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Commit 162d69a2 authored by peastman's avatar peastman
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Merge pull request #827 from peastman/reference 

Lots of cleanup to reference platform
parents 2379b982 c44c956d
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plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 162d69a2
......@@ -77,7 +77,7 @@ public:
*
* @return global cubicK term
*/
double getAmoebaGlobalAngleCubic( void ) const;
double getAmoebaGlobalAngleCubic() const;
/**
* Set the global quartic term
......@@ -91,7 +91,7 @@ public:
*
* @return global quartic term
*/
double getAmoebaGlobalAngleQuartic( void ) const;
double getAmoebaGlobalAngleQuartic() const;
/**
* Set the global pentic term
......@@ -105,7 +105,7 @@ public:
*
* @return global penticK term
*/
double getAmoebaGlobalAnglePentic( void ) const;
double getAmoebaGlobalAnglePentic() const;
/**
* Set the global sextic term
......@@ -119,7 +119,7 @@ public:
*
* @return global sextic term
*/
double getAmoebaGlobalAngleSextic( void ) const;
double getAmoebaGlobalAngleSextic() const;
/**
* Add an angle term to the force field.
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ 162d69a2
......@@ -78,7 +78,7 @@ public:
*
* @return global cubicK term
*/
double getAmoebaGlobalBondCubic( void ) const;
double getAmoebaGlobalBondCubic() const;
/**
* Set the global quartic term
......@@ -92,7 +92,7 @@ public:
*
* @return global quartic term
*/
double getAmoebaGlobalBondQuartic( void ) const;
double getAmoebaGlobalBondQuartic() const;
/**
* Add a bond term to the force field.
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ 162d69a2
......@@ -127,7 +127,7 @@ public:
/**
* Get the flag signaling whether the cavity term should be included
*/
int getIncludeCavityTerm( ) const;
int getIncludeCavityTerm() const;
/**
* Set the flag signaling whether the cavity term should be included
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ 162d69a2
......@@ -77,7 +77,7 @@ public:
*
* @return global cubicK term
*/
double getAmoebaGlobalInPlaneAngleCubic( void ) const;
double getAmoebaGlobalInPlaneAngleCubic() const;
/**
* Set the global quartic term
......@@ -91,7 +91,7 @@ public:
*
* @return global quartic term
*/
double getAmoebaGlobalInPlaneAngleQuartic( void ) const;
double getAmoebaGlobalInPlaneAngleQuartic() const;
/**
* Set the global pentic term
......@@ -105,7 +105,7 @@ public:
*
* @return global penticK term
*/
double getAmoebaGlobalInPlaneAnglePentic( void ) const;
double getAmoebaGlobalInPlaneAnglePentic() const;
/**
* Set the global sextic term
......@@ -119,7 +119,7 @@ public:
*
* @return global sextic term
*/
double getAmoebaGlobalInPlaneAngleSextic( void ) const;
double getAmoebaGlobalInPlaneAngleSextic() const;
/**
* Add an angle term to the force field.
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ 162d69a2
......@@ -97,7 +97,7 @@ private:
static int CovalentDegrees[AmoebaMultipoleForce::CovalentEnd];
static bool initializedCovalentDegrees;
static const int* getCovalentDegrees( void );
static const int* getCovalentDegrees();
};
} // namespace OpenMM
......
plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ 162d69a2
......@@ -63,7 +63,7 @@ void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle
angles[index].quadraticK = quadraticK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleCubic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
return _globalCubicK;
}
......@@ -71,7 +71,7 @@ void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
_globalCubicK = cubicK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleQuartic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
return _globalQuarticK;
}
......@@ -79,7 +79,7 @@ void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaAngleForce::getAmoebaGlobalAnglePentic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
return _globalPenticK;
}
......@@ -87,7 +87,7 @@ void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
_globalPenticK = penticK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleSextic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const {
return _globalSexticK;
}
......
plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ 162d69a2
......@@ -67,11 +67,11 @@ void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaBondForce::getAmoebaGlobalBondCubic( void ) const {
double AmoebaBondForce::getAmoebaGlobalBondCubic() const {
return _globalCubicK;
}
double AmoebaBondForce::getAmoebaGlobalBondQuartic( void ) const {
double AmoebaBondForce::getAmoebaGlobalBondQuartic() const {
return _globalQuarticK;
}
......
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ 162d69a2
......@@ -73,11 +73,11 @@ void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK
_globalQuarticK = quarticK;
}
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic() const {
return _globalCubicK;
}
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic() const {
return _globalQuarticK;
}
......@@ -89,11 +89,11 @@ void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK
_globalSexticK = quarticK;
}
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic() const {
return _globalPenticK;
}
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic() const {
return _globalSexticK;
}
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 162d69a2
......@@ -45,7 +45,7 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
}
AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
return nonbondedMethod;
}
......@@ -53,7 +53,7 @@ void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMe
nonbondedMethod = method;
}
AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType() const {
return polarizationType;
}
......@@ -77,7 +77,7 @@ void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
aewald = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const {
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
return pmeBSplineOrder;
}
......@@ -103,7 +103,7 @@ void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDim
return;
}
int AmoebaMultipoleForce::getMutualInducedMaxIterations( void ) const {
int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
return mutualInducedMaxIterations;
}
......@@ -111,7 +111,7 @@ void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInduced
mutualInducedMaxIterations = inputMutualInducedMaxIterations;
}
double AmoebaMultipoleForce::getMutualInducedTargetEpsilon( void ) const {
double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const {
return mutualInducedTargetEpsilon;
}
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 162d69a2
......@@ -138,7 +138,7 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
return names;
}
const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
if( !initializedCovalentDegrees ){
initializedCovalentDegrees = true;
CovalentDegrees[AmoebaMultipoleForce::Covalent12] = 1;
......
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp
View file @ 162d69a2
......@@ -44,7 +44,7 @@ AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
return _globalCubicK;
}
......@@ -52,7 +52,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK
_globalCubicK = cubicK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
return _globalQuarticK;
}
......@@ -60,7 +60,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quar
_globalQuarticK = quarticK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
return _globalPenticK;
}
......@@ -68,7 +68,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penti
_globalPenticK = penticK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const {
return _globalSexticK;
}
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ 162d69a2
......@@ -66,7 +66,7 @@ void AmoebaVdwForce::setSigmaCombiningRule( const std::string& inputSigmaCombini
sigmaCombiningRule = inputSigmaCombiningRule;
}
const std::string& AmoebaVdwForce::getSigmaCombiningRule( void ) const {
const std::string& AmoebaVdwForce::getSigmaCombiningRule() const {
return sigmaCombiningRule;
}
......@@ -74,7 +74,7 @@ void AmoebaVdwForce::setEpsilonCombiningRule( const std::string& inputEpsilonCom
epsilonCombiningRule = inputEpsilonCombiningRule;
}
const std::string& AmoebaVdwForce::getEpsilonCombiningRule( void ) const {
const std::string& AmoebaVdwForce::getEpsilonCombiningRule() const {
return epsilonCombiningRule;
}
......
plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForce.cpp
View file @ 162d69a2
......@@ -63,35 +63,35 @@ void AmoebaWcaDispersionForce::setParticleParameters(int particleIndex, double r
parameters[particleIndex].epsilon = epsilon;
}
double AmoebaWcaDispersionForce::getEpso( void ) const {
double AmoebaWcaDispersionForce::getEpso() const {
return epso;
}
double AmoebaWcaDispersionForce::getEpsh( void ) const {
double AmoebaWcaDispersionForce::getEpsh() const {
return epsh;
}
double AmoebaWcaDispersionForce::getRmino( void ) const {
double AmoebaWcaDispersionForce::getRmino() const {
return rmino;
}
double AmoebaWcaDispersionForce::getRminh( void ) const {
double AmoebaWcaDispersionForce::getRminh() const {
return rminh;
}
double AmoebaWcaDispersionForce::getAwater( void ) const {
double AmoebaWcaDispersionForce::getAwater() const {
return awater;
}
double AmoebaWcaDispersionForce::getShctd( void ) const {
double AmoebaWcaDispersionForce::getShctd() const {
return shctd;
}
double AmoebaWcaDispersionForce::getDispoff( void ) const {
double AmoebaWcaDispersionForce::getDispoff() const {
return dispoff;
}
double AmoebaWcaDispersionForce::getSlevy( void ) const {
double AmoebaWcaDispersionForce::getSlevy() const {
return slevy;
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 162d69a2
......@@ -91,16 +91,16 @@ ReferenceCalcAmoebaBondForceKernel::~ReferenceCalcAmoebaBondForceKernel() {
void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const AmoebaBondForce& force) {
numBonds = force.getNumBonds();
for( int ii = 0; ii < numBonds; ii++) {
for (int ii = 0; ii < numBonds; ii++) {
int particle1Index, particle2Index;
double lengthValue, kValue;
force.getBondParameters(ii, particle1Index, particle2Index, lengthValue, kValue );
force.getBondParameters(ii, particle1Index, particle2Index, lengthValue, kValue);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
length.push_back( static_cast<RealOpenMM>( lengthValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( kValue ) );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
length.push_back( static_cast<RealOpenMM>(lengthValue));
kQuadratic.push_back(static_cast<RealOpenMM>(kValue));
}
globalBondCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
globalBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondQuartic());
......@@ -110,9 +110,9 @@ double ReferenceCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool in
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceBondForce amoebaReferenceBondForce;
RealOpenMM energy = amoebaReferenceBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic,
RealOpenMM energy = amoebaReferenceBondForce.calculateForceAndEnergy(numBonds, posData, particle1, particle2, length, kQuadratic,
globalBondCubic, globalBondQuartic,
forceData );
forceData);
return static_cast<double>(energy);
}
......@@ -150,11 +150,11 @@ void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const
int particle1Index, particle2Index, particle3Index;
double angleValue, k;
force.getAngleParameters(ii, particle1Index, particle2Index, particle3Index, angleValue, k);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
angle.push_back( static_cast<RealOpenMM>( angleValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( k) );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
angle.push_back( static_cast<RealOpenMM>(angleValue));
kQuadratic.push_back(static_cast<RealOpenMM>(k));
}
globalAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleCubic());
globalAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleQuartic());
......@@ -166,8 +166,8 @@ double ReferenceCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool i
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceAngleForce amoebaReferenceAngleForce;
RealOpenMM energy = amoebaReferenceAngleForce.calculateForceAndEnergy( numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData );
RealOpenMM energy = amoebaReferenceAngleForce.calculateForceAndEnergy(numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData);
return static_cast<double>(energy);
}
......@@ -202,12 +202,12 @@ void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system
int particle1Index, particle2Index, particle3Index, particle4Index;
double angleValue, k;
force.getAngleParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, angleValue, k);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
particle4.push_back( particle4Index );
angle.push_back( static_cast<RealOpenMM>( angleValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( k ) );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
particle4.push_back(particle4Index);
angle.push_back( static_cast<RealOpenMM>(angleValue));
kQuadratic.push_back( static_cast<RealOpenMM>(k));
}
globalInPlaneAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleCubic());
globalInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
......@@ -220,9 +220,9 @@ double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context,
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceInPlaneAngleForce amoebaReferenceInPlaneAngleForce;
RealOpenMM energy = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4,
RealOpenMM energy = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy(numAngles, posData, particle1, particle2, particle3, particle4,
angle, kQuadratic, globalInPlaneAngleCubic, globalInPlaneAngleQuartic,
globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData );
globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData);
return static_cast<double>(energy);
}
......@@ -257,14 +257,14 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c
int particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index;
double kTorsionParameter;
force.getPiTorsionParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index, kTorsionParameter );
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
particle4.push_back( particle4Index );
particle5.push_back( particle5Index );
particle6.push_back( particle6Index );
kTorsion.push_back( static_cast<RealOpenMM>(kTorsionParameter) );
force.getPiTorsionParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index, kTorsionParameter);
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
particle4.push_back(particle4Index);
particle5.push_back(particle5Index);
particle6.push_back(particle6Index);
kTorsion.push_back(static_cast<RealOpenMM>(kTorsionParameter));
}
}
......@@ -272,9 +272,9 @@ double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bo
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy( numPiTorsions, posData, particle1, particle2,
RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy(numPiTorsions, posData, particle1, particle2,
particle3, particle4, particle5, particle6,
kTorsion, forceData );
kTorsion, forceData);
return static_cast<double>(energy);
}
......@@ -305,18 +305,18 @@ ReferenceCalcAmoebaStretchBendForceKernel::~ReferenceCalcAmoebaStretchBendForceK
void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system, const AmoebaStretchBendForce& force) {
numStretchBends = force.getNumStretchBends();
for ( int ii = 0; ii < numStretchBends; ii++) {
for (int ii = 0; ii < numStretchBends; ii++) {
int particle1Index, particle2Index, particle3Index;
double lengthAB, lengthCB, angle, k1, k2;
force.getStretchBendParameters(ii, particle1Index, particle2Index, particle3Index, lengthAB, lengthCB, angle, k1, k2);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
lengthABParameters.push_back( static_cast<RealOpenMM>(lengthAB) );
lengthCBParameters.push_back( static_cast<RealOpenMM>(lengthCB) );
angleParameters.push_back( static_cast<RealOpenMM>(angle) );
k1Parameters.push_back( static_cast<RealOpenMM>(k1) );
k2Parameters.push_back( static_cast<RealOpenMM>(k2) );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
lengthABParameters.push_back(static_cast<RealOpenMM>(lengthAB));
lengthCBParameters.push_back(static_cast<RealOpenMM>(lengthCB));
angleParameters.push_back( static_cast<RealOpenMM>(angle));
k1Parameters.push_back( static_cast<RealOpenMM>(k1));
k2Parameters.push_back( static_cast<RealOpenMM>(k2));
}
}
......@@ -324,9 +324,9 @@ double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context,
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy( numStretchBends, posData, particle1, particle2, particle3,
RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy(numStretchBends, posData, particle1, particle2, particle3,
lengthABParameters, lengthCBParameters, angleParameters, k1Parameters,
k2Parameters, forceData );
k2Parameters, forceData);
return static_cast<double>(energy);
}
......@@ -366,16 +366,16 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst
double k;
force.getOutOfPlaneBendParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, k);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
particle4.push_back( particle4Index );
kParameters.push_back( static_cast<RealOpenMM>(k) );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
particle4.push_back(particle4Index);
kParameters.push_back(static_cast<RealOpenMM>(k));
}
globalOutOfPlaneBendAngleCubic = static_cast<RealOpenMM>( force.getAmoebaGlobalOutOfPlaneBendCubic());
globalOutOfPlaneBendAngleQuartic = static_cast<RealOpenMM>( force.getAmoebaGlobalOutOfPlaneBendQuartic());
globalOutOfPlaneBendAnglePentic = static_cast<RealOpenMM>( force.getAmoebaGlobalOutOfPlaneBendPentic());
globalOutOfPlaneBendAngleSextic = static_cast<RealOpenMM>( force.getAmoebaGlobalOutOfPlaneBendSextic());
globalOutOfPlaneBendAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendCubic());
globalOutOfPlaneBendAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendQuartic());
globalOutOfPlaneBendAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendPentic());
globalOutOfPlaneBendAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendSextic());
}
......@@ -383,13 +383,13 @@ double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& contex
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy( numOutOfPlaneBends, posData,
RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy(numOutOfPlaneBends, posData,
particle1, particle2, particle3, particle4,
kParameters,
globalOutOfPlaneBendAngleCubic,
globalOutOfPlaneBendAngleQuartic,
globalOutOfPlaneBendAnglePentic,
globalOutOfPlaneBendAngleSextic, forceData );
globalOutOfPlaneBendAngleSextic, forceData);
return static_cast<double>(energy);
}
......@@ -426,13 +426,13 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst
int particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, chiralCheckAtomIndex, gridIndex;
force.getTorsionTorsionParameters(ii, particle1Index, particle2Index, particle3Index,
particle4Index, particle5Index, chiralCheckAtomIndex, gridIndex);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
particle4.push_back( particle4Index );
particle5.push_back( particle5Index );
chiralCheckAtom.push_back( chiralCheckAtomIndex );
gridIndices.push_back( gridIndex );
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
particle4.push_back(particle4Index);
particle5.push_back(particle5Index);
chiralCheckAtom.push_back(chiralCheckAtomIndex);
gridIndices.push_back(gridIndex);
}
// torsion-torsion grids
......@@ -441,25 +441,25 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst
torsionTorsionGrids.resize(numTorsionTorsionGrids);
for (int ii = 0; ii < numTorsionTorsionGrids; ii++) {
const TorsionTorsionGrid grid = force.getTorsionTorsionGrid( ii );
torsionTorsionGrids[ii].resize( grid.size() );
const TorsionTorsionGrid grid = force.getTorsionTorsionGrid(ii);
torsionTorsionGrids[ii].resize(grid.size());
// check if grid needs to be reordered: x-angle should be 'slow' index
TorsionTorsionGrid reorderedGrid;
int reorder = 0;
if( grid[0][0][0] != grid[0][1][0] ){
AmoebaTorsionTorsionForceImpl::reorderGrid( grid, reorderedGrid );
if (grid[0][0][0] != grid[0][1][0]) {
AmoebaTorsionTorsionForceImpl::reorderGrid(grid, reorderedGrid);
reorder = 1;
}
for (unsigned int kk = 0; kk < grid.size(); kk++) {
torsionTorsionGrids[ii][kk].resize( grid[kk].size() );
torsionTorsionGrids[ii][kk].resize(grid[kk].size());
for (unsigned int jj = 0; jj < grid[kk].size(); jj++) {
torsionTorsionGrids[ii][kk][jj].resize( grid[kk][jj].size() );
if( reorder ){
torsionTorsionGrids[ii][kk][jj].resize(grid[kk][jj].size());
if (reorder) {
for (unsigned int ll = 0; ll < grid[ll][jj].size(); ll++) {
torsionTorsionGrids[ii][kk][jj][ll] = static_cast<RealOpenMM>(reorderedGrid[kk][jj][ll]);
}
......@@ -478,9 +478,9 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy( numTorsionTorsions, posData,
RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy(numTorsionTorsions, posData,
particle1, particle2, particle3, particle4, particle5,
chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData );
chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData);
return static_cast<double>(energy);
}
......@@ -517,7 +517,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
int quadrupoleIndex = 0;
int maxCovalentRange = 0;
double totalCharge = 0.0;
for( int ii = 0; ii < numMultipoles; ii++ ){
for (int ii = 0; ii < numMultipoles; ii++) {
// multipoles
......@@ -526,7 +526,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
std::vector<double> dipolesD;
std::vector<double> quadrupolesD;
force.getMultipoleParameters(ii, charge, dipolesD, quadrupolesD, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
tholeD, dampingFactorD, polarityD );
tholeD, dampingFactorD, polarityD);
totalCharge += charge;
axisTypes[ii] = axisType;
......@@ -556,13 +556,13 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
// covalent info
std::vector< std::vector<int> > covalentLists;
force.getCovalentMaps(ii, covalentLists );
force.getCovalentMaps(ii, covalentLists);
multipoleAtomCovalentInfo[ii] = covalentLists;
}
polarizationType = force.getPolarizationType();
if( polarizationType == AmoebaMultipoleForce::Mutual ){
if (polarizationType == AmoebaMultipoleForce::Mutual) {
mutualInducedMaxIterations = force.getMutualInducedMaxIterations();
mutualInducedTargetEpsilon = force.getMutualInducedTargetEpsilon();
}
......@@ -570,7 +570,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
// PME
nonbondedMethod = force.getNonbondedMethod();
if( nonbondedMethod == AmoebaMultipoleForce::PME ){
if (nonbondedMethod == AmoebaMultipoleForce::PME) {
usePme = true;
alphaEwald = force.getAEwald();
cutoffDistance = force.getCutoffDistance();
......@@ -591,7 +591,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
return;
}
AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmoebaReferenceMultipoleForce(ContextImpl& context )
AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmoebaReferenceMultipoleForce(ContextImpl& context)
{
// amoebaReferenceMultipoleForce is set to AmoebaReferenceGeneralizedKirkwoodForce if AmoebaGeneralizedKirkwoodForce is present
......@@ -609,66 +609,66 @@ AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmo
}
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = NULL;
if( gkKernel ){
if (gkKernel) {
// amoebaReferenceGeneralizedKirkwoodForce is deleted in AmoebaReferenceGeneralizedKirkwoodMultipoleForce
// destructor
AmoebaReferenceGeneralizedKirkwoodForce* amoebaReferenceGeneralizedKirkwoodForce = new AmoebaReferenceGeneralizedKirkwoodForce();
amoebaReferenceGeneralizedKirkwoodForce->setNumParticles( gkKernel->getNumParticles() );
amoebaReferenceGeneralizedKirkwoodForce->setSoluteDielectric( gkKernel->getSoluteDielectric() );
amoebaReferenceGeneralizedKirkwoodForce->setSolventDielectric( gkKernel->getSolventDielectric() );
amoebaReferenceGeneralizedKirkwoodForce->setDielectricOffset( gkKernel->getDielectricOffset() );
amoebaReferenceGeneralizedKirkwoodForce->setProbeRadius( gkKernel->getProbeRadius() );
amoebaReferenceGeneralizedKirkwoodForce->setSurfaceAreaFactor( gkKernel->getSurfaceAreaFactor() );
amoebaReferenceGeneralizedKirkwoodForce->setIncludeCavityTerm( gkKernel->getIncludeCavityTerm() );
amoebaReferenceGeneralizedKirkwoodForce->setDirectPolarization( gkKernel->getDirectPolarization() );
amoebaReferenceGeneralizedKirkwoodForce->setNumParticles(gkKernel->getNumParticles());
amoebaReferenceGeneralizedKirkwoodForce->setSoluteDielectric(gkKernel->getSoluteDielectric());
amoebaReferenceGeneralizedKirkwoodForce->setSolventDielectric(gkKernel->getSolventDielectric());
amoebaReferenceGeneralizedKirkwoodForce->setDielectricOffset(gkKernel->getDielectricOffset());
amoebaReferenceGeneralizedKirkwoodForce->setProbeRadius(gkKernel->getProbeRadius());
amoebaReferenceGeneralizedKirkwoodForce->setSurfaceAreaFactor(gkKernel->getSurfaceAreaFactor());
amoebaReferenceGeneralizedKirkwoodForce->setIncludeCavityTerm(gkKernel->getIncludeCavityTerm());
amoebaReferenceGeneralizedKirkwoodForce->setDirectPolarization(gkKernel->getDirectPolarization());
vector<RealOpenMM> parameters;
gkKernel->getAtomicRadii( parameters );
amoebaReferenceGeneralizedKirkwoodForce->setAtomicRadii( parameters );
gkKernel->getAtomicRadii(parameters);
amoebaReferenceGeneralizedKirkwoodForce->setAtomicRadii(parameters);
gkKernel->getScaleFactors( parameters );
amoebaReferenceGeneralizedKirkwoodForce->setScaleFactors( parameters );
gkKernel->getScaleFactors(parameters);
amoebaReferenceGeneralizedKirkwoodForce->setScaleFactors(parameters);
gkKernel->getCharges( parameters );
amoebaReferenceGeneralizedKirkwoodForce->setCharges( parameters );
gkKernel->getCharges(parameters);
amoebaReferenceGeneralizedKirkwoodForce->setCharges(parameters);
// calculate Grycuk Born radii
vector<RealVec>& posData = extractPositions(context);
amoebaReferenceGeneralizedKirkwoodForce->calculateGrycukBornRadii( posData );
amoebaReferenceGeneralizedKirkwoodForce->calculateGrycukBornRadii(posData);
amoebaReferenceMultipoleForce = new AmoebaReferenceGeneralizedKirkwoodMultipoleForce( amoebaReferenceGeneralizedKirkwoodForce );
amoebaReferenceMultipoleForce = new AmoebaReferenceGeneralizedKirkwoodMultipoleForce(amoebaReferenceGeneralizedKirkwoodForce);
} else if( usePme ) {
} else if (usePme) {
AmoebaReferencePmeMultipoleForce* amoebaReferencePmeMultipoleForce = new AmoebaReferencePmeMultipoleForce( );
amoebaReferencePmeMultipoleForce->setAlphaEwald( alphaEwald );
amoebaReferencePmeMultipoleForce->setCutoffDistance( cutoffDistance );
amoebaReferencePmeMultipoleForce->setPmeGridDimensions( pmeGridDimension );
AmoebaReferencePmeMultipoleForce* amoebaReferencePmeMultipoleForce = new AmoebaReferencePmeMultipoleForce();
amoebaReferencePmeMultipoleForce->setAlphaEwald(alphaEwald);
amoebaReferencePmeMultipoleForce->setCutoffDistance(cutoffDistance);
amoebaReferencePmeMultipoleForce->setPmeGridDimensions(pmeGridDimension);
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 1.999999*cutoffDistance;
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize){
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize) {
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
}
amoebaReferencePmeMultipoleForce->setPeriodicBoxSize(boxVectors);
amoebaReferenceMultipoleForce = static_cast<AmoebaReferenceMultipoleForce*>(amoebaReferencePmeMultipoleForce);
} else {
amoebaReferenceMultipoleForce = new AmoebaReferenceMultipoleForce( AmoebaReferenceMultipoleForce::NoCutoff );
amoebaReferenceMultipoleForce = new AmoebaReferenceMultipoleForce(AmoebaReferenceMultipoleForce::NoCutoff);
}
// set polarization type
if( polarizationType == AmoebaMultipoleForce::Mutual ){
amoebaReferenceMultipoleForce->setPolarizationType( AmoebaReferenceMultipoleForce::Mutual );
amoebaReferenceMultipoleForce->setMutualInducedDipoleTargetEpsilon( mutualInducedTargetEpsilon );
amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations( mutualInducedMaxIterations );
} else if( polarizationType == AmoebaMultipoleForce::Direct ){
amoebaReferenceMultipoleForce->setPolarizationType( AmoebaReferenceMultipoleForce::Direct );
if (polarizationType == AmoebaMultipoleForce::Mutual) {
amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Mutual);
amoebaReferenceMultipoleForce->setMutualInducedDipoleTargetEpsilon(mutualInducedTargetEpsilon);
amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations(mutualInducedMaxIterations);
} else if (polarizationType == AmoebaMultipoleForce::Direct) {
amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Direct);
} else {
throw OpenMMException("Polarization type not recognzied." );
throw OpenMMException("Polarization type not recognzied.");
}
return amoebaReferenceMultipoleForce;
......@@ -677,11 +677,11 @@ AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmo
double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = amoebaReferenceMultipoleForce->calculateForceAndEnergy( posData, charges, dipoles, quadrupoles, tholes,
RealOpenMM energy = amoebaReferenceMultipoleForce->calculateForceAndEnergy(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes,
multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, forceData);
......@@ -697,7 +697,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the induced dipoles.
......@@ -711,44 +711,44 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
}
void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ){
std::vector< double >& outputElectrostaticPotential) {
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
vector<RealVec> grid( inputGrid.size() );
vector<RealOpenMM> potential( inputGrid.size() );
for( unsigned int ii = 0; ii < inputGrid.size(); ii++ ){
vector<RealVec> grid(inputGrid.size());
vector<RealOpenMM> potential(inputGrid.size());
for (unsigned int ii = 0; ii < inputGrid.size(); ii++) {
grid[ii] = inputGrid[ii];
}
amoebaReferenceMultipoleForce->calculateElectrostaticPotential( posData, charges, dipoles, quadrupoles, tholes,
amoebaReferenceMultipoleForce->calculateElectrostaticPotential(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes,
multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, grid, potential );
multipoleAtomCovalentInfo, grid, potential);
outputElectrostaticPotential.resize( inputGrid.size() );
for( unsigned int ii = 0; ii < inputGrid.size(); ii++ ){
outputElectrostaticPotential.resize(inputGrid.size());
for (unsigned int ii = 0; ii < inputGrid.size(); ii++) {
outputElectrostaticPotential[ii] = potential[ii];
}
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments){
void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) {
// retrieve masses
const System& system = context.getSystem();
vector<RealOpenMM> masses;
for (int i = 0; i < system.getNumParticles(); ++i) {
masses.push_back( static_cast<RealOpenMM>(system.getParticleMass(i)) );
masses.push_back(static_cast<RealOpenMM>(system.getParticleMass(i)));
}
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
amoebaReferenceMultipoleForce->calculateAmoebaSystemMultipoleMoments( masses, posData, charges, dipoles, quadrupoles, tholes,
amoebaReferenceMultipoleForce->calculateAmoebaSystemMultipoleMoments(masses, posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes,
multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, outputMultipoleMoments );
multipoleAtomCovalentInfo, outputMultipoleMoments);
delete amoebaReferenceMultipoleForce;
}
......@@ -801,51 +801,51 @@ ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::ReferenceCalcAmoebaGeneralize
ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::~ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel() {
}
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getNumParticles( void ) const {
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getNumParticles() const {
return numParticles;
}
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getIncludeCavityTerm( void ) const {
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getIncludeCavityTerm() const {
return includeCavityTerm;
}
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDirectPolarization( void ) const {
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDirectPolarization() const {
return directPolarization;
}
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSoluteDielectric( void ) const {
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSoluteDielectric() const {
return soluteDielectric;
}
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSolventDielectric( void ) const {
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSolventDielectric() const {
return solventDielectric;
}
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDielectricOffset( void ) const {
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDielectricOffset() const {
return dielectricOffset;
}
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getProbeRadius( void ) const {
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getProbeRadius() const {
return probeRadius;
}
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSurfaceAreaFactor( void ) const {
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSurfaceAreaFactor() const {
return surfaceAreaFactor;
}
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getAtomicRadii( vector<RealOpenMM>& outputAtomicRadii ) const {
outputAtomicRadii.resize( atomicRadii.size() );
copy( atomicRadii.begin(), atomicRadii.end(), outputAtomicRadii.begin() );
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getAtomicRadii(vector<RealOpenMM>& outputAtomicRadii) const {
outputAtomicRadii.resize(atomicRadii.size());
copy(atomicRadii.begin(), atomicRadii.end(), outputAtomicRadii.begin());
}
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getScaleFactors( vector<RealOpenMM>& outputScaleFactors ) const {
outputScaleFactors.resize( scaleFactors.size() );
copy( scaleFactors.begin(), scaleFactors.end(), outputScaleFactors.begin() );
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getScaleFactors(vector<RealOpenMM>& outputScaleFactors) const {
outputScaleFactors.resize(scaleFactors.size());
copy(scaleFactors.begin(), scaleFactors.end(), outputScaleFactors.begin());
}
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getCharges( vector<RealOpenMM>& outputCharges ) const {
outputCharges.resize( charges.size() );
copy( charges.begin(), charges.end(), outputCharges.begin() );
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getCharges(vector<RealOpenMM>& outputCharges) const {
outputCharges.resize(charges.size());
copy(charges.begin(), charges.end(), outputCharges.begin());
}
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) {
......@@ -861,37 +861,37 @@ void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System&
throw OpenMMException("AmoebaGeneralizedKirkwoodForce requires the System to also contain an AmoebaMultipoleForce.");
}
if (amoebaMultipoleForce->getNonbondedMethod() != AmoebaMultipoleForce::NoCutoff ) {
if (amoebaMultipoleForce->getNonbondedMethod() != AmoebaMultipoleForce::NoCutoff) {
throw OpenMMException("AmoebaGeneralizedKirkwoodForce requires the AmoebaMultipoleForce use the NoCutoff nonbonded method.");
}
numParticles = system.getNumParticles();
for( int ii = 0; ii < numParticles; ii++ ){
for (int ii = 0; ii < numParticles; ii++) {
double particleCharge, particleRadius, scalingFactor;
force.getParticleParameters(ii, particleCharge, particleRadius, scalingFactor);
atomicRadii.push_back( static_cast<RealOpenMM>( particleRadius ) );
scaleFactors.push_back( static_cast<RealOpenMM>( scalingFactor ) );
charges.push_back( static_cast<RealOpenMM>( particleCharge ) );
atomicRadii.push_back(static_cast<RealOpenMM>(particleRadius));
scaleFactors.push_back(static_cast<RealOpenMM>(scalingFactor));
charges.push_back(static_cast<RealOpenMM>(particleCharge));
// Make sure the charge matches the one specified by the AmoebaMultipoleForce.
double charge2, thole, damping, polarity;
int axisType, atomX, atomY, atomZ;
vector<double> dipole, quadrupole;
amoebaMultipoleForce->getMultipoleParameters( ii, charge2, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
if ( particleCharge != charge2 ){
amoebaMultipoleForce->getMultipoleParameters(ii, charge2, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
if (particleCharge != charge2) {
throw OpenMMException("AmoebaGeneralizedKirkwoodForce and AmoebaMultipoleForce must specify the same charge for every atom.");
}
}
includeCavityTerm = force.getIncludeCavityTerm();
soluteDielectric = static_cast<RealOpenMM>( force.getSoluteDielectric() );
solventDielectric = static_cast<RealOpenMM>( force.getSolventDielectric() );
dielectricOffset = static_cast<RealOpenMM>( 0.009 );
probeRadius = static_cast<RealOpenMM>( force.getProbeRadius() ),
surfaceAreaFactor = static_cast<RealOpenMM>( force.getSurfaceAreaFactor() );
soluteDielectric = static_cast<RealOpenMM>(force.getSoluteDielectric());
solventDielectric = static_cast<RealOpenMM>(force.getSolventDielectric());
dielectricOffset = static_cast<RealOpenMM>(0.009);
probeRadius = static_cast<RealOpenMM>(force.getProbeRadius()),
surfaceAreaFactor = static_cast<RealOpenMM>(force.getSurfaceAreaFactor());
directPolarization = amoebaMultipoleForce->getPolarizationType() == AmoebaMultipoleForce::Direct ? 1 : 0;
}
......@@ -924,7 +924,7 @@ ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string
}
ReferenceCalcAmoebaVdwForceKernel::~ReferenceCalcAmoebaVdwForceKernel() {
if( neighborList ){
if (neighborList) {
delete neighborList;
}
}
......@@ -935,28 +935,28 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
numParticles = system.getNumParticles();
indexIVs.resize( numParticles );
allExclusions.resize( numParticles );
sigmas.resize( numParticles );
epsilons.resize( numParticles );
reductions.resize( numParticles );
indexIVs.resize(numParticles);
allExclusions.resize(numParticles);
sigmas.resize(numParticles);
epsilons.resize(numParticles);
reductions.resize(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
for (int ii = 0; ii < numParticles; ii++) {
int indexIV;
double sigma, epsilon, reduction;
std::vector<int> exclusions;
force.getParticleParameters( ii, indexIV, sigma, epsilon, reduction );
force.getParticleExclusions( ii, exclusions );
for( unsigned int jj = 0; jj < exclusions.size(); jj++ ){
allExclusions[ii].insert( exclusions[jj] );
force.getParticleParameters(ii, indexIV, sigma, epsilon, reduction);
force.getParticleExclusions(ii, exclusions);
for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
allExclusions[ii].insert(exclusions[jj]);
}
indexIVs[ii] = indexIV;
sigmas[ii] = static_cast<RealOpenMM>( sigma );
epsilons[ii] = static_cast<RealOpenMM>( epsilon );
reductions[ii] = static_cast<RealOpenMM>( reduction );
sigmas[ii] = static_cast<RealOpenMM>(sigma);
epsilons[ii] = static_cast<RealOpenMM>(epsilon);
reductions[ii] = static_cast<RealOpenMM>(reduction);
}
sigmaCombiningRule = force.getSigmaCombiningRule();
epsilonCombiningRule = force.getEpsilonCombiningRule();
......@@ -972,27 +972,27 @@ double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool inc
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceVdwForce vdwForce( sigmaCombiningRule, epsilonCombiningRule );
AmoebaReferenceVdwForce vdwForce(sigmaCombiningRule, epsilonCombiningRule);
RealOpenMM energy;
if( useCutoff ){
vdwForce.setCutoff( cutoff );
computeNeighborListVoxelHash( *neighborList, numParticles, posData, allExclusions, extractBoxVectors(context), usePBC, cutoff, 0.0);
if( usePBC ){
vdwForce.setNonbondedMethod( AmoebaReferenceVdwForce::CutoffPeriodic);
if (useCutoff) {
vdwForce.setCutoff(cutoff);
computeNeighborListVoxelHash(*neighborList, numParticles, posData, allExclusions, extractBoxVectors(context), usePBC, cutoff, 0.0);
if (usePBC) {
vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::CutoffPeriodic);
RealVec* boxVectors = extractBoxVectors(context);
double minAllowedSize = 1.999999*cutoff;
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize){
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize) {
throw OpenMMException("The periodic box size has decreased to less than twice the cutoff.");
}
vdwForce.setPeriodicBox(boxVectors);
energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, sigmas, epsilons, reductions, *neighborList, forceData);
energy = vdwForce.calculateForceAndEnergy(numParticles, posData, indexIVs, sigmas, epsilons, reductions, *neighborList, forceData);
energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
} else {
vdwForce.setNonbondedMethod( AmoebaReferenceVdwForce::CutoffNonPeriodic);
vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::CutoffNonPeriodic);
}
} else {
vdwForce.setNonbondedMethod( AmoebaReferenceVdwForce::NoCutoff );
energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, sigmas, epsilons, reductions, allExclusions, forceData);
vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::NoCutoff);
energy = vdwForce.calculateForceAndEnergy(numParticles, posData, indexIVs, sigmas, epsilons, reductions, allExclusions, forceData);
}
return static_cast<double>(energy);
}
......@@ -1032,32 +1032,32 @@ void ReferenceCalcAmoebaWcaDispersionForceKernel::initialize(const System& syste
numParticles = system.getNumParticles();
radii.resize(numParticles);
epsilons.resize(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
for (int ii = 0; ii < numParticles; ii++) {
double radius, epsilon;
force.getParticleParameters( ii, radius, epsilon );
force.getParticleParameters(ii, radius, epsilon);
radii[ii] = static_cast<RealOpenMM>( radius );
epsilons[ii] = static_cast<RealOpenMM>( epsilon );
radii[ii] = static_cast<RealOpenMM>(radius);
epsilons[ii] = static_cast<RealOpenMM>(epsilon);
}
totalMaximumDispersionEnergy = static_cast<RealOpenMM>( AmoebaWcaDispersionForceImpl::getTotalMaximumDispersionEnergy( force ) );
totalMaximumDispersionEnergy = static_cast<RealOpenMM>(AmoebaWcaDispersionForceImpl::getTotalMaximumDispersionEnergy(force));
epso = static_cast<RealOpenMM>( force.getEpso() );
epsh = static_cast<RealOpenMM>( force.getEpsh() );
rmino = static_cast<RealOpenMM>( force.getRmino() );
rminh = static_cast<RealOpenMM>( force.getRminh() );
awater = static_cast<RealOpenMM>( force.getAwater() );
shctd = static_cast<RealOpenMM>( force.getShctd() );
dispoff = static_cast<RealOpenMM>( force.getDispoff());
slevy = static_cast<RealOpenMM>( force.getSlevy() );
epso = static_cast<RealOpenMM>(force.getEpso() );
epsh = static_cast<RealOpenMM>(force.getEpsh() );
rmino = static_cast<RealOpenMM>(force.getRmino() );
rminh = static_cast<RealOpenMM>(force.getRminh() );
awater = static_cast<RealOpenMM>(force.getAwater());
shctd = static_cast<RealOpenMM>(force.getShctd() );
dispoff = static_cast<RealOpenMM>(force.getDispoff());
slevy = static_cast<RealOpenMM>(force.getSlevy() );
}
double ReferenceCalcAmoebaWcaDispersionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceWcaDispersionForce amoebaReferenceWcaDispersionForce( epso, epsh, rmino, rminh, awater, shctd, dispoff, slevy );
RealOpenMM energy = amoebaReferenceWcaDispersionForce.calculateForceAndEnergy( numParticles, posData, radii, epsilons, totalMaximumDispersionEnergy, forceData);
AmoebaReferenceWcaDispersionForce amoebaReferenceWcaDispersionForce(epso, epsh, rmino, rminh, awater, shctd, dispoff, slevy);
RealOpenMM energy = amoebaReferenceWcaDispersionForce.calculateForceAndEnergy(numParticles, posData, radii, epsilons, totalMaximumDispersionEnergy, forceData);
return static_cast<double>(energy);
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 162d69a2
......@@ -357,7 +357,7 @@ public:
*
* @return pointer to initialized instance of AmoebaReferenceMultipoleForce
*/
AmoebaReferenceMultipoleForce* setupAmoebaReferenceMultipoleForce(ContextImpl& context );
AmoebaReferenceMultipoleForce* setupAmoebaReferenceMultipoleForce(ContextImpl& context);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -382,7 +382,7 @@ public:
* @param outputElectrostaticPotential output potential
*/
void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential );
std::vector< double >& outputElectrostaticPotential);
/**
* Get the system multipole moments.
......@@ -393,7 +393,7 @@ public:
dipole_x, dipole_y, dipole_z,
quadrupole_xx, quadrupole_xy, quadrupole_xz,
quadrupole_yx, quadrupole_yy, quadrupole_yz,
quadrupole_zx, quadrupole_zy, quadrupole_zz )
quadrupole_zx, quadrupole_zy, quadrupole_zz)
*/
void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
/**
......@@ -555,14 +555,14 @@ public:
*
* @return includeCavityTerm
*/
int getIncludeCavityTerm( void ) const;
int getIncludeCavityTerm() const;
/**
* Get the number of particles.
*
* @return number of particles
*/
int getNumParticles( void ) const;
int getNumParticles() const;
/**
* Get Direct Polarization flag.
......@@ -570,7 +570,7 @@ public:
* @return directPolarization
*
*/
int getDirectPolarization( void ) const;
int getDirectPolarization() const;
/**
* Get the solute dielectric.
......@@ -578,7 +578,7 @@ public:
* @return soluteDielectric
*
*/
RealOpenMM getSoluteDielectric( void ) const;
RealOpenMM getSoluteDielectric() const;
/**
* Get the solvent dielectric.
......@@ -586,7 +586,7 @@ public:
* @return solventDielectric
*
*/
RealOpenMM getSolventDielectric( void ) const;
RealOpenMM getSolventDielectric() const;
/**
* Get the dielectric offset.
......@@ -594,7 +594,7 @@ public:
* @return dielectricOffset
*
*/
RealOpenMM getDielectricOffset( void ) const;
RealOpenMM getDielectricOffset() const;
/**
* Get the probe radius.
......@@ -602,7 +602,7 @@ public:
* @return probeRadius
*
*/
RealOpenMM getProbeRadius( void ) const;
RealOpenMM getProbeRadius() const;
/**
* Get the surface area factor.
......@@ -610,7 +610,7 @@ public:
* @return surfaceAreaFactor
*
*/
RealOpenMM getSurfaceAreaFactor( void ) const;
RealOpenMM getSurfaceAreaFactor() const;
/**
* Get the vector of particle radii.
......@@ -618,7 +618,7 @@ public:
* @param atomicRadii vector of atomic radii
*
*/
void getAtomicRadii( std::vector<RealOpenMM>& atomicRadii ) const;
void getAtomicRadii(std::vector<RealOpenMM>& atomicRadii) const;
/**
* Get the vector of scale factors.
......@@ -626,7 +626,7 @@ public:
* @param scaleFactors vector of scale factors
*
*/
void getScaleFactors( std::vector<RealOpenMM>& scaleFactors ) const;
void getScaleFactors(std::vector<RealOpenMM>& scaleFactors) const;
/**
* Get the vector of charges.
......@@ -634,7 +634,7 @@ public:
* @param charges vector of charges
*
*/
void getCharges( std::vector<RealOpenMM>& charges ) const;
void getCharges(std::vector<RealOpenMM>& charges) const;
/**
* Copy changed parameters over to a context.
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.cpp
View file @ 162d69a2
......@@ -26,7 +26,7 @@
#include "AmoebaReferenceAngleForce.h"
using std::vector;
using OpenMM::RealVec;
using namespace OpenMM;
/**---------------------------------------------------------------------------------------
......@@ -46,11 +46,11 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine,
RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine(RealOpenMM cosine,
RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ) const {
RealOpenMM* dEdR) const {
// ---------------------------------------------------------------------------------------
......@@ -67,9 +67,9 @@ RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM
// ---------------------------------------------------------------------------------------
RealOpenMM angle;
if( cosine >= one ){
if (cosine >= one) {
angle = zero;
} else if( cosine <= -one ){
} else if (cosine <= -one) {
angle = RADIAN*PI_M;
} else {
angle = RADIAN*ACOS(cosine);
......@@ -79,10 +79,10 @@ RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM
RealOpenMM deltaIdeal3 = deltaIdeal*deltaIdeal2;
RealOpenMM deltaIdeal4 = deltaIdeal2*deltaIdeal2;
*dEdR = ( two + three*angleCubic*deltaIdeal +
*dEdR = (two + three*angleCubic*deltaIdeal +
four*angleQuartic*deltaIdeal2 +
five*anglePentic*deltaIdeal3 +
six*angleSextic*deltaIdeal4 );
six*angleSextic*deltaIdeal4);
*dEdR *= RADIAN*angleK*deltaIdeal;
......@@ -113,12 +113,12 @@ RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn(const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealVec& positionAtomC,
RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealVec* forces ) const {
RealVec* forces) const {
// ---------------------------------------------------------------------------------------
......@@ -132,30 +132,30 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& position
// ---------------------------------------------------------------------------------------
std::vector<RealOpenMM> deltaR[2];
AmoebaReferenceForce::loadDeltaR( positionAtomA, positionAtomB, deltaR[0] );
RealOpenMM rAB2 = AmoebaReferenceForce::getNormSquared3( deltaR[0] );
RealOpenMM rAB = SQRT( rAB2 );
AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[0]);
RealOpenMM rAB2 = AmoebaReferenceForce::getNormSquared3(deltaR[0]);
RealOpenMM rAB = SQRT(rAB2);
AmoebaReferenceForce::loadDeltaR( positionAtomC, positionAtomB, deltaR[1] );
RealOpenMM rCB2 = AmoebaReferenceForce::getNormSquared3( deltaR[1] );
RealOpenMM rCB = SQRT( rCB2 );
AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[1]);
RealOpenMM rCB2 = AmoebaReferenceForce::getNormSquared3(deltaR[1]);
RealOpenMM rCB = SQRT(rCB2);
if( rAB <= zero || rCB <= zero ){
if (rAB <= zero || rCB <= zero) {
return zero;
}
std::vector<RealOpenMM> pVector(3);
AmoebaReferenceForce::getCrossProduct( deltaR[0], deltaR[1], pVector );
RealOpenMM rp = AmoebaReferenceForce::getNorm3( pVector );
if( rp < 1.0e-06 ){
AmoebaReferenceForce::getCrossProduct(deltaR[0], deltaR[1], pVector);
RealOpenMM rp = AmoebaReferenceForce::getNorm3(pVector);
if (rp < 1.0e-06) {
rp = 1.0e-06;
}
RealOpenMM dot = AmoebaReferenceForce::getDotProduct3( deltaR[0], deltaR[1] );
RealOpenMM dot = AmoebaReferenceForce::getDotProduct3(deltaR[0], deltaR[1]);
RealOpenMM cosine = dot/(rAB*rCB);
RealOpenMM dEdR;
RealOpenMM energy = getPrefactorsGivenAngleCosine( cosine, angle, angleK, angleCubic, angleQuartic,
anglePentic, angleSextic, &dEdR );
RealOpenMM energy = getPrefactorsGivenAngleCosine(cosine, angle, angleK, angleCubic, angleQuartic,
anglePentic, angleSextic, &dEdR);
RealOpenMM termA = dEdR/(rAB2*rp);
RealOpenMM termC = -dEdR/(rCB2*rp);
......@@ -164,9 +164,9 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& position
deltaCrossP[0].resize(3);
deltaCrossP[1].resize(3);
deltaCrossP[2].resize(3);
AmoebaReferenceForce::getCrossProduct( deltaR[0], pVector, deltaCrossP[0] );
AmoebaReferenceForce::getCrossProduct( deltaR[1], pVector, deltaCrossP[2] );
for( unsigned int ii = 0; ii < 3; ii++ ){
AmoebaReferenceForce::getCrossProduct(deltaR[0], pVector, deltaCrossP[0]);
AmoebaReferenceForce::getCrossProduct(deltaR[1], pVector, deltaCrossP[2]);
for (unsigned int ii = 0; ii < 3; ii++) {
deltaCrossP[0][ii] *= termA;
deltaCrossP[2][ii] *= termC;
deltaCrossP[1][ii] = -1.0f*(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
......@@ -174,7 +174,7 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& position
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
for (int jj = 0; jj < 3; jj++) {
forces[jj][0] = deltaCrossP[jj][0];
forces[jj][1] = deltaCrossP[jj][1];
forces[jj][2] = deltaCrossP[jj][2];
......@@ -183,7 +183,7 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& position
return energy;
}
RealOpenMM AmoebaReferenceAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
RealOpenMM AmoebaReferenceAngleForce::calculateForceAndEnergy(int numAngles, vector<RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
......@@ -202,10 +202,10 @@ RealOpenMM AmoebaReferenceAngleForce::calculateForceAndEnergy( int numAngles, ve
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealVec forces[3];
energy += calculateAngleIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
energy += calculateAngleIxn(posData[particle1Index], posData[particle2Index], posData[particle3Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces);
for( unsigned int jj = 0; jj < 3; jj++ ){
for (unsigned int jj = 0; jj < 3; jj++) {
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] += forces[1][jj];
forceData[particle3Index][jj] += forces[2][jj];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.h
View file @ 162d69a2
......@@ -28,7 +28,7 @@
#include "RealVec.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class AmoebaReferenceAngleForce {
......@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceAngleForce( ){};
AmoebaReferenceAngleForce() {};
/**---------------------------------------------------------------------------------------
......@@ -48,7 +48,7 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceAngleForce( ){};
~AmoebaReferenceAngleForce() {};
/**---------------------------------------------------------------------------------------
......@@ -72,7 +72,7 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, std::vector<OpenMM::RealVec>& posData,
RealOpenMM calculateForceAndEnergy(int numAngles, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
......@@ -82,7 +82,7 @@ public:
RealOpenMM globalAngleQuartic,
RealOpenMM globalAnglePentic,
RealOpenMM globalAngleSextic,
std::vector<OpenMM::RealVec>& forceData ) const;
std::vector<OpenMM::RealVec>& forceData) const;
private:
......@@ -104,10 +104,10 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ) const;
RealOpenMM* dEdR) const;
/**---------------------------------------------------------------------------------------
......@@ -128,15 +128,15 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateAngleIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
RealOpenMM calculateAngleIxn(const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const OpenMM::RealVec& positionAtomC,
RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
OpenMM::RealVec* forces ) const;
OpenMM::RealVec* forces) const;
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // _AmoebaReferenceAngleForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.cpp
View file @ 162d69a2
......@@ -26,7 +26,7 @@
#include "AmoebaReferenceForce.h"
using std::vector;
using OpenMM::RealVec;
using namespace OpenMM;
/**---------------------------------------------------------------------------------------
......@@ -44,10 +44,10 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceBondForce::calculateBondIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM AmoebaReferenceBondForce::calculateBondIxn(const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealVec* forces ) const {
RealVec* forces) const {
// ---------------------------------------------------------------------------------------
......@@ -63,8 +63,8 @@ RealOpenMM AmoebaReferenceBondForce::calculateBondIxn( const RealVec& positionAt
// get deltaR, R2, and R between 2 atoms
std::vector<RealOpenMM> deltaR;
AmoebaReferenceForce::loadDeltaR( positionAtomA, positionAtomB, deltaR );
RealOpenMM r = AmoebaReferenceForce::getNorm3( deltaR );
AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR);
RealOpenMM r = AmoebaReferenceForce::getNorm3(deltaR);
// deltaIdeal = r - r_0
......@@ -84,11 +84,11 @@ RealOpenMM AmoebaReferenceBondForce::calculateBondIxn( const RealVec& positionAt
forces[1][1] = dEdR*deltaR[1];
forces[1][2] = dEdR*deltaR[2];
RealOpenMM energy = bondK*deltaIdeal2*( one + bondCubic*deltaIdeal + bondQuartic*deltaIdeal2 );
RealOpenMM energy = bondK*deltaIdeal2*(one + bondCubic*deltaIdeal + bondQuartic*deltaIdeal2);
return energy;
}
RealOpenMM AmoebaReferenceBondForce::calculateForceAndEnergy( int numBonds,
RealOpenMM AmoebaReferenceBondForce::calculateForceAndEnergy(int numBonds,
vector<RealVec>& particlePositions,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
......@@ -96,20 +96,20 @@ RealOpenMM AmoebaReferenceBondForce::calculateForceAndEnergy( int numBonds,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalBondCubic,
RealOpenMM globalBondQuartic,
vector<RealVec>& forceData ) const {
vector<RealVec>& forceData) const {
RealOpenMM energy = 0.0;
for( int ii = 0; ii < numBonds; ii++ ){
for (int ii = 0; ii < numBonds; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
RealOpenMM bondLength = length[ii];
RealOpenMM bondK = kQuadratic[ii];
RealVec forces[2];
energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index],
energy += calculateBondIxn(particlePositions[particle1Index], particlePositions[particle2Index],
bondLength, bondK, globalBondCubic, globalBondQuartic,
forces );
forces);
for( int jj = 0; jj < 3; jj++ ){
for (int jj = 0; jj < 3; jj++) {
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] += forces[1][jj];
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.h
View file @ 162d69a2
......@@ -28,7 +28,7 @@
#include "RealVec.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class AmoebaReferenceBondForce {
......@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceBondForce( ){};
AmoebaReferenceBondForce() {};
/**---------------------------------------------------------------------------------------
......@@ -48,7 +48,7 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceBondForce( ){};
~AmoebaReferenceBondForce() {};
/**---------------------------------------------------------------------------------------
......@@ -69,13 +69,13 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numBonds, std::vector<OpenMM::RealVec>& posData,
RealOpenMM calculateForceAndEnergy(int numBonds, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<RealOpenMM>& bondLength,
const std::vector<RealOpenMM>& bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic,
std::vector<OpenMM::RealVec>& forceData ) const;
std::vector<OpenMM::RealVec>& forceData) const;
private:
......@@ -95,13 +95,13 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateBondIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
RealOpenMM calculateBondIxn(const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic,
OpenMM::RealVec* forces ) const;
OpenMM::RealVec* forces) const;
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // _AmoebaReferenceBondForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.cpp
View file @ 162d69a2
......@@ -25,7 +25,7 @@
#include "AmoebaReferenceForce.h"
#include <vector>
using OpenMM::RealVec;
using namespace OpenMM;
/**---------------------------------------------------------------------------------------
......@@ -37,8 +37,8 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
void AmoebaReferenceForce::loadDeltaR( const RealVec& xVector, const RealVec& yVector,
std::vector<RealOpenMM>& deltaR ){
void AmoebaReferenceForce::loadDeltaR(const RealVec& xVector, const RealVec& yVector,
std::vector<RealOpenMM>& deltaR) {
// ---------------------------------------------------------------------------------------
......@@ -48,9 +48,9 @@ void AmoebaReferenceForce::loadDeltaR( const RealVec& xVector, const RealVec& yV
// ---------------------------------------------------------------------------------------
deltaR.resize(0);
deltaR.push_back( yVector[0] - xVector[0] );
deltaR.push_back( yVector[1] - xVector[1] );
deltaR.push_back( yVector[2] - xVector[2] );
deltaR.push_back(yVector[0] - xVector[0]);
deltaR.push_back(yVector[1] - xVector[1]);
deltaR.push_back(yVector[2] - xVector[2]);
}
/**---------------------------------------------------------------------------------------
......@@ -63,7 +63,7 @@ void AmoebaReferenceForce::loadDeltaR( const RealVec& xVector, const RealVec& yV
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getNormSquared3( const std::vector<RealOpenMM>& inputVector ){
RealOpenMM AmoebaReferenceForce::getNormSquared3(const std::vector<RealOpenMM>& inputVector) {
// ---------------------------------------------------------------------------------------
......@@ -73,7 +73,7 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3( const std::vector<RealOpenMM>&
// get 3 norm
return ( inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2] );
return (inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
}
/**---------------------------------------------------------------------------------------
......@@ -86,7 +86,7 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3( const std::vector<RealOpenMM>&
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getNormSquared3( const RealOpenMM* inputVector ){
RealOpenMM AmoebaReferenceForce::getNormSquared3(const RealOpenMM* inputVector) {
// ---------------------------------------------------------------------------------------
......@@ -96,7 +96,7 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3( const RealOpenMM* inputVector
// get 3 norm
return ( inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2] );
return (inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
}
/**---------------------------------------------------------------------------------------
......@@ -109,7 +109,7 @@ RealOpenMM AmoebaReferenceForce::getNormSquared3( const RealOpenMM* inputVector
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getNorm3( const std::vector<RealOpenMM>& inputVector ){
RealOpenMM AmoebaReferenceForce::getNorm3(const std::vector<RealOpenMM>& inputVector) {
// ---------------------------------------------------------------------------------------
......@@ -119,10 +119,10 @@ RealOpenMM AmoebaReferenceForce::getNorm3( const std::vector<RealOpenMM>& inputV
// get 3 norm
return SQRT( inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2] );
return SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
}
RealOpenMM AmoebaReferenceForce::getNorm3( const RealOpenMM* inputVector ){
RealOpenMM AmoebaReferenceForce::getNorm3(const RealOpenMM* inputVector) {
// ---------------------------------------------------------------------------------------
......@@ -132,10 +132,10 @@ RealOpenMM AmoebaReferenceForce::getNorm3( const RealOpenMM* inputVector ){
// get 3 norm
return SQRT( inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2] );
return SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
}
RealOpenMM AmoebaReferenceForce::normalizeVector3( RealOpenMM* inputVector ){
RealOpenMM AmoebaReferenceForce::normalizeVector3(RealOpenMM* inputVector) {
// ---------------------------------------------------------------------------------------
......@@ -143,8 +143,8 @@ RealOpenMM AmoebaReferenceForce::normalizeVector3( RealOpenMM* inputVector ){
// ---------------------------------------------------------------------------------------
RealOpenMM norm = SQRT( inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2] );
if( norm > 0.0 ){
RealOpenMM norm = SQRT(inputVector[0]*inputVector[0] + inputVector[1]*inputVector[1] + inputVector[2]*inputVector[2]);
if (norm > 0.0) {
RealOpenMM normI = 1.0/norm;
inputVector[0] *= normI;
inputVector[1] *= normI;
......@@ -165,7 +165,7 @@ RealOpenMM AmoebaReferenceForce::normalizeVector3( RealOpenMM* inputVector ){
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getDotProduct3( const std::vector<RealOpenMM>& xVector, const std::vector<RealOpenMM>& yVector ){
RealOpenMM AmoebaReferenceForce::getDotProduct3(const std::vector<RealOpenMM>& xVector, const std::vector<RealOpenMM>& yVector) {
// ---------------------------------------------------------------------------------------
......@@ -189,7 +189,7 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3( const std::vector<RealOpenMM>&
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getDotProduct3( const RealOpenMM* xVector, const RealOpenMM* yVector ){
RealOpenMM AmoebaReferenceForce::getDotProduct3(const RealOpenMM* xVector, const RealOpenMM* yVector) {
// ---------------------------------------------------------------------------------------
......@@ -202,7 +202,7 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3( const RealOpenMM* xVector, cons
return xVector[0]*yVector[0] + xVector[1]*yVector[1] + xVector[2]*yVector[2];
}
RealOpenMM AmoebaReferenceForce::getDotProduct3( const RealOpenMM* xVector, const OpenMM::Vec3& yVector ){
RealOpenMM AmoebaReferenceForce::getDotProduct3(const RealOpenMM* xVector, const OpenMM::Vec3& yVector) {
// ---------------------------------------------------------------------------------------
......@@ -227,7 +227,7 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3( const RealOpenMM* xVector, cons
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceForce::getDotProduct3( unsigned int vectorOffset, const std::vector<RealOpenMM>& xVector, const RealOpenMM* yVector ){
RealOpenMM AmoebaReferenceForce::getDotProduct3(unsigned int vectorOffset, const std::vector<RealOpenMM>& xVector, const RealOpenMM* yVector) {
// ---------------------------------------------------------------------------------------
......@@ -250,9 +250,9 @@ RealOpenMM AmoebaReferenceForce::getDotProduct3( unsigned int vectorOffset, cons
--------------------------------------------------------------------------------------- */
void AmoebaReferenceForce::getCrossProduct( const std::vector<RealOpenMM>& xVector,
void AmoebaReferenceForce::getCrossProduct(const std::vector<RealOpenMM>& xVector,
const std::vector<RealOpenMM>& yVector,
std::vector<RealOpenMM>& zVector ){
std::vector<RealOpenMM>& zVector) {
// ---------------------------------------------------------------------------------------
......@@ -277,9 +277,9 @@ void AmoebaReferenceForce::getCrossProduct( const std::vector<RealOpenMM>& xVect
--------------------------------------------------------------------------------------- */
void AmoebaReferenceForce::getCrossProduct( const RealOpenMM* xVector,
void AmoebaReferenceForce::getCrossProduct(const RealOpenMM* xVector,
const RealOpenMM* yVector,
RealOpenMM* zVector ){
RealOpenMM* zVector) {
// ---------------------------------------------------------------------------------------
......
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