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Commit eb232608 authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Merge remote-tracking branch 'upstream/master'

parents 62581e9c 7f8c5089
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Showing with 178 additions and 198 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ eb232608
......@@ -71,28 +71,28 @@ public:
*
* @param cubicK the cubic force constant for the bond
*/
void setAmoebaGlobalBondCubic( double cubicK );
void setAmoebaGlobalBondCubic(double cubicK);
/**
* Get the global cubic term
*
* @return global cubicK term
*/
double getAmoebaGlobalBondCubic( void ) const;
double getAmoebaGlobalBondCubic() const;
/**
* Set the global quartic term
*
* @param quarticK the quartic force constant for the bond
*/
void setAmoebaGlobalBondQuartic( double quarticK );
void setAmoebaGlobalBondQuartic(double quarticK);
/**
* Get the global quartic term
*
* @return global quartic term
*/
double getAmoebaGlobalBondQuartic( void ) const;
double getAmoebaGlobalBondQuartic() const;
/**
* Add a bond term to the force field.
......@@ -104,7 +104,7 @@ public:
* @return the index of the bond that was added
*/
int addBond(int particle1, int particle2, double length, double quadraticK );
int addBond(int particle1, int particle2, double length, double quadraticK);
/**
* Get the force field parameters for a bond term.
......@@ -116,7 +116,7 @@ public:
* @param quadratic k the quadratic force constant for the bond
*/
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK) const;
/**
* Set the force field parameters for a bond term.
......@@ -127,7 +127,7 @@ public:
* @param length the equilibrium length of the bond, measured in nm
* @param k the quadratic force constant for the bond
*/
void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK);
/**
* Update the per-bond parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
......@@ -167,7 +167,7 @@ public:
particle1 = particle2 = -1;
length = quadraticK = 0.0;
}
BondInfo(int particle1, int particle2, double length, double quadraticK ) :
BondInfo(int particle1, int particle2, double length, double quadraticK) :
particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
}
};
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ eb232608
......@@ -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
......@@ -152,7 +152,7 @@ public:
/**
* Set the surface area factor kJ/(nm*nm) used in SASA contribution
*/
void setSurfaceAreaFactor( double surfaceAreaFactor );
void setSurfaceAreaFactor(double surfaceAreaFactor);
/**
* Update the per-particle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ eb232608
......@@ -70,56 +70,56 @@ public:
*
* @param cubicK the cubic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleCubic( double cubicK );
void setAmoebaGlobalInPlaneAngleCubic(double cubicK);
/**
* Get the global cubic term
*
* @return global cubicK term
*/
double getAmoebaGlobalInPlaneAngleCubic( void ) const;
double getAmoebaGlobalInPlaneAngleCubic() const;
/**
* Set the global quartic term
*
* @param quarticK the quartic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleQuartic( double quarticK );
void setAmoebaGlobalInPlaneAngleQuartic(double quarticK);
/**
* Get the global quartic term
*
* @return global quartic term
*/
double getAmoebaGlobalInPlaneAngleQuartic( void ) const;
double getAmoebaGlobalInPlaneAngleQuartic() const;
/**
* Set the global pentic term
*
* @param penticK the pentic force constant for the angle
*/
void setAmoebaGlobalInPlaneAnglePentic( double penticK );
void setAmoebaGlobalInPlaneAnglePentic(double penticK);
/**
* Get the global pentic term
*
* @return global penticK term
*/
double getAmoebaGlobalInPlaneAnglePentic( void ) const;
double getAmoebaGlobalInPlaneAnglePentic() const;
/**
* Set the global sextic term
*
* @param sexticK the sextic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleSextic( double sexticK );
void setAmoebaGlobalInPlaneAngleSextic(double sexticK);
/**
* Get the global sextic term
*
* @return global sextic term
*/
double getAmoebaGlobalInPlaneAngleSextic( void ) const;
double getAmoebaGlobalInPlaneAngleSextic() const;
/**
* Add an angle term to the force field.
......@@ -133,7 +133,7 @@ public:
* @return the index of the angle that was added
*/
int addAngle(int particle1, int particle2, int particle3, int particle4, double length,
double quadraticK );
double quadraticK);
/**
* Get the force field parameters for an angle term.
......@@ -147,7 +147,7 @@ public:
* @param quadratic k the quadratic force constant for the angle measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& length,
double& quadraticK ) const;
double& quadraticK) const;
/**
* Set the force field parameters for an angle term.
......@@ -160,7 +160,7 @@ public:
* @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
*/
void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK );
void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK);
/**
* Update the per-angle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
......@@ -200,7 +200,7 @@ public:
particle1 = particle2 = particle3 = particle4 = -1;
length = quadraticK = 0.0;
}
AngleInfo(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK ) :
AngleInfo(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK) :
particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4),
length(length), quadraticK(quadraticK) {
}
......
plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ eb232608
......@@ -148,7 +148,7 @@ public:
lengthAB = lengthCB = angle = k1 = k2 = 0.0;
}
StretchBendInfo(int particle1, int particle2, int particle3,
double lengthAB, double lengthCB, double angle, double k1, double k2 ) :
double lengthAB, double lengthCB, double angle, double k1, double k2) :
particle1(particle1), particle2(particle2), particle3(particle3),
lengthAB(lengthAB), lengthCB(lengthCB), angle(angle), k1(k1), k2(k2) {
}
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ eb232608
......@@ -350,10 +350,10 @@ public:
virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ) = 0;
virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) = 0;
virtual void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments ) = 0;
virtual void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) = 0;
/**
* Copy changed parameters over to a context.
*
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ eb232608
......@@ -70,9 +70,9 @@ public:
* @param minCovalentIndex minimum covalent index
* @param maxCovalentIndex maximum covalent index
*/
static void getCovalentRange( const AmoebaMultipoleForce& force, int index,
const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex );
static void getCovalentRange(const AmoebaMultipoleForce& force, int index,
const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex);
/**
* Get the covalent degree for the CovalentEnd lists
......@@ -80,14 +80,14 @@ public:
* @param force AmoebaMultipoleForce force reference
* @param covalentDegree covalent degrees for the CovalentEnd lists
*/
static void getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree );
static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree);
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential );
void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential);
void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments );
void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
void updateParametersInContext(ContextImpl& context);
......@@ -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/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h
View file @ eb232608
......@@ -61,7 +61,7 @@ public:
}
std::vector<std::string> getKernelNames();
OPENMM_EXPORT_AMOEBA static void reorderGrid( const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid );
OPENMM_EXPORT_AMOEBA static void reorderGrid(const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid);
private:
const AmoebaTorsionTorsionForce& owner;
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaWcaDispersionForceImpl.h
View file @ eb232608
......@@ -69,7 +69,7 @@ public:
* @param particleIndex the particle index
* @param maxDispersionEnergy maximum dispersion energy
*/
static void getMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy );
static void getMaximumDispersionEnergy(const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy);
/**
* Get the total maximum dispersion energy
......@@ -78,7 +78,7 @@ public:
*
* @return total maximum dispersion energy for the system
*/
static double getTotalMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force);
static double getTotalMaximumDispersionEnergy(const AmoebaWcaDispersionForce& force);
void updateParametersInContext(ContextImpl& context);
private:
......
plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ eb232608
......@@ -46,7 +46,7 @@ int AmoebaAngleForce::addAngle(int particle1, int particle2, int particle3, dou
}
void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3,
double& length, double& quadraticK ) const {
double& length, double& quadraticK) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
particle3 = angles[index].particle3;
......@@ -55,7 +55,7 @@ void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& partic
}
void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3,
double length, double quadraticK ) {
double length, double quadraticK) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
angles[index].particle3 = particle3;
......@@ -63,35 +63,35 @@ void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle
angles[index].quadraticK = quadraticK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleCubic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
return _globalCubicK;
}
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK) {
_globalCubicK = cubicK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleQuartic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
return _globalQuarticK;
}
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK) {
_globalQuarticK = quarticK;
}
double AmoebaAngleForce::getAmoebaGlobalAnglePentic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
return _globalPenticK;
}
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK) {
_globalPenticK = penticK;
}
double AmoebaAngleForce::getAmoebaGlobalAngleSextic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const {
return _globalSexticK;
}
void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK) {
_globalSexticK = sexticK;
}
......
plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ eb232608
......@@ -41,37 +41,37 @@ AmoebaBondForce::AmoebaBondForce() {
}
int AmoebaBondForce::addBond(int particle1, int particle2, double length, double quadraticK) {
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK ));
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK));
return bonds.size()-1;
}
void AmoebaBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const {
void AmoebaBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK) const {
particle1 = bonds[index].particle1;
particle2 = bonds[index].particle2;
length = bonds[index].length;
quadraticK = bonds[index].quadraticK;
}
void AmoebaBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK ) {
void AmoebaBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK) {
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].length = length;
bonds[index].quadraticK = quadraticK;
}
void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK ) {
void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK) {
_globalCubicK = cubicK;
}
void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) {
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/AmoebaGeneralizedKirkwoodForce.cpp
View file @ eb232608
......@@ -62,7 +62,7 @@ double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
return dielectricOffset;
}
void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset ) {
void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset) {
dielectricOffset = inputDielectricOffset;
} */
......@@ -70,7 +70,7 @@ int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const {
return includeCavityTerm;
}
void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm ) {
void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm) {
includeCavityTerm = inputIncludeCavityTerm;
}
......@@ -78,7 +78,7 @@ double AmoebaGeneralizedKirkwoodForce::getProbeRadius() const {
return probeRadius;
}
void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius ) {
void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius) {
probeRadius = inputProbeRadius;
}
......@@ -86,7 +86,7 @@ double AmoebaGeneralizedKirkwoodForce::getSurfaceAreaFactor() const {
return surfaceAreaFactor;
}
void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor ) {
void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor) {
surfaceAreaFactor = inputSurfaceAreaFactor;
}
......
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ eb232608
......@@ -40,13 +40,13 @@ AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
int AmoebaInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK ) {
angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK ));
int AmoebaInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK) {
angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK));
return angles.size()-1;
}
void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
double& length, double& quadraticK ) const {
double& length, double& quadraticK) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
particle3 = angles[index].particle3;
......@@ -56,7 +56,7 @@ void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int&
}
void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4,
double length, double quadraticK ) {
double length, double quadraticK) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
angles[index].particle3 = particle3;
......@@ -65,35 +65,35 @@ void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int p
angles[index].quadraticK = quadraticK;
}
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK) {
_globalCubicK = cubicK;
}
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK ) {
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;
}
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK) {
_globalPenticK = cubicK;
}
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK ) {
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 @ eb232608
......@@ -45,19 +45,19 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
}
AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
return nonbondedMethod;
}
void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMethod method) {
void AmoebaMultipoleForce::setNonbondedMethod(AmoebaMultipoleForce::NonbondedMethod method) {
nonbondedMethod = method;
}
AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType() const {
return polarizationType;
}
void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::PolarizationType type ) {
void AmoebaMultipoleForce::setPolarizationType(AmoebaMultipoleForce::PolarizationType type) {
polarizationType = type;
}
......@@ -73,19 +73,19 @@ double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const {
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
return pmeBSplineOrder;
}
void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ) const {
if( gridDimension.size() < 3 ){
void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
if (gridDimension.size() < 3) {
gridDimension.resize(3);
}
if( pmeGridDimension.size() > 2 ){
if (pmeGridDimension.size() > 2) {
gridDimension[0] = pmeGridDimension[0];
gridDimension[1] = pmeGridDimension[1];
gridDimension[2] = pmeGridDimension[2];
......@@ -95,7 +95,7 @@ void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension
return;
}
void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDimension ) {
void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1];
......@@ -103,19 +103,19 @@ void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDim
return;
}
int AmoebaMultipoleForce::getMutualInducedMaxIterations( void ) const {
int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
return mutualInducedMaxIterations;
}
void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInducedMaxIterations ) {
void AmoebaMultipoleForce::setMutualInducedMaxIterations(int inputMutualInducedMaxIterations) {
mutualInducedMaxIterations = inputMutualInducedMaxIterations;
}
double AmoebaMultipoleForce::getMutualInducedTargetEpsilon( void ) const {
double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const {
return mutualInducedTargetEpsilon;
}
void AmoebaMultipoleForce::setMutualInducedTargetEpsilon( double inputMutualInducedTargetEpsilon ) {
void AmoebaMultipoleForce::setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon) {
mutualInducedTargetEpsilon = inputMutualInducedTargetEpsilon;
}
......@@ -127,22 +127,22 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = tol;
}
int AmoebaMultipoleForce::addMultipole( double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
multipoles.push_back(MultipoleInfo(charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
return multipoles.size()-1;
}
void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity ) const {
int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const {
charge = multipoles[index].charge;
molecularDipole.resize( 3 );
molecularDipole.resize(3);
molecularDipole[0] = multipoles[index].molecularDipole[0];
molecularDipole[1] = multipoles[index].molecularDipole[1];
molecularDipole[2] = multipoles[index].molecularDipole[2];
molecularQuadrupole.resize( 9 );
molecularQuadrupole.resize(9);
molecularQuadrupole[0] = multipoles[index].molecularQuadrupole[0];
molecularQuadrupole[1] = multipoles[index].molecularQuadrupole[1];
molecularQuadrupole[2] = multipoles[index].molecularQuadrupole[2];
......@@ -164,7 +164,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
}
void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole,
int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity ) {
int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles[index].charge = charge;
......@@ -192,34 +192,34 @@ void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, cons
}
void AmoebaMultipoleForce::setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms ) {
void AmoebaMultipoleForce::setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms) {
std::vector<int>& covalentList = multipoles[index].covalentInfo[typeId];
covalentList.resize( covalentAtoms.size() );
for( unsigned int ii = 0; ii < covalentAtoms.size(); ii++ ){
covalentList.resize(covalentAtoms.size());
for (unsigned int ii = 0; ii < covalentAtoms.size(); ii++) {
covalentList[ii] = covalentAtoms[ii];
}
}
void AmoebaMultipoleForce::getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms ) const {
void AmoebaMultipoleForce::getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms) const {
// load covalent atom index entries for atomId==index and covalentId==typeId into covalentAtoms
std::vector<int> covalentList = multipoles[index].covalentInfo[typeId];
covalentAtoms.resize( covalentList.size() );
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
covalentAtoms.resize(covalentList.size());
for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
covalentAtoms[ii] = covalentList[ii];
}
}
void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<int> >& covalentLists ) const {
void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<int> >& covalentLists) const {
covalentLists.resize( CovalentEnd );
for( unsigned int jj = 0; jj < CovalentEnd; jj++ ){
covalentLists.resize(CovalentEnd);
for (unsigned int jj = 0; jj < CovalentEnd; jj++) {
std::vector<int> covalentList = multipoles[index].covalentInfo[jj];
std::vector<int> covalentAtoms;
covalentAtoms.resize( covalentList.size() );
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
covalentAtoms.resize(covalentList.size());
for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
covalentAtoms[ii] = covalentList[ii];
}
covalentLists[jj] = covalentAtoms;
......@@ -230,11 +230,11 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles);
}
void AmoebaMultipoleForce::getElectrostaticPotential( const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential ){
void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
}
void AmoebaMultipoleForce::getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments ){
void AmoebaMultipoleForce::getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments) {
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getSystemMultipoleMoments(getContextImpl(context), outputMultipoleMoments);
}
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ eb232608
......@@ -64,26 +64,26 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
}
double quadrupoleValidationTolerance = 1.0e-05;
for( int ii = 0; ii < system.getNumParticles(); ii++ ){
for (int ii = 0; ii < system.getNumParticles(); ii++) {
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity ;
std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole;
owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity );
owner.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity);
// check quadrupole is traceless and symmetric
double trace = fabs( molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8] );
if( trace > quadrupoleValidationTolerance ){
double trace = fabs(molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8]);
if (trace > quadrupoleValidationTolerance) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii;
buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[1] - molecularQuadrupole[3] ) > quadrupoleValidationTolerance ){
if (fabs(molecularQuadrupole[1] - molecularQuadrupole[3]) > quadrupoleValidationTolerance ) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];";
......@@ -91,7 +91,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[2] - molecularQuadrupole[6] ) > quadrupoleValidationTolerance ){
if (fabs(molecularQuadrupole[2] - molecularQuadrupole[6]) > quadrupoleValidationTolerance ) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];";
......@@ -99,7 +99,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[5] - molecularQuadrupole[7] ) > quadrupoleValidationTolerance ){
if (fabs(molecularQuadrupole[5] - molecularQuadrupole[7]) > quadrupoleValidationTolerance ) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];";
......@@ -109,9 +109,9 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
// only 'Z-then-X', 'Bisector', Z-Bisect, ThreeFold currently handled
if( axisType != AmoebaMultipoleForce::ZThenX && axisType != AmoebaMultipoleForce::Bisector &&
if (axisType != AmoebaMultipoleForce::ZThenX && axisType != AmoebaMultipoleForce::Bisector &&
axisType != AmoebaMultipoleForce::ZBisect && axisType != AmoebaMultipoleForce::ThreeFold &&
axisType != AmoebaMultipoleForce::ZOnly && axisType != AmoebaMultipoleForce::NoAxisType ) {
axisType != AmoebaMultipoleForce::ZOnly && axisType != AmoebaMultipoleForce::NoAxisType) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: axis type=" << axisType;
buffer << " not currently handled - only axisTypes[ ";
......@@ -138,8 +138,8 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
return names;
}
const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
if( !initializedCovalentDegrees ){
const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
if (!initializedCovalentDegrees) {
initializedCovalentDegrees = true;
CovalentDegrees[AmoebaMultipoleForce::Covalent12] = 1;
CovalentDegrees[AmoebaMultipoleForce::Covalent13] = 2;
......@@ -153,20 +153,20 @@ const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
return CovalentDegrees;
}
void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex ){
void AmoebaMultipoleForceImpl::getCovalentRange(const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex) {
*minCovalentIndex = 999999999;
*maxCovalentIndex = -999999999;
for( unsigned int kk = 0; kk < lists.size(); kk++ ){
for (unsigned int kk = 0; kk < lists.size(); kk++) {
AmoebaMultipoleForce::CovalentType jj = lists[kk];
std::vector<int> covalentList;
force.getCovalentMap( atomIndex, jj, covalentList );
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
if( *minCovalentIndex > covalentList[ii] ){
force.getCovalentMap(atomIndex, jj, covalentList);
for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
if (*minCovalentIndex > covalentList[ii]) {
*minCovalentIndex = covalentList[ii];
}
if( *maxCovalentIndex < covalentList[ii] ){
if (*maxCovalentIndex < covalentList[ii]) {
*maxCovalentIndex = covalentList[ii];
}
}
......@@ -174,10 +174,10 @@ void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& for
return;
}
void AmoebaMultipoleForceImpl::getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree ){
covalentDegree.resize( AmoebaMultipoleForce::CovalentEnd );
void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree) {
covalentDegree.resize(AmoebaMultipoleForce::CovalentEnd);
const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees();
for( unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++ ){
for (unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++) {
covalentDegree[kk] = CovalentDegrees[kk];
}
return;
......@@ -187,12 +187,12 @@ void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Ve
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles);
}
void AmoebaMultipoleForceImpl::getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ){
void AmoebaMultipoleForceImpl::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, outputElectrostaticPotential);
}
void AmoebaMultipoleForceImpl::getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments ){
void AmoebaMultipoleForceImpl::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getSystemMultipoleMoments(context, outputMultipoleMoments);
}
......
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp
View file @ eb232608
......@@ -44,35 +44,35 @@ AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
return _globalCubicK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK) {
_globalCubicK = cubicK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
return _globalQuarticK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK) {
_globalQuarticK = quarticK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
return _globalPenticK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK) {
_globalPenticK = penticK;
}
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic( void ) const {
double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const {
return _globalSexticK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK) {
_globalSexticK = sexticK;
}
......@@ -82,7 +82,7 @@ int AmoebaOutOfPlaneBendForce::addOutOfPlaneBend(int particle1, int particle2, i
}
void AmoebaOutOfPlaneBendForce::getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
double& k ) const {
double& k) const {
particle1 = outOfPlaneBends[index].particle1;
particle2 = outOfPlaneBends[index].particle2;
particle3 = outOfPlaneBends[index].particle3;
......
plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp
View file @ eb232608
......@@ -44,7 +44,7 @@ int AmoebaPiTorsionForce::addPiTorsion(int particle1, int particle2, int particl
return piTorsions.size()-1;
}
void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k ) const {
void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k) const {
particle1 = piTorsions[index].particle1;
particle2 = piTorsions[index].particle2;
particle3 = piTorsions[index].particle3;
......@@ -54,7 +54,7 @@ void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int
k = piTorsions[index].k;
}
void AmoebaPiTorsionForce::setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k ) {
void AmoebaPiTorsionForce::setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k) {
piTorsions[index].particle1 = particle1;
piTorsions[index].particle2 = particle2;
piTorsions[index].particle3 = particle3;
......
plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp
View file @ eb232608
......@@ -46,7 +46,7 @@ int AmoebaStretchBendForce::addStretchBend(int particle1, int particle2, int par
}
void AmoebaStretchBendForce::getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3,
double& lengthAB, double& lengthCB, double& angle, double& k1, double& k2 ) const {
double& lengthAB, double& lengthCB, double& angle, double& k1, double& k2) const {
particle1 = stretchBends[index].particle1;
particle2 = stretchBends[index].particle2;
particle3 = stretchBends[index].particle3;
......
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp
View file @ eb232608
......@@ -70,13 +70,13 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionParameters(int index, int parti
torsionTorsions[index].gridIndex = gridIndex;
}
const TorsionTorsionGrid& AmoebaTorsionTorsionForce::getTorsionTorsionGrid(int index ) const {
const TorsionTorsionGrid& AmoebaTorsionTorsionForce::getTorsionTorsionGrid(int index) const {
return torsionTorsionGrids[index].getTorsionTorsionGrid();
}
void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTorsionGrid& grid ) {
if( index >= static_cast<int>(torsionTorsionGrids.size()) ){
torsionTorsionGrids.resize( index + 1);
void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTorsionGrid& grid) {
if (index >= static_cast<int>(torsionTorsionGrids.size())) {
torsionTorsionGrids.resize(index + 1);
}
torsionTorsionGrids[index] = grid;
}
......
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForceImpl.cpp
View file @ eb232608
......@@ -70,12 +70,11 @@ typedef std::map< double, Map_Double_IntPair > Map_Double_MapDoubleIntPair;
typedef Map_Double_MapDoubleIntPair::iterator Map_Double_MapDoubleIntPairI;
typedef Map_Double_MapDoubleIntPair::const_iterator Map_Double_MapDoubleIntPairCI;
void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid ){
void AmoebaTorsionTorsionForceImpl::reorderGrid(const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid) {
reorderedGrid.resize( grid.size() );
std::vector<Map_Double_IntPair> map_Double_IntPair_Vector( grid.size() );
reorderedGrid.resize(grid.size());
std::vector<Map_Double_IntPair> map_Double_IntPair_Vector(grid.size());
Map_Double_MapDoubleIntPair mapAngles;
//(void) fprintf( stderr, "AmoebaTorsionTorsionForceImpl::reorder grid\n" );
// (1) set dimensions for reorderd grid
// (2) build map:
......@@ -84,27 +83,27 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
for (unsigned int ii = 0; ii < grid.size(); ii++) {
reorderedGrid[ii].resize( grid[ii].size() );
reorderedGrid[ii].resize(grid[ii].size());
for (unsigned int jj = 0; jj < grid[ii].size(); jj++) {
reorderedGrid[ii][jj].resize( grid[ii][jj].size() );
reorderedGrid[ii][jj].resize(grid[ii][jj].size());
double angleX = grid[ii][jj][0];
double angleY = grid[ii][jj][1];
if( mapAngles.find( angleX ) == mapAngles.end() ){
if( map_Double_IntPair_Vector[ii].size() > 0 ){
if (mapAngles.find(angleX) == mapAngles.end()) {
if (map_Double_IntPair_Vector[ii].size() > 0) {
char buffer[1024];
(void) sprintf( buffer, "TorsionTorsion grid reorder: x-angle not set correctly: x=%15.7e y=%15.7e size=%u should be zero; ii/jj indies=%u %u.\n",
angleX, angleY, static_cast<unsigned int>(map_Double_IntPair_Vector[ii].size()), ii, jj );
(void) sprintf(buffer, "TorsionTorsion grid reorder: x-angle not set correctly: x=%15.7e y=%15.7e size=%u should be zero; ii/jj indies=%u %u.\n",
angleX, angleY, static_cast<unsigned int>(map_Double_IntPair_Vector[ii].size()), ii, jj);
throw OpenMMException(buffer);
}
mapAngles[angleX] = map_Double_IntPair_Vector[ii];
}
Map_Double_IntPair& map_Double_IntPair = mapAngles[angleX];
if( map_Double_IntPair.find( angleY ) != map_Double_IntPair.end() ){
if (map_Double_IntPair.find(angleY) != map_Double_IntPair.end()) {
char buffer[1024];
(void) sprintf( buffer, "TorsionTorsion grid reorder: angle pair found twice: %15.7e %15.7e %u\n", angleX, angleY, static_cast<unsigned int>(map_Double_IntPair.size()) );
(void) sprintf(buffer, "TorsionTorsion grid reorder: angle pair found twice: %15.7e %15.7e %u\n", angleX, angleY, static_cast<unsigned int>(map_Double_IntPair.size()));
throw OpenMMException(buffer);
}
struct IntPair pair;
......@@ -114,24 +113,6 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
}
}
#if 0
(void) fprintf( stderr, "TorsionTorsion grid reorder map\n" );
for( Map_Double_MapDoubleIntPairCI ii = mapAngles.begin(); ii != mapAngles.end(); ii++ ){
double angleX = ii->first;
Map_Double_IntPair map_Double_IntPair = ii->second;
(void) fprintf( stderr, " %15.7e %u \n", angleX, static_cast<unsigned int>(map_Double_IntPair.size()) );
}
for( Map_Double_MapDoubleIntPairCI ii = mapAngles.begin(); ii != mapAngles.end(); ii++ ){
double angleX = ii->first;
Map_Double_IntPair map_Double_IntPair = ii->second;
for( Map_Double_IntPairCI jj = map_Double_IntPair.begin(); jj != map_Double_IntPair.end(); jj++ ){
double angle = jj->first;
struct IntPair pair = jj->second;
(void) fprintf( stderr, " %15.7e %15.7e %d %d\n", angleX, angle, pair.index1, pair.index2 );
}
}
#endif
// load reordered entries
Map_Double_MapDoubleIntPairCI mapII = mapAngles.begin();
......@@ -144,7 +125,6 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
struct IntPair pair = mapJJ->second;
int index1 = pair.index1;
int index2 = pair.index2;
//(void) fprintf( stderr, " %3d %3d %15.7e %15.7e %3d %3d zzz\n", ii, jj, mapII->first, mapJJ->first, index1, index2 );
for (unsigned int kk = 0; kk < grid[ii][jj].size(); kk++) {
reorderedGrid[ii][jj][kk] = static_cast<float>(grid[index1][index2][kk]);
......@@ -153,12 +133,12 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
// increment map iterators
mapJJ++;
if( mapJJ == map_Double_IntPair.end() ){
if (mapJJ == map_Double_IntPair.end()) {
mapII++;
if( mapII == mapAngles.end() ){
if( (jj != (grid[ii].size()-1)) && (ii != (grid.size()-1)) ){
if (mapII == mapAngles.end()) {
if ((jj != (grid[ii].size()-1)) && (ii != (grid.size()-1))) {
char buffer[1024];
(void) sprintf( buffer, "AmoebaTorsionTorsionForceImpl::reorderGrid: error detected with map iterators.\n" );
(void) sprintf(buffer, "AmoebaTorsionTorsionForceImpl::reorderGrid: error detected with map iterators.\n");
throw OpenMMException(buffer);
}
} else {
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ eb232608
......@@ -41,13 +41,13 @@ using std::vector;
AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), cutoff(1.0e+10), useDispersionCorrection(true) {
}
int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor ) {
int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor) {
parameters.push_back(VdwInfo(parentIndex, sigma, epsilon, reductionFactor));
return parameters.size()-1;
}
void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
double& sigma, double& epsilon, double& reductionFactor ) const {
double& sigma, double& epsilon, double& reductionFactor) const {
parentIndex = parameters[particleIndex].parentIndex;
sigma = parameters[particleIndex].sigma;
epsilon = parameters[particleIndex].epsilon;
......@@ -55,54 +55,54 @@ void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
}
void AmoebaVdwForce::setParticleParameters(int particleIndex, int parentIndex,
double sigma, double epsilon, double reductionFactor ) {
double sigma, double epsilon, double reductionFactor) {
parameters[particleIndex].parentIndex = parentIndex;
parameters[particleIndex].sigma = sigma;
parameters[particleIndex].epsilon = epsilon;
parameters[particleIndex].reductionFactor = reductionFactor;
}
void AmoebaVdwForce::setSigmaCombiningRule( const std::string& inputSigmaCombiningRule ) {
void AmoebaVdwForce::setSigmaCombiningRule(const std::string& inputSigmaCombiningRule) {
sigmaCombiningRule = inputSigmaCombiningRule;
}
const std::string& AmoebaVdwForce::getSigmaCombiningRule( void ) const {
const std::string& AmoebaVdwForce::getSigmaCombiningRule() const {
return sigmaCombiningRule;
}
void AmoebaVdwForce::setEpsilonCombiningRule( const std::string& inputEpsilonCombiningRule ) {
void AmoebaVdwForce::setEpsilonCombiningRule(const std::string& inputEpsilonCombiningRule) {
epsilonCombiningRule = inputEpsilonCombiningRule;
}
const std::string& AmoebaVdwForce::getEpsilonCombiningRule( void ) const {
const std::string& AmoebaVdwForce::getEpsilonCombiningRule() const {
return epsilonCombiningRule;
}
void AmoebaVdwForce::setParticleExclusions( int particleIndex, const std::vector< int >& inputExclusions ) {
void AmoebaVdwForce::setParticleExclusions(int particleIndex, const std::vector< int >& inputExclusions) {
if( exclusions.size() < parameters.size() ){
exclusions.resize( parameters.size() );
if (exclusions.size() < parameters.size()) {
exclusions.resize(parameters.size());
}
if( static_cast<int>(exclusions.size()) < particleIndex ){
exclusions.resize( particleIndex + 10 );
if (static_cast<int>(exclusions.size()) < particleIndex) {
exclusions.resize(particleIndex + 10);
}
for( unsigned int ii = 0; ii < inputExclusions.size(); ii++ ){
exclusions[particleIndex].push_back( inputExclusions[ii] );
for (unsigned int ii = 0; ii < inputExclusions.size(); ii++) {
exclusions[particleIndex].push_back(inputExclusions[ii]);
}
}
void AmoebaVdwForce::getParticleExclusions( int particleIndex, std::vector< int >& outputExclusions ) const {
void AmoebaVdwForce::getParticleExclusions(int particleIndex, std::vector< int >& outputExclusions) const {
if( particleIndex < static_cast<int>(exclusions.size()) ){
outputExclusions.resize( exclusions[particleIndex].size() );
for( unsigned int ii = 0; ii < exclusions[particleIndex].size(); ii++ ){
if (particleIndex < static_cast<int>(exclusions.size())) {
outputExclusions.resize(exclusions[particleIndex].size());
for (unsigned int ii = 0; ii < exclusions[particleIndex].size(); ii++) {
outputExclusions[ii] = exclusions[particleIndex][ii];
}
}
}
void AmoebaVdwForce::setCutoff( double inputCutoff ){
void AmoebaVdwForce::setCutoff(double inputCutoff) {
cutoff = inputCutoff;
}
......
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