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Commit d95b90b9 authored by peastman's avatar peastman
Browse files

Cleaned up formatting in AMOEBA code

parent a568bb12
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Showing with 169 additions and 169 deletions
libraries/validate/include/ValidateOpenMM.h
View file @ d95b90b9
......@@ -83,7 +83,7 @@ typedef StringStringVectorMap::const_iterator StringStringVectorMapCI;
class ValidateOpenMM {
public:
ValidateOpenMM( void );
ValidateOpenMM();
~ValidateOpenMM();
// force names
......@@ -166,7 +166,7 @@ public:
* @return log
*
*/
FILE* getLog( ) const;
FILE* getLog() const;
/**
*
......
libraries/validate/include/ValidateOpenMMForces.h
View file @ d95b90b9
......@@ -41,7 +41,7 @@ typedef MapIntInt::const_iterator MapIntIntCI;
class ForceValidationResult {
public:
ForceValidationResult( const Context& context1, const Context& context2, StringUIntMap& forceNamesMap );
ForceValidationResult(const Context& context1, const Context& context2, StringUIntMap& forceNamesMap);
~ForceValidationResult();
/**
......@@ -51,7 +51,7 @@ public:
*
* @throws OpenMMException if energyIndex is not 0 or 1
*/
double getPotentialEnergy( int energyIndex ) const;
double getPotentialEnergy(int energyIndex) const;
/**
* Get array of forces at specified platform index (0 || 1)
......@@ -60,7 +60,7 @@ public:
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<double> getForceNorms( int forceIndex ) const;
std::vector<double> getForceNorms(int forceIndex) const;
/**
* Get array of forces at platform index (0 || 1)
......@@ -69,7 +69,7 @@ public:
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<Vec3> getForces( int forceIndex ) const;
std::vector<Vec3> getForces(int forceIndex) const;
/**
* Get maximum delta in force norm
......@@ -78,7 +78,7 @@ public:
*
* @return max delta in norm of forces
*/
double getMaxDeltaForceNorm( int* maxIndex = NULL ) const;
double getMaxDeltaForceNorm(int* maxIndex = NULL) const;
/**
* Get maximum relative delta in force norm
......@@ -87,7 +87,7 @@ public:
*
* @return max relative delta in norm of forces
*/
double getMaxRelativeDeltaForceNorm( int* maxIndex = NULL ) const;
double getMaxRelativeDeltaForceNorm(int* maxIndex = NULL) const;
/**
* Get maximum dot product between forces
......@@ -96,7 +96,7 @@ public:
*
* @return max dot product between forces
*/
double getMaxDotProduct( int* maxIndex = NULL ) const;
double getMaxDotProduct(int* maxIndex = NULL) const;
/**
* Get name of force associated w/ computed results
......@@ -104,7 +104,7 @@ public:
* @return force name(s); if more than one force active in computation,
* then names are concatenated and separated by '::' (e.g., 'NB_FORCE::GBSA_OBC_FORCE')
*/
std::string getForceName( void ) const;
std::string getForceName() const;
/**
* Get platform name
......@@ -115,7 +115,7 @@ public:
*
* @throws OpenMMException if index is not 0 or 1
*/
std::string getPlatformName( int index ) const;
std::string getPlatformName(int index) const;
/**
* Register index of two entries that differ by a specified tolerance
......@@ -123,46 +123,46 @@ public:
* @param index inconsistent index
*
*/
void registerInconsistentForceIndex( int index, int value = 1 );
void registerInconsistentForceIndex(int index, int value = 1);
/**
* Clear list of entries that differ by a specified tolerance
*
*/
void clearInconsistentForceIndexList( void );
void clearInconsistentForceIndexList();
/**
* Get list of entries that differ by a specified tolerance
*
*/
void getInconsistentForceIndexList( std::vector<int>& inconsistentIndices ) const;
void getInconsistentForceIndexList(std::vector<int>& inconsistentIndices) const;
/**
* Get number of entries in inconsistent index list
*
*/
int getNumberOfInconsistentForceEntries( void ) const;
int getNumberOfInconsistentForceEntries() const;
/**
* Return true if nans were detected
*
* @return true if nans were detected
*/
int nansDetected( void ) const;
int nansDetected() const;
/**
* Determine if force norms are valid
*
* @param tolerance tolerance
*/
void compareForceNorms( double tolerance );
void compareForceNorms(double tolerance);
/**
* Determine if forces are valid
*
* @param tolerance tolerance
*/
void compareForces( double tolerance );
void compareForces(double tolerance);
private:
......@@ -193,13 +193,13 @@ private:
* Calculate norms of vectors
*
*/
void _calculateNorms( void );
void _calculateNorms();
/**
* Calculate norms of specified vector
*
*/
void _calculateNormOfForceVector( int forceIndex );
void _calculateNormOfForceVector(int forceIndex);
// stat indices
......@@ -216,7 +216,7 @@ private:
* Find vector stats
*
*/
void _findStatsForDouble( const std::vector<double>& array, std::vector<double>& statVector ) const;
void _findStatsForDouble(const std::vector<double>& array, std::vector<double>& statVector) const;
};
// Class used to compare forces/potential energies on two platforms
......@@ -224,7 +224,7 @@ private:
class ValidateOpenMMForces : public ValidateOpenMM {
public:
OPENMM_VALIDATE_EXPORT ValidateOpenMMForces( void );
OPENMM_VALIDATE_EXPORT ValidateOpenMMForces();
OPENMM_VALIDATE_EXPORT ~ValidateOpenMMForces();
/**
......@@ -236,7 +236,7 @@ public:
*
* @return number of inconsistent entries
*/
int OPENMM_VALIDATE_EXPORT compareWithReferencePlatform(Context& context, std::string* summaryString = NULL );
int OPENMM_VALIDATE_EXPORT compareWithReferencePlatform(Context& context, std::string* summaryString = NULL);
/**
* Validate force/energy by comparing the results between the forces/energies computed on two different platforms
......@@ -250,7 +250,7 @@ public:
* on the two input platforms
*/
ForceValidationResult* compareForce(Context& context, std::vector<int>& compareForces,
Platform& platform1, Platform& platform2 ) const;
Platform& platform1, Platform& platform2) const;
/**
* Compare individual forces by comparing calculations across two platforms (platform associated w/ input context and
......@@ -261,42 +261,42 @@ public:
* @param forceValidationResults output vector of ForceValidationResult ptrs (user is responsible for deleting
* individual ForceValidationResult objects)
*/
void compareOpenMMForces(Context& context, Platform& comparisonPlatform, std::vector<ForceValidationResult*>& forceValidationResults ) const;
void compareOpenMMForces(Context& context, Platform& comparisonPlatform, std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Determine if results are consistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
void checkForInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const;
void checkForInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Get total number of force entries that are inconsistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
int getTotalNumberOfInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const;
int getTotalNumberOfInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Get summary string of results
*
* @param forceValidationResults vector of ForceValidationResult ptrs
*/
std::string getSummary( std::vector<ForceValidationResult*>& forceValidationResults ) const;
std::string getSummary(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Set force tolerance
*
* @param tolerance force tolerance
*/
void setForceTolerance( double tolerance );
void setForceTolerance(double tolerance);
/**
* Get force tolerance
*
* @return force tolerance
*/
double getForceTolerance( void ) const;
double getForceTolerance() const;
/*
* Get force tolerance for specified force
......@@ -307,7 +307,7 @@ public:
*
* */
double getForceTolerance( const std::string& forceName ) const;
double getForceTolerance(const std::string& forceName) const;
/*
* Get max errors to print in summary string
......@@ -316,7 +316,7 @@ public:
*
* */
int getMaxErrorsToPrint( void ) const;
int getMaxErrorsToPrint() const;
/*
* Set max errors to print in summary string
......@@ -325,7 +325,7 @@ public:
*
* */
void setMaxErrorsToPrint( int maxErrorsToPrint );
void setMaxErrorsToPrint(int maxErrorsToPrint);
/*
* Return true if force is not to be validated (Andersen thermostat, CM motion remover, ...)
......@@ -335,13 +335,13 @@ public:
* @return true if force is not currently validated
**/
int isExcludedForce( std::string forceName ) const;
int isExcludedForce(std::string forceName) const;
private:
// initialize class entries
void _initialize( void );
void _initialize();
/*
* Format output line
......@@ -354,9 +354,9 @@ private:
*
* */
std::string _getLine( const std::string& tab,
std::string _getLine(const std::string& tab,
const std::string& description,
const std::string& value ) const;
const std::string& value) const;
std::vector<ForceValidationResult*> _forceValidationResults;
......
libraries/validate/src/ValidateOpenMM.cpp
View file @ d95b90b9
......@@ -54,7 +54,7 @@ const std::string ValidateOpenMM::CUSTOM_EXTERNAL_FORCE = "CustomExter
const std::string ValidateOpenMM::CUSTOM_NONBONDED_FORCE = "CustomNonBonded";
ValidateOpenMM::ValidateOpenMM( void ) {
ValidateOpenMM::ValidateOpenMM() {
_log = NULL;
......@@ -82,7 +82,7 @@ int ValidateOpenMM::isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
FILE* ValidateOpenMM::getLog( void ) const {
FILE* ValidateOpenMM::getLog() const {
return _log;
}
......
libraries/validate/src/ValidateOpenMMForces.cpp
View file @ d95b90b9
......@@ -68,7 +68,7 @@ ForceValidationResult::ForceValidationResult( const Context& context1, const Con
ForceValidationResult::~ForceValidationResult( ){
}
void ForceValidationResult::_calculateNorms( void ){
void ForceValidationResult::_calculateNorms(){
// ---------------------------------------------------------------------------------------
......@@ -195,7 +195,7 @@ std::vector<double> ForceValidationResult::getForceNorms( int forceIndex ) cons
}
}
int ForceValidationResult::nansDetected( void ) const {
int ForceValidationResult::nansDetected() const {
return _nansDetected;
}
......@@ -203,7 +203,7 @@ void ForceValidationResult::registerInconsistentForceIndex( int index, int value
_inconsistentForceIndicies[index] = value;
}
void ForceValidationResult::clearInconsistentForceIndexList( void ){
void ForceValidationResult::clearInconsistentForceIndexList(){
_inconsistentForceIndicies.clear();
}
......@@ -213,7 +213,7 @@ void ForceValidationResult::getInconsistentForceIndexList( std::vector<int>& inc
}
}
int ForceValidationResult::getNumberOfInconsistentForceEntries( void ) const {
int ForceValidationResult::getNumberOfInconsistentForceEntries() const {
return static_cast<int>(_inconsistentForceIndicies.size() );
}
......@@ -329,7 +329,7 @@ double ForceValidationResult::getMaxDotProduct( int* maxIndex ) const {
return maxDotProduct;
}
std::string ForceValidationResult::getForceName( void ) const {
std::string ForceValidationResult::getForceName() const {
// ---------------------------------------------------------------------------------------
......@@ -376,7 +376,7 @@ void ForceValidationResult::compareForces( double tolerance ){
std::vector<Vec3> forces2 = getForces( 1 );
std::vector<double> forceNorms2 = getForceNorms( 1 );
clearInconsistentForceIndexList( );
clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forces1.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms2[jj] ) ){
registerInconsistentForceIndex( jj );
......@@ -406,7 +406,7 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
std::vector<double> forceNorms0 = getForceNorms( 0 );
std::vector<double> forceNorms1 = getForceNorms( 1 );
clearInconsistentForceIndexList( );
clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forceNorms0.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms0[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ){
registerInconsistentForceIndex( jj );
......@@ -420,11 +420,11 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
}
}
ValidateOpenMMForces::ValidateOpenMMForces( void ) {
ValidateOpenMMForces::ValidateOpenMMForces() {
_initialize();
}
void ValidateOpenMMForces::_initialize( void ){
void ValidateOpenMMForces::_initialize(){
_forceTolerance = 1.0e-02;
_maxErrorsToPrint = 25;
......@@ -450,7 +450,7 @@ void ValidateOpenMMForces::_initialize( void ){
_forcesToBeExcluded[ANDERSEN_THERMOSTAT] = 1;
}
ValidateOpenMMForces::~ValidateOpenMMForces( ){
ValidateOpenMMForces::~ValidateOpenMMForces(){
for( unsigned int ii = 0; ii < _forceValidationResults.size(); ii++ ){
delete _forceValidationResults[ii];
......@@ -459,7 +459,7 @@ ValidateOpenMMForces::~ValidateOpenMMForces( ){
}
double ValidateOpenMMForces::getForceTolerance( void ) const {
double ValidateOpenMMForces::getForceTolerance() const {
return _forceTolerance;
}
......@@ -706,7 +706,7 @@ double ValidateOpenMMForces::getForceTolerance( const std::string& forceName ) c
return _forceTolerance;
}
int ValidateOpenMMForces::getMaxErrorsToPrint( void ) const {
int ValidateOpenMMForces::getMaxErrorsToPrint() const {
return _maxErrorsToPrint;
}
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ d95b90b9
......@@ -70,7 +70,7 @@ public:
*
* @param cubicK the cubic force constant for the angle
*/
void setAmoebaGlobalAngleCubic( double cubicK );
void setAmoebaGlobalAngleCubic(double cubicK);
/**
* Get the global cubic term
......@@ -84,7 +84,7 @@ public:
*
* @param quarticK the quartic force constant for the angle
*/
void setAmoebaGlobalAngleQuartic( double quarticK );
void setAmoebaGlobalAngleQuartic(double quarticK);
/**
* Get the global quartic term
......@@ -98,7 +98,7 @@ public:
*
* @param penticK the pentic force constant for the angle
*/
void setAmoebaGlobalAnglePentic( double penticK );
void setAmoebaGlobalAnglePentic(double penticK);
/**
* Get the global pentic term
......@@ -112,7 +112,7 @@ public:
*
* @param sexticK the sextic force constant for the angle
*/
void setAmoebaGlobalAngleSextic( double sexticK );
void setAmoebaGlobalAngleSextic(double sexticK);
/**
* Get the global sextic term
......@@ -131,7 +131,7 @@ public:
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @return the index of the angle that was added
*/
int addAngle(int particle1, int particle2, int particle3, double length, double quadraticK );
int addAngle(int particle1, int particle2, int particle3, double length, double quadraticK);
/**
* Get the force field parameters for an angle term.
......@@ -143,7 +143,7 @@ public:
* @param length the equilibrium angle, measured in degress
* @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, double& length, double& quadraticK ) const;
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK) const;
/**
* Set the force field parameters for an angle term.
......@@ -155,7 +155,7 @@ public:
* @param length the equilibrium angle, measured in degrees
* @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, double length, double quadraticK );
void setAngleParameters(int index, int particle1, int particle2, int particle3, 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.
......@@ -195,7 +195,7 @@ public:
particle1 = particle2 = particle3 = -1;
length = quadraticK = 0.0;
}
AngleInfo(int particle1, int particle2, int particle3, double length, double quadraticK ) :
AngleInfo(int particle1, int particle2, int particle3, double length, double quadraticK) :
particle1(particle1), particle2(particle2), particle3(particle3), length(length), quadraticK(quadraticK) {
}
};
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ d95b90b9
......@@ -71,7 +71,7 @@ public:
*
* @param cubicK the cubic force constant for the bond
*/
void setAmoebaGlobalBondCubic( double cubicK );
void setAmoebaGlobalBondCubic(double cubicK);
/**
* Get the global cubic term
......@@ -85,7 +85,7 @@ public:
*
* @param quarticK the quartic force constant for the bond
*/
void setAmoebaGlobalBondQuartic( double quarticK );
void setAmoebaGlobalBondQuartic(double quarticK);
/**
* Get the global quartic term
......@@ -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 @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -70,7 +70,7 @@ public:
*
* @param cubicK the cubic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleCubic( double cubicK );
void setAmoebaGlobalInPlaneAngleCubic(double cubicK);
/**
* Get the global cubic term
......@@ -84,7 +84,7 @@ public:
*
* @param quarticK the quartic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleQuartic( double quarticK );
void setAmoebaGlobalInPlaneAngleQuartic(double quarticK);
/**
* Get the global quartic term
......@@ -98,7 +98,7 @@ public:
*
* @param penticK the pentic force constant for the angle
*/
void setAmoebaGlobalInPlaneAnglePentic( double penticK );
void setAmoebaGlobalInPlaneAnglePentic(double penticK);
/**
* Get the global pentic term
......@@ -112,7 +112,7 @@ public:
*
* @param sexticK the sextic force constant for the angle
*/
void setAmoebaGlobalInPlaneAngleSextic( double sexticK );
void setAmoebaGlobalInPlaneAngleSextic(double sexticK);
/**
* Get the global sextic term
......@@ -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 @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -70,9 +70,9 @@ public:
* @param minCovalentIndex minimum covalent index
* @param maxCovalentIndex maximum covalent index
*/
static void getCovalentRange( const AmoebaMultipoleForce& force, int index,
static void getCovalentRange(const AmoebaMultipoleForce& force, int index,
const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex );
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);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h
View file @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -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;
......@@ -67,7 +67,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
return _globalCubicK;
}
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK) {
_globalCubicK = cubicK;
}
......@@ -75,7 +75,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
return _globalQuarticK;
}
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK) {
_globalQuarticK = quarticK;
}
......@@ -83,7 +83,7 @@ double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
return _globalPenticK;
}
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK) {
_globalPenticK = penticK;
}
......@@ -91,7 +91,7 @@ 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 @ d95b90b9
......@@ -41,29 +41,29 @@ 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;
}
......
plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp
View file @ d95b90b9
......@@ -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 @ d95b90b9
......@@ -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;
......@@ -65,11 +65,11 @@ 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;
}
......@@ -81,11 +81,11 @@ 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;
}
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ d95b90b9
......@@ -49,7 +49,7 @@ AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod()
return nonbondedMethod;
}
void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMethod method) {
void AmoebaMultipoleForce::setNonbondedMethod(AmoebaMultipoleForce::NonbondedMethod method) {
nonbondedMethod = method;
}
......@@ -57,7 +57,7 @@ AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType
return polarizationType;
}
void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::PolarizationType type ) {
void AmoebaMultipoleForce::setPolarizationType(AmoebaMultipoleForce::PolarizationType type) {
polarizationType = type;
}
......@@ -73,7 +73,7 @@ double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
}
......@@ -81,11 +81,11 @@ 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];
......@@ -107,7 +107,7 @@ int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
return mutualInducedMaxIterations;
}
void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInducedMaxIterations ) {
void AmoebaMultipoleForce::setMutualInducedMaxIterations(int inputMutualInducedMaxIterations) {
mutualInducedMaxIterations = inputMutualInducedMaxIterations;
}
......@@ -115,7 +115,7 @@ 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 @ d95b90b9
......@@ -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[ ";
......@@ -139,7 +139,7 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
}
const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
if( !initializedCovalentDegrees ){
if (!initializedCovalentDegrees) {
initializedCovalentDegrees = true;
CovalentDegrees[AmoebaMultipoleForce::Covalent12] = 1;
CovalentDegrees[AmoebaMultipoleForce::Covalent13] = 2;
......@@ -153,20 +153,20 @@ const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
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 @ d95b90b9
......@@ -48,7 +48,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
return _globalCubicK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK) {
_globalCubicK = cubicK;
}
......@@ -56,7 +56,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
return _globalQuarticK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK) {
_globalQuarticK = quarticK;
}
......@@ -64,7 +64,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
return _globalPenticK;
}
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK ) {
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK) {
_globalPenticK = penticK;
}
......@@ -72,7 +72,7 @@ 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;
......
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