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Commit ebcfba84 authored by Andrew Heather's avatar Andrew Heather
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formatting changes

parent 1ae68a17
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src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
View file @ ebcfba84
......@@ -135,7 +135,7 @@ scalar distribution::median()
scalar runningSum = 0.0;
List< Pair<scalar> > normDist(normalised());
List<Pair<scalar> > normDist(normalised());
if (normDist.size())
{
......@@ -259,7 +259,7 @@ List< Pair<scalar> > distribution::normalised()
sort(keys);
List< Pair<scalar> > normDist(size());
List<Pair<scalar> > normDist(size());
forAll(keys,k)
{
......@@ -282,9 +282,9 @@ List< Pair<scalar> > distribution::normalisedMinusMean()
List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
{
List< Pair<scalar> > oldDist(normalised());
List<Pair<scalar> > oldDist(normalised());
List< Pair<scalar> > newDist(oldDist.size());
List<Pair<scalar> > newDist(oldDist.size());
forAll(oldDist,u)
{
......@@ -383,7 +383,7 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
}
List< Pair<scalar> > distribution::raw()
List<Pair<scalar> > distribution::raw()
{
insertMissingKeys();
......@@ -391,7 +391,7 @@ List< Pair<scalar> > distribution::raw()
sort(keys);
List< Pair<scalar> > rawDist(size());
List<Pair<scalar> > rawDist(size());
forAll(keys,k)
{
......
src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
View file @ ebcfba84
......@@ -94,13 +94,14 @@ public:
void insertMissingKeys();
List< Pair<scalar> > normalised();
List<Pair<scalar> > normalised();
List< Pair<scalar> > normalisedMinusMean();
List<Pair<scalar> > normalisedMinusMean();
List< Pair<scalar> > normalisedShifted(const scalar shiftValue);
List<Pair<scalar> > normalisedShifted(const scalar shiftValue);
List<Pair<scalar> > raw();
List< Pair<scalar> > raw();
// Access
......
src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
View file @ ebcfba84
......@@ -24,19 +24,12 @@ License
\*---------------------------------------------------------------------------*/
namespace Foam
{
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline scalar distribution::binWidth() const
inline Foam::scalar Foam::distribution::binWidth() const
{
return binWidth_;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //
src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
View file @ ebcfba84
......@@ -24,9 +24,6 @@ License
\*---------------------------------------------------------------------------*/
namespace Foam
{
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
......@@ -35,8 +32,4 @@ inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //
src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
View file @ ebcfba84
......@@ -98,6 +98,7 @@ public:
const referredMolecule& b
);
// IOstream Operators
friend Istream& operator>>
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
View file @ ebcfba84
......@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
energyScalingFunction
Foam::energyScalingFunction
Description
......@@ -59,11 +59,12 @@ protected:
// Protected data
word name_;
dictionary energyScalingFunctionProperties_;
const pairPotential& pairPot_;
// Private Member Functions
//- Disallow copy construct
......@@ -72,6 +73,7 @@ protected:
//- Disallow default bitwise assignment
void operator=(const energyScalingFunction&);
public:
//- Runtime type information
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
doubleSigmoid
Foam::energyScalingFunctions::doubleSigmoid
Description
SourceFiles
doubleSigmoid.C
......@@ -54,14 +54,14 @@ class doubleSigmoid
public energyScalingFunction
{
// Private data
dictionary doubleSigmoidCoeffs_;
scalar shift1_;
scalar scale1_;
scalar shift2_;
scalar scale2_;
// Private Member Functions
scalar sigmoidScale
......@@ -71,6 +71,7 @@ class doubleSigmoid
const scalar scale
) const;
public:
//- Runtime type information
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
noScaling
Foam::energyScalingFunctions::noScaling
Description
SourceFiles
noScaling.C
......@@ -53,7 +53,6 @@ class noScaling
:
public energyScalingFunction
{
// Private data
public:
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
shifted
Foam::energyScalingFunctions::shifted
Description
SourceFiles
shifted.C
......@@ -54,9 +54,10 @@ class shifted
public energyScalingFunction
{
// Private data
scalar e_at_rCut_;
public:
//- Runtime type information
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
shiftedForce
Foam::energyScalingFunctions::shiftedForce
Description
SourceFiles
shiftedForce.C
......@@ -54,14 +54,13 @@ class shiftedForce
public energyScalingFunction
{
// Private data
scalar rCut_;
scalar e_at_rCut_;
scalar de_dr_at_rCut_;
// Private Member Functions
public:
......@@ -85,8 +84,9 @@ public:
~shiftedForce()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Read transportProperties dictionary
......
src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
sigmoid
Foam::energyScalingFunctions::sigmoid
Description
SourceFiles
sigmoid.C
......@@ -54,12 +54,13 @@ class sigmoid
public energyScalingFunction
{
// Private data
dictionary sigmoidCoeffs_;
scalar shift_;
scalar scale_;
// Private Member Functions
scalar sigmoidScale
......@@ -69,6 +70,7 @@ class sigmoid
const scalar scale
) const;
public:
//- Runtime type information
......@@ -91,6 +93,7 @@ public:
~sigmoid()
{}
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
......
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
View file @ ebcfba84
......@@ -52,7 +52,7 @@ void Foam::pairPotential::scaleEnergy(scalar& e, const scalar r) const
name_, pairPotentialProperties_, *this
).ptr();
}
esfPtr_->scaleEnergy(e, r);
}
......@@ -77,6 +77,7 @@ Foam::pairPotential::pairPotential
writeTables_(Switch(pairPotentialProperties_.lookup("writeTables")))
{}
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void Foam::pairPotential::setLookupTables()
......@@ -91,7 +92,7 @@ void Foam::pairPotential::setLookupTables()
{
energyLookup_[k] = scaledEnergy(k*dr_ + rMin_);
forceLookup_[k] = -energyDerivative( (k * dr_ + rMin_), true);
forceLookup_[k] = -energyDerivative((k*dr_ + rMin_), true);
}
}
......@@ -105,8 +106,8 @@ Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
<< "r less than rMin" << nl
<< abort(FatalError);
<< "r less than rMin" << nl
<< abort(FatalError);
}
scalar f =
......@@ -120,7 +121,7 @@ Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
Foam::List< Foam::Pair< Foam::scalar > >
Foam::pairPotential::forceTable() const
{
List< Pair<scalar> > forceTab(forceLookup_.size());
List<Pair<scalar> > forceTab(forceLookup_.size());
forAll(forceLookup_,k)
{
......@@ -142,8 +143,8 @@ Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
<< "r less than rMin" << nl
<< abort(FatalError);
<< "r less than rMin" << nl
<< abort(FatalError);
}
scalar e =
......@@ -157,7 +158,7 @@ Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
Foam::List< Foam::Pair< Foam::scalar > >
Foam::pairPotential::energyTable() const
{
List< Pair<scalar> > energyTab(energyLookup_.size());
List<Pair<scalar> > energyTab(energyLookup_.size());
forAll(energyLookup_,k)
{
......@@ -173,7 +174,7 @@ Foam::List< Foam::Pair< Foam::scalar > >
Foam::scalar Foam::pairPotential::scaledEnergy(const scalar r) const
{
scalar e = unscaledEnergy(r);
scaleEnergy(e, r);
return e;
......@@ -192,7 +193,7 @@ Foam::scalar Foam::pairPotential::energyDerivative
scalar ra = r - dr_;
scalar rf = r;
scalar rb = r + dr_;
scalar Ea, Ef, Eb;
if (scaledEnergyDerivative)
......@@ -207,20 +208,20 @@ Foam::scalar Foam::pairPotential::energyDerivative
Ef = unscaledEnergy(rf);
Eb = unscaledEnergy(rb);
}
scalar denominator = (ra - rf)*(ra - rb)*(rf - rb);
scalar a1 =
(
rb*rb*(Ea - Ef) + ra*ra*(Ef - Eb) + rf*rf*(Eb - Ea)
) / denominator;
scalar a2 =
scalar a2 =
(
rb*(Ef - Ea) + rf*(Ea - Eb) + ra*(Eb - Ef)
) / denominator;
return a1 + 2.0 * a2 * r;
return a1 + 2.0*a2*r;
}
......@@ -231,6 +232,7 @@ bool Foam::pairPotential::read(const dictionary& pairPotentialProperties)
return true;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
......
src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
View file @ ebcfba84
......@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
pairPotential
Foam::pairPotential
Description
......@@ -82,13 +82,14 @@ protected:
// Private Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
//- Disallow copy construct
pairPotential(const pairPotential&);
//- Disallow default bitwise assignment
void operator=(const pairPotential&);
public:
//- Runtime type information
......@@ -152,9 +153,9 @@ public:
scalar forceLookup (const scalar r) const;
List< Pair <scalar> > energyTable() const;
List<Pair<scalar> > energyTable() const;
List< Pair <scalar> > forceTable() const;
List<Pair<scalar> > forceTable() const;
inline bool writeTables() const;
......
src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
View file @ ebcfba84
......@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
azizChen
Foam::pairPotentials::azizChen
Description
......
src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
View file @ ebcfba84
......@@ -74,7 +74,7 @@ scalar lennardJones::unscaledEnergy(const scalar r) const
// (rIJ/sigma)^-6
scalar ir6 = ir2*ir2*ir2;
return 4.0 * epsilon_ * (ir6 * (ir6 - 1.0));
return 4.0 * epsilon_*(ir6*(ir6 - 1.0));
}
......@@ -86,7 +86,7 @@ bool lennardJones::read(const dictionary& pairPotentialProperties)
lennardJonesCoeffs_.lookup("sigma") >> sigma_;
lennardJonesCoeffs_.lookup("epsilon") >> epsilon_;
return true;
}
......
src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
View file @ ebcfba84
......@@ -23,10 +23,10 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
lennardJones
Foam::pairPotentials::lennardJones
Description
SourceFiles
lennardJones.C
......
src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
View file @ ebcfba84
......@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
maitlandSmith
Foam::pairPotentials::maitlandSmith
Description
......
src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
View file @ ebcfba84
......@@ -36,54 +36,55 @@ void Foam::pairPotentialList::readPairPotentialDict
const polyMesh& mesh
)
{
Info<< nl << "Building pair potentials." << endl;
Info<< nl << "Building pair potentials." << endl;
rCutMax_ = 0.0;
for (label a = 0; a < nIds(); ++a)
{
word idA = idList_[a];
for (label b = a; b < nIds(); ++b)
{
word idB = idList_[b];
word pairPotentialName;
if (a==b)
if (a == b)
{
if(pairPotentialDict.found(idA+"-"+idB))
if (pairPotentialDict.found(idA + "-" + idB))
{
pairPotentialName = idA+"-"+idB;
pairPotentialName = idA + "-" + idB;
}
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "
<< idA+"-"+idB << " not found"
<< abort(FatalError);
<< idA << "-" << idB << " not found"
<< nl << abort(FatalError);
}
}
else
{
if(pairPotentialDict.found(idA+"-"+idB))
if (pairPotentialDict.found(idA + "-" + idB))
{
pairPotentialName = idA+"-"+idB;
pairPotentialName = idA + "-" + idB;
}
else if(pairPotentialDict.found(idB+"-"+idA))
else if (pairPotentialDict.found(idB + "-" + idA))
{
pairPotentialName = idB+"-"+idA;
pairPotentialName = idB + "-" + idA;
}
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "
<< idA+"-"+idB << " or " << idB+"-"+idA << " not found"
<< abort(FatalError);
<< idA << "-" << idB << " or "
<< idB << "-" << idA << " not found"
<< nl << abort(FatalError);
}
if
(
pairPotentialDict.found(idA+"-"+idB)
......@@ -92,15 +93,15 @@ void Foam::pairPotentialList::readPairPotentialDict
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
<< "Pair pairPotential specification subDict "