++ b/src/lagrangian/molecularDynamics/potential/potential/potential.H
@@ -49,7 +49,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class potential Declaration
+ Class potential Declaration
\*---------------------------------------------------------------------------*/
class potential
@@ -74,6 +74,7 @@ class potential
vector gravity_;
+
// Private Member Functions
void setSiteIdList(const IOdictionary& moleculePropertiesDict);
@@ -108,6 +109,7 @@ public:
IOdictionary& idListDict
);
+
// Destructor
~potential();
diff --git a/src/lagrangian/molecularDynamics/potential/potential/potentialI.H b/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
index 0b72556152c..38ba6344557 100644
--- a/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
+++ b/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::potential::nIds() const
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
index d8c4e575326..85c8a703596 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
@@ -39,7 +39,11 @@ autoPtr<tetherPotential> tetherPotential::New
const dictionary& tetherPotentialProperties
)
{
- word tetherPotentialTypeName(tetherPotentialProperties.lookup("tetherPotential"));
+ word
+ tetherPotentialTypeName
+ (
+ tetherPotentialProperties.lookup("tetherPotential")
+ );
Info<< nl << "Selecting tether potential "
<< tetherPotentialTypeName << " for "
@@ -54,8 +58,8 @@ autoPtr<tetherPotential> tetherPotential::New
(
"tetherPotential::New()"
) << "Unknown tetherPotential type "
- << tetherPotentialTypeName << endl << endl
- << "Valid tetherPotentials are : " << endl
+ << tetherPotentialTypeName << nl << nl
+ << "Valid tetherPotentials are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
index a70da011778..f65e5bb6b85 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
@@ -48,7 +48,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class tetherPotential Declaration
+ Class tetherPotential Declaration
\*---------------------------------------------------------------------------*/
class tetherPotential
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
index 90b3251c171..4af51cfdff8 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class harmonicSpring Declaration
+ Class harmonicSpring Declaration
\*---------------------------------------------------------------------------*/
class harmonicSpring
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
index f78a3aa7c26..2bb98e39bd2 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class pitchForkRing Declaration
+ Class pitchForkRing Declaration
\*---------------------------------------------------------------------------*/
class pitchForkRing
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
index 289190798f0..5396013a173 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -88,6 +86,7 @@ scalar restrainedHarmonicSpring::energy(const vector r) const
}
}
+
vector restrainedHarmonicSpring::force(const vector r) const
{
scalar magR = mag(r);
@@ -102,7 +101,11 @@ vector restrainedHarmonicSpring::force(const vector r) const
}
}
-bool restrainedHarmonicSpring::read(const dictionary& tetherPotentialProperties)
+
+bool restrainedHarmonicSpring::read
+(
+ const dictionary& tetherPotentialProperties
+)
{
tetherPotential::read(tetherPotentialProperties);
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
index 028809010ab..1711c4f5f3e 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class restrainedHarmonicSpring Declaration
+ Class restrainedHarmonicSpring Declaration
\*---------------------------------------------------------------------------*/
class restrainedHarmonicSpring
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
index d0b514b9b59..93498b8f711 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
@@ -154,6 +154,5 @@ Foam::scalar Foam::tetherPotentialList::energy
return (*this)[tetherPotentialIndex(a)].energy(rIT);
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
index cb9bf9633b1..8ca770f5235 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
@@ -57,6 +57,7 @@ class tetherPotentialList
List<label> idMap_;
+
// Private Member Functions
inline label tetherPotentialIndex
@@ -92,10 +93,12 @@ public:
const List<word>& tetherSiteIdList
);
+
// Destructor
~tetherPotentialList();
+
// Member Functions
void buildPotentials
--
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