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"platforms/cpu/src/CpuConstantPotentialForceVec4.cpp" did not exist on "b06fc4a7a47478beacbaf5cc108f755653bc7abb"
Commit f11bafd9 authored by peastman's avatar peastman
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Merge pull request #828 from peastman/cleanup 

Cleanup to AMOEBA code
parents 162d69a2 d95b90b9
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Showing with 169 additions and 169 deletions
libraries/validate/include/ValidateOpenMM.h
View file @ f11bafd9
...@@ -83,7 +83,7 @@ typedef StringStringVectorMap::const_iterator StringStringVectorMapCI; ...@@ -83,7 +83,7 @@ typedef StringStringVectorMap::const_iterator StringStringVectorMapCI;
class ValidateOpenMM { class ValidateOpenMM {
public: public:
ValidateOpenMM( void ); ValidateOpenMM();
~ValidateOpenMM(); ~ValidateOpenMM();
// force names // force names
...@@ -166,7 +166,7 @@ public: ...@@ -166,7 +166,7 @@ public:
* @return log * @return log
* *
*/ */
FILE* getLog( ) const; FILE* getLog() const;
/** /**
* *
......
libraries/validate/include/ValidateOpenMMForces.h
View file @ f11bafd9
...@@ -41,7 +41,7 @@ typedef MapIntInt::const_iterator MapIntIntCI; ...@@ -41,7 +41,7 @@ typedef MapIntInt::const_iterator MapIntIntCI;
class ForceValidationResult { class ForceValidationResult {
public: public:
ForceValidationResult( const Context& context1, const Context& context2, StringUIntMap& forceNamesMap ); ForceValidationResult(const Context& context1, const Context& context2, StringUIntMap& forceNamesMap);
~ForceValidationResult(); ~ForceValidationResult();
/** /**
...@@ -51,7 +51,7 @@ public: ...@@ -51,7 +51,7 @@ public:
* *
* @throws OpenMMException if energyIndex is not 0 or 1 * @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) * Get array of forces at specified platform index (0 || 1)
...@@ -60,7 +60,7 @@ public: ...@@ -60,7 +60,7 @@ public:
* *
* @throws OpenMMException if forceIndex is not 0 or 1 * @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) * Get array of forces at platform index (0 || 1)
...@@ -69,7 +69,7 @@ public: ...@@ -69,7 +69,7 @@ public:
* *
* @throws OpenMMException if forceIndex is not 0 or 1 * @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 * Get maximum delta in force norm
...@@ -78,7 +78,7 @@ public: ...@@ -78,7 +78,7 @@ public:
* *
* @return max delta in norm of forces * @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 * Get maximum relative delta in force norm
...@@ -87,7 +87,7 @@ public: ...@@ -87,7 +87,7 @@ public:
* *
* @return max relative delta in norm of forces * @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 * Get maximum dot product between forces
...@@ -96,7 +96,7 @@ public: ...@@ -96,7 +96,7 @@ public:
* *
* @return max dot product between forces * @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 * Get name of force associated w/ computed results
...@@ -104,7 +104,7 @@ public: ...@@ -104,7 +104,7 @@ public:
* @return force name(s); if more than one force active in computation, * @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') * 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 * Get platform name
...@@ -115,7 +115,7 @@ public: ...@@ -115,7 +115,7 @@ public:
* *
* @throws OpenMMException if index is not 0 or 1 * @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 * Register index of two entries that differ by a specified tolerance
...@@ -123,46 +123,46 @@ public: ...@@ -123,46 +123,46 @@ public:
* @param index inconsistent index * @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 * 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 * 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 * 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
* *
* @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 * Determine if force norms are valid
* *
* @param tolerance tolerance * @param tolerance tolerance
*/ */
void compareForceNorms( double tolerance ); void compareForceNorms(double tolerance);
/** /**
* Determine if forces are valid * Determine if forces are valid
* *
* @param tolerance tolerance * @param tolerance tolerance
*/ */
void compareForces( double tolerance ); void compareForces(double tolerance);
private: private:
...@@ -193,13 +193,13 @@ private: ...@@ -193,13 +193,13 @@ private:
* Calculate norms of vectors * Calculate norms of vectors
* *
*/ */
void _calculateNorms( void ); void _calculateNorms();
/** /**
* Calculate norms of specified vector * Calculate norms of specified vector
* *
*/ */
void _calculateNormOfForceVector( int forceIndex ); void _calculateNormOfForceVector(int forceIndex);
// stat indices // stat indices
...@@ -216,7 +216,7 @@ private: ...@@ -216,7 +216,7 @@ private:
* Find vector stats * 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 // Class used to compare forces/potential energies on two platforms
...@@ -224,7 +224,7 @@ private: ...@@ -224,7 +224,7 @@ private:
class ValidateOpenMMForces : public ValidateOpenMM { class ValidateOpenMMForces : public ValidateOpenMM {
public: public:
OPENMM_VALIDATE_EXPORT ValidateOpenMMForces( void ); OPENMM_VALIDATE_EXPORT ValidateOpenMMForces();
OPENMM_VALIDATE_EXPORT ~ValidateOpenMMForces(); OPENMM_VALIDATE_EXPORT ~ValidateOpenMMForces();
/** /**
...@@ -236,7 +236,7 @@ public: ...@@ -236,7 +236,7 @@ public:
* *
* @return number of inconsistent entries * @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 * Validate force/energy by comparing the results between the forces/energies computed on two different platforms
...@@ -250,7 +250,7 @@ public: ...@@ -250,7 +250,7 @@ public:
* on the two input platforms * on the two input platforms
*/ */
ForceValidationResult* compareForce(Context& context, std::vector<int>& compareForces, 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 * Compare individual forces by comparing calculations across two platforms (platform associated w/ input context and
...@@ -261,42 +261,42 @@ public: ...@@ -261,42 +261,42 @@ public:
* @param forceValidationResults output vector of ForceValidationResult ptrs (user is responsible for deleting * @param forceValidationResults output vector of ForceValidationResult ptrs (user is responsible for deleting
* individual ForceValidationResult objects) * 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 * Determine if results are consistent
* *
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces 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 * Get total number of force entries that are inconsistent
* *
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent * @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 * Get summary string of results
* *
* @param forceValidationResults vector of ForceValidationResult ptrs * @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 * Set force tolerance
* *
* @param tolerance force tolerance * @param tolerance force tolerance
*/ */
void setForceTolerance( double tolerance ); void setForceTolerance(double tolerance);
/** /**
* Get force tolerance * Get force tolerance
* *
* @return force tolerance * @return force tolerance
*/ */
double getForceTolerance( void ) const; double getForceTolerance() const;
/* /*
* Get force tolerance for specified force * Get force tolerance for specified force
...@@ -307,7 +307,7 @@ public: ...@@ -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 * Get max errors to print in summary string
...@@ -316,7 +316,7 @@ public: ...@@ -316,7 +316,7 @@ public:
* *
* */ * */
int getMaxErrorsToPrint( void ) const; int getMaxErrorsToPrint() const;
/* /*
* Set max errors to print in summary string * Set max errors to print in summary string
...@@ -325,7 +325,7 @@ public: ...@@ -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, ...) * Return true if force is not to be validated (Andersen thermostat, CM motion remover, ...)
...@@ -335,13 +335,13 @@ public: ...@@ -335,13 +335,13 @@ public:
* @return true if force is not currently validated * @return true if force is not currently validated
**/ **/
int isExcludedForce( std::string forceName ) const; int isExcludedForce(std::string forceName) const;
private: private:
// initialize class entries // initialize class entries
void _initialize( void ); void _initialize();
/* /*
* Format output line * Format output line
...@@ -354,9 +354,9 @@ private: ...@@ -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& description,
const std::string& value ) const; const std::string& value) const;
std::vector<ForceValidationResult*> _forceValidationResults; std::vector<ForceValidationResult*> _forceValidationResults;
......
libraries/validate/src/ValidateOpenMM.cpp
View file @ f11bafd9
...@@ -54,7 +54,7 @@ const std::string ValidateOpenMM::CUSTOM_EXTERNAL_FORCE = "CustomExter ...@@ -54,7 +54,7 @@ const std::string ValidateOpenMM::CUSTOM_EXTERNAL_FORCE = "CustomExter
const std::string ValidateOpenMM::CUSTOM_NONBONDED_FORCE = "CustomNonBonded"; const std::string ValidateOpenMM::CUSTOM_NONBONDED_FORCE = "CustomNonBonded";
ValidateOpenMM::ValidateOpenMM( void ) { ValidateOpenMM::ValidateOpenMM() {
_log = NULL; _log = NULL;
...@@ -82,7 +82,7 @@ int ValidateOpenMM::isNanOrInfinity( double number ){ ...@@ -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; 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; return _log;
} }
......
libraries/validate/src/ValidateOpenMMForces.cpp
View file @ f11bafd9
...@@ -68,7 +68,7 @@ ForceValidationResult::ForceValidationResult( const Context& context1, const Con ...@@ -68,7 +68,7 @@ ForceValidationResult::ForceValidationResult( const Context& context1, const Con
ForceValidationResult::~ForceValidationResult( ){ ForceValidationResult::~ForceValidationResult( ){
} }
void ForceValidationResult::_calculateNorms( void ){ void ForceValidationResult::_calculateNorms(){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -195,7 +195,7 @@ std::vector<double> ForceValidationResult::getForceNorms( int forceIndex ) cons ...@@ -195,7 +195,7 @@ std::vector<double> ForceValidationResult::getForceNorms( int forceIndex ) cons
} }
} }
int ForceValidationResult::nansDetected( void ) const { int ForceValidationResult::nansDetected() const {
return _nansDetected; return _nansDetected;
} }
...@@ -203,7 +203,7 @@ void ForceValidationResult::registerInconsistentForceIndex( int index, int value ...@@ -203,7 +203,7 @@ void ForceValidationResult::registerInconsistentForceIndex( int index, int value
_inconsistentForceIndicies[index] = value; _inconsistentForceIndicies[index] = value;
} }
void ForceValidationResult::clearInconsistentForceIndexList( void ){ void ForceValidationResult::clearInconsistentForceIndexList(){
_inconsistentForceIndicies.clear(); _inconsistentForceIndicies.clear();
} }
...@@ -213,7 +213,7 @@ void ForceValidationResult::getInconsistentForceIndexList( std::vector<int>& inc ...@@ -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() ); return static_cast<int>(_inconsistentForceIndicies.size() );
} }
...@@ -329,7 +329,7 @@ double ForceValidationResult::getMaxDotProduct( int* maxIndex ) const { ...@@ -329,7 +329,7 @@ double ForceValidationResult::getMaxDotProduct( int* maxIndex ) const {
return maxDotProduct; return maxDotProduct;
} }
std::string ForceValidationResult::getForceName( void ) const { std::string ForceValidationResult::getForceName() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -376,7 +376,7 @@ void ForceValidationResult::compareForces( double tolerance ){ ...@@ -376,7 +376,7 @@ void ForceValidationResult::compareForces( double tolerance ){
std::vector<Vec3> forces2 = getForces( 1 ); std::vector<Vec3> forces2 = getForces( 1 );
std::vector<double> forceNorms2 = getForceNorms( 1 ); std::vector<double> forceNorms2 = getForceNorms( 1 );
clearInconsistentForceIndexList( ); clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forces1.size(); jj++ ){ for( unsigned int jj = 0; jj < forces1.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms2[jj] ) ){ if( ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms2[jj] ) ){
registerInconsistentForceIndex( jj ); registerInconsistentForceIndex( jj );
...@@ -406,7 +406,7 @@ void ForceValidationResult::compareForceNorms( double tolerance ){ ...@@ -406,7 +406,7 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
std::vector<double> forceNorms0 = getForceNorms( 0 ); std::vector<double> forceNorms0 = getForceNorms( 0 );
std::vector<double> forceNorms1 = getForceNorms( 1 ); std::vector<double> forceNorms1 = getForceNorms( 1 );
clearInconsistentForceIndexList( ); clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forceNorms0.size(); jj++ ){ for( unsigned int jj = 0; jj < forceNorms0.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms0[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ){ if( ValidateOpenMM::isNanOrInfinity( forceNorms0[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ){
registerInconsistentForceIndex( jj ); registerInconsistentForceIndex( jj );
...@@ -420,11 +420,11 @@ void ForceValidationResult::compareForceNorms( double tolerance ){ ...@@ -420,11 +420,11 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
} }
} }
ValidateOpenMMForces::ValidateOpenMMForces( void ) { ValidateOpenMMForces::ValidateOpenMMForces() {
_initialize(); _initialize();
} }
void ValidateOpenMMForces::_initialize( void ){ void ValidateOpenMMForces::_initialize(){
_forceTolerance = 1.0e-02; _forceTolerance = 1.0e-02;
_maxErrorsToPrint = 25; _maxErrorsToPrint = 25;
...@@ -450,7 +450,7 @@ void ValidateOpenMMForces::_initialize( void ){ ...@@ -450,7 +450,7 @@ void ValidateOpenMMForces::_initialize( void ){
_forcesToBeExcluded[ANDERSEN_THERMOSTAT] = 1; _forcesToBeExcluded[ANDERSEN_THERMOSTAT] = 1;
} }
ValidateOpenMMForces::~ValidateOpenMMForces( ){ ValidateOpenMMForces::~ValidateOpenMMForces(){
for( unsigned int ii = 0; ii < _forceValidationResults.size(); ii++ ){ for( unsigned int ii = 0; ii < _forceValidationResults.size(); ii++ ){
delete _forceValidationResults[ii]; delete _forceValidationResults[ii];
...@@ -459,7 +459,7 @@ ValidateOpenMMForces::~ValidateOpenMMForces( ){ ...@@ -459,7 +459,7 @@ ValidateOpenMMForces::~ValidateOpenMMForces( ){
} }
double ValidateOpenMMForces::getForceTolerance( void ) const { double ValidateOpenMMForces::getForceTolerance() const {
return _forceTolerance; return _forceTolerance;
} }
...@@ -706,7 +706,7 @@ double ValidateOpenMMForces::getForceTolerance( const std::string& forceName ) c ...@@ -706,7 +706,7 @@ double ValidateOpenMMForces::getForceTolerance( const std::string& forceName ) c
return _forceTolerance; return _forceTolerance;
} }
int ValidateOpenMMForces::getMaxErrorsToPrint( void ) const { int ValidateOpenMMForces::getMaxErrorsToPrint() const {
return _maxErrorsToPrint; return _maxErrorsToPrint;
} }
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ f11bafd9
...@@ -70,7 +70,7 @@ public: ...@@ -70,7 +70,7 @@ public:
* *
* @param cubicK the cubic force constant for the angle * @param cubicK the cubic force constant for the angle
*/ */
void setAmoebaGlobalAngleCubic( double cubicK ); void setAmoebaGlobalAngleCubic(double cubicK);
/** /**
* Get the global cubic term * Get the global cubic term
...@@ -84,7 +84,7 @@ public: ...@@ -84,7 +84,7 @@ public:
* *
* @param quarticK the quartic force constant for the angle * @param quarticK the quartic force constant for the angle
*/ */
void setAmoebaGlobalAngleQuartic( double quarticK ); void setAmoebaGlobalAngleQuartic(double quarticK);
/** /**
* Get the global quartic term * Get the global quartic term
...@@ -98,7 +98,7 @@ public: ...@@ -98,7 +98,7 @@ public:
* *
* @param penticK the pentic force constant for the angle * @param penticK the pentic force constant for the angle
*/ */
void setAmoebaGlobalAnglePentic( double penticK ); void setAmoebaGlobalAnglePentic(double penticK);
/** /**
* Get the global pentic term * Get the global pentic term
...@@ -112,7 +112,7 @@ public: ...@@ -112,7 +112,7 @@ public:
* *
* @param sexticK the sextic force constant for the angle * @param sexticK the sextic force constant for the angle
*/ */
void setAmoebaGlobalAngleSextic( double sexticK ); void setAmoebaGlobalAngleSextic(double sexticK);
/** /**
* Get the global sextic term * Get the global sextic term
...@@ -131,7 +131,7 @@ public: ...@@ -131,7 +131,7 @@ public:
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @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 * @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. * Get the force field parameters for an angle term.
...@@ -143,7 +143,7 @@ public: ...@@ -143,7 +143,7 @@ public:
* @param length the equilibrium angle, measured in degress * @param length the equilibrium angle, measured in degress
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @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. * Set the force field parameters for an angle term.
...@@ -155,7 +155,7 @@ public: ...@@ -155,7 +155,7 @@ public:
* @param length the equilibrium angle, measured in degrees * @param length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @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 * 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. * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
...@@ -195,7 +195,7 @@ public: ...@@ -195,7 +195,7 @@ public:
particle1 = particle2 = particle3 = -1; particle1 = particle2 = particle3 = -1;
length = quadraticK = 0.0; 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) { particle1(particle1), particle2(particle2), particle3(particle3), length(length), quadraticK(quadraticK) {
} }
}; };
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ f11bafd9
...@@ -71,7 +71,7 @@ public: ...@@ -71,7 +71,7 @@ public:
* *
* @param cubicK the cubic force constant for the bond * @param cubicK the cubic force constant for the bond
*/ */
void setAmoebaGlobalBondCubic( double cubicK ); void setAmoebaGlobalBondCubic(double cubicK);
/** /**
* Get the global cubic term * Get the global cubic term
...@@ -85,7 +85,7 @@ public: ...@@ -85,7 +85,7 @@ public:
* *
* @param quarticK the quartic force constant for the bond * @param quarticK the quartic force constant for the bond
*/ */
void setAmoebaGlobalBondQuartic( double quarticK ); void setAmoebaGlobalBondQuartic(double quarticK);
/** /**
* Get the global quartic term * Get the global quartic term
...@@ -104,7 +104,7 @@ public: ...@@ -104,7 +104,7 @@ public:
* @return the index of the bond that was added * @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. * Get the force field parameters for a bond term.
...@@ -116,7 +116,7 @@ public: ...@@ -116,7 +116,7 @@ public:
* @param quadratic k the quadratic force constant for the bond * @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. * Set the force field parameters for a bond term.
...@@ -127,7 +127,7 @@ public: ...@@ -127,7 +127,7 @@ public:
* @param length the equilibrium length of the bond, measured in nm * @param length the equilibrium length of the bond, measured in nm
* @param k the quadratic force constant for the bond * @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 * 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. * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
...@@ -167,7 +167,7 @@ public: ...@@ -167,7 +167,7 @@ public:
particle1 = particle2 = -1; particle1 = particle2 = -1;
length = quadraticK = 0.0; 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) { particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
} }
}; };
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ f11bafd9
...@@ -152,7 +152,7 @@ public: ...@@ -152,7 +152,7 @@ public:
/** /**
* Set the surface area factor kJ/(nm*nm) used in SASA contribution * 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 * 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. * 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 @ f11bafd9
...@@ -70,7 +70,7 @@ public: ...@@ -70,7 +70,7 @@ public:
* *
* @param cubicK the cubic force constant for the angle * @param cubicK the cubic force constant for the angle
*/ */
void setAmoebaGlobalInPlaneAngleCubic( double cubicK ); void setAmoebaGlobalInPlaneAngleCubic(double cubicK);
/** /**
* Get the global cubic term * Get the global cubic term
...@@ -84,7 +84,7 @@ public: ...@@ -84,7 +84,7 @@ public:
* *
* @param quarticK the quartic force constant for the angle * @param quarticK the quartic force constant for the angle
*/ */
void setAmoebaGlobalInPlaneAngleQuartic( double quarticK ); void setAmoebaGlobalInPlaneAngleQuartic(double quarticK);
/** /**
* Get the global quartic term * Get the global quartic term
...@@ -98,7 +98,7 @@ public: ...@@ -98,7 +98,7 @@ public:
* *
* @param penticK the pentic force constant for the angle * @param penticK the pentic force constant for the angle
*/ */
void setAmoebaGlobalInPlaneAnglePentic( double penticK ); void setAmoebaGlobalInPlaneAnglePentic(double penticK);
/** /**
* Get the global pentic term * Get the global pentic term
...@@ -112,7 +112,7 @@ public: ...@@ -112,7 +112,7 @@ public:
* *
* @param sexticK the sextic force constant for the angle * @param sexticK the sextic force constant for the angle
*/ */
void setAmoebaGlobalInPlaneAngleSextic( double sexticK ); void setAmoebaGlobalInPlaneAngleSextic(double sexticK);
/** /**
* Get the global sextic term * Get the global sextic term
...@@ -133,7 +133,7 @@ public: ...@@ -133,7 +133,7 @@ public:
* @return the index of the angle that was added * @return the index of the angle that was added
*/ */
int addAngle(int particle1, int particle2, int particle3, int particle4, double length, 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. * Get the force field parameters for an angle term.
...@@ -147,7 +147,7 @@ public: ...@@ -147,7 +147,7 @@ public:
* @param quadratic k the quadratic force constant for the angle measured in kJ/mol/radian^2 * @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, 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. * Set the force field parameters for an angle term.
...@@ -160,7 +160,7 @@ public: ...@@ -160,7 +160,7 @@ public:
* @param length the equilibrium angle, measured in radians * @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @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 * 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. * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
...@@ -200,7 +200,7 @@ public: ...@@ -200,7 +200,7 @@ public:
particle1 = particle2 = particle3 = particle4 = -1; particle1 = particle2 = particle3 = particle4 = -1;
length = quadraticK = 0.0; 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), particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4),
length(length), quadraticK(quadraticK) { length(length), quadraticK(quadraticK) {
} }
......
plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ f11bafd9
...@@ -148,7 +148,7 @@ public: ...@@ -148,7 +148,7 @@ public:
lengthAB = lengthCB = angle = k1 = k2 = 0.0; lengthAB = lengthCB = angle = k1 = k2 = 0.0;
} }
StretchBendInfo(int particle1, int particle2, int particle3, 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), particle1(particle1), particle2(particle2), particle3(particle3),
lengthAB(lengthAB), lengthCB(lengthCB), angle(angle), k1(k1), k2(k2) { lengthAB(lengthAB), lengthCB(lengthCB), angle(angle), k1(k1), k2(k2) {
} }
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ f11bafd9
...@@ -350,10 +350,10 @@ public: ...@@ -350,10 +350,10 @@ public:
virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0; virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
virtual void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid, virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ) = 0; 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. * Copy changed parameters over to a context.
* *
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h
View file @ f11bafd9
...@@ -70,9 +70,9 @@ public: ...@@ -70,9 +70,9 @@ public:
* @param minCovalentIndex minimum covalent index * @param minCovalentIndex minimum covalent index
* @param maxCovalentIndex maximum 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, const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex ); int* minCovalentIndex, int* maxCovalentIndex);
/** /**
* Get the covalent degree for the CovalentEnd lists * Get the covalent degree for the CovalentEnd lists
...@@ -80,14 +80,14 @@ public: ...@@ -80,14 +80,14 @@ public:
* @param force AmoebaMultipoleForce force reference * @param force AmoebaMultipoleForce force reference
* @param covalentDegree covalent degrees for the CovalentEnd lists * @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 getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid, void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ); std::vector< double >& outputElectrostaticPotential);
void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments ); void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
void updateParametersInContext(ContextImpl& context); void updateParametersInContext(ContextImpl& context);
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h
View file @ f11bafd9
...@@ -61,7 +61,7 @@ public: ...@@ -61,7 +61,7 @@ public:
} }
std::vector<std::string> getKernelNames(); 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: private:
const AmoebaTorsionTorsionForce& owner; const AmoebaTorsionTorsionForce& owner;
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaWcaDispersionForceImpl.h
View file @ f11bafd9
...@@ -69,7 +69,7 @@ public: ...@@ -69,7 +69,7 @@ public:
* @param particleIndex the particle index * @param particleIndex the particle index
* @param maxDispersionEnergy maximum dispersion energy * @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 * Get the total maximum dispersion energy
...@@ -78,7 +78,7 @@ public: ...@@ -78,7 +78,7 @@ public:
* *
* @return total maximum dispersion energy for the system * @return total maximum dispersion energy for the system
*/ */
static double getTotalMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force); static double getTotalMaximumDispersionEnergy(const AmoebaWcaDispersionForce& force);
void updateParametersInContext(ContextImpl& context); void updateParametersInContext(ContextImpl& context);
private: private:
......
plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ f11bafd9
...@@ -46,7 +46,7 @@ int AmoebaAngleForce::addAngle(int particle1, int particle2, int particle3, dou ...@@ -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, 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; particle1 = angles[index].particle1;
particle2 = angles[index].particle2; particle2 = angles[index].particle2;
particle3 = angles[index].particle3; particle3 = angles[index].particle3;
...@@ -55,7 +55,7 @@ void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& partic ...@@ -55,7 +55,7 @@ void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& partic
} }
void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, 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].particle1 = particle1;
angles[index].particle2 = particle2; angles[index].particle2 = particle2;
angles[index].particle3 = particle3; angles[index].particle3 = particle3;
...@@ -67,7 +67,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const { ...@@ -67,7 +67,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
return _globalCubicK; return _globalCubicK;
} }
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) { void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK) {
_globalCubicK = cubicK; _globalCubicK = cubicK;
} }
...@@ -75,7 +75,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const { ...@@ -75,7 +75,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
return _globalQuarticK; return _globalQuarticK;
} }
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) { void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK) {
_globalQuarticK = quarticK; _globalQuarticK = quarticK;
} }
...@@ -83,7 +83,7 @@ double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const { ...@@ -83,7 +83,7 @@ double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
return _globalPenticK; return _globalPenticK;
} }
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) { void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK) {
_globalPenticK = penticK; _globalPenticK = penticK;
} }
...@@ -91,7 +91,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const { ...@@ -91,7 +91,7 @@ double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const {
return _globalSexticK; return _globalSexticK;
} }
void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK ) { void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK) {
_globalSexticK = sexticK; _globalSexticK = sexticK;
} }
......
plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ f11bafd9
...@@ -41,29 +41,29 @@ AmoebaBondForce::AmoebaBondForce() { ...@@ -41,29 +41,29 @@ AmoebaBondForce::AmoebaBondForce() {
} }
int AmoebaBondForce::addBond(int particle1, int particle2, double length, double quadraticK) { 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; 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; particle1 = bonds[index].particle1;
particle2 = bonds[index].particle2; particle2 = bonds[index].particle2;
length = bonds[index].length; length = bonds[index].length;
quadraticK = bonds[index].quadraticK; 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].particle1 = particle1;
bonds[index].particle2 = particle2; bonds[index].particle2 = particle2;
bonds[index].length = length; bonds[index].length = length;
bonds[index].quadraticK = quadraticK; bonds[index].quadraticK = quadraticK;
} }
void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK ) { void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK) {
_globalCubicK = cubicK; _globalCubicK = cubicK;
} }
void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) { void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK) {
_globalQuarticK = quarticK; _globalQuarticK = quarticK;
} }
......
plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp
View file @ f11bafd9
...@@ -62,7 +62,7 @@ double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const { ...@@ -62,7 +62,7 @@ double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
return dielectricOffset; return dielectricOffset;
} }
void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset ) { void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset) {
dielectricOffset = inputDielectricOffset; dielectricOffset = inputDielectricOffset;
} */ } */
...@@ -70,7 +70,7 @@ int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const { ...@@ -70,7 +70,7 @@ int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const {
return includeCavityTerm; return includeCavityTerm;
} }
void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm ) { void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm) {
includeCavityTerm = inputIncludeCavityTerm; includeCavityTerm = inputIncludeCavityTerm;
} }
...@@ -78,7 +78,7 @@ double AmoebaGeneralizedKirkwoodForce::getProbeRadius() const { ...@@ -78,7 +78,7 @@ double AmoebaGeneralizedKirkwoodForce::getProbeRadius() const {
return probeRadius; return probeRadius;
} }
void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius ) { void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius) {
probeRadius = inputProbeRadius; probeRadius = inputProbeRadius;
} }
...@@ -86,7 +86,7 @@ double AmoebaGeneralizedKirkwoodForce::getSurfaceAreaFactor() const { ...@@ -86,7 +86,7 @@ double AmoebaGeneralizedKirkwoodForce::getSurfaceAreaFactor() const {
return surfaceAreaFactor; return surfaceAreaFactor;
} }
void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor ) { void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor) {
surfaceAreaFactor = inputSurfaceAreaFactor; surfaceAreaFactor = inputSurfaceAreaFactor;
} }
......
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ f11bafd9
...@@ -40,13 +40,13 @@ AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() { ...@@ -40,13 +40,13 @@ AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0; _globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
} }
int AmoebaInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4, double length, double 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 )); angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK));
return angles.size()-1; return angles.size()-1;
} }
void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, 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; particle1 = angles[index].particle1;
particle2 = angles[index].particle2; particle2 = angles[index].particle2;
particle3 = angles[index].particle3; particle3 = angles[index].particle3;
...@@ -56,7 +56,7 @@ void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& ...@@ -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, 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].particle1 = particle1;
angles[index].particle2 = particle2; angles[index].particle2 = particle2;
angles[index].particle3 = particle3; angles[index].particle3 = particle3;
...@@ -65,11 +65,11 @@ void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int p ...@@ -65,11 +65,11 @@ void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int p
angles[index].quadraticK = quadraticK; angles[index].quadraticK = quadraticK;
} }
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK ) { void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK) {
_globalCubicK = cubicK; _globalCubicK = cubicK;
} }
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK ) { void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK) {
_globalQuarticK = quarticK; _globalQuarticK = quarticK;
} }
...@@ -81,11 +81,11 @@ double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic() const { ...@@ -81,11 +81,11 @@ double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic() const {
return _globalQuarticK; return _globalQuarticK;
} }
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK ) { void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK) {
_globalPenticK = cubicK; _globalPenticK = cubicK;
} }
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK ) { void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK) {
_globalSexticK = quarticK; _globalSexticK = quarticK;
} }
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ f11bafd9
...@@ -49,7 +49,7 @@ AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() ...@@ -49,7 +49,7 @@ AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod()
return nonbondedMethod; return nonbondedMethod;
} }
void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMethod method) { void AmoebaMultipoleForce::setNonbondedMethod(AmoebaMultipoleForce::NonbondedMethod method) {
nonbondedMethod = method; nonbondedMethod = method;
} }
...@@ -57,7 +57,7 @@ AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType ...@@ -57,7 +57,7 @@ AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType
return polarizationType; return polarizationType;
} }
void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::PolarizationType type ) { void AmoebaMultipoleForce::setPolarizationType(AmoebaMultipoleForce::PolarizationType type) {
polarizationType = type; polarizationType = type;
} }
...@@ -73,7 +73,7 @@ double AmoebaMultipoleForce::getAEwald() const { ...@@ -73,7 +73,7 @@ double AmoebaMultipoleForce::getAEwald() const {
return aewald; return aewald;
} }
void AmoebaMultipoleForce::setAEwald(double inputAewald ) { void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald; aewald = inputAewald;
} }
...@@ -81,11 +81,11 @@ int AmoebaMultipoleForce::getPmeBSplineOrder() const { ...@@ -81,11 +81,11 @@ int AmoebaMultipoleForce::getPmeBSplineOrder() const {
return pmeBSplineOrder; return pmeBSplineOrder;
} }
void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ) const { void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
if( gridDimension.size() < 3 ){ if (gridDimension.size() < 3) {
gridDimension.resize(3); gridDimension.resize(3);
} }
if( pmeGridDimension.size() > 2 ){ if (pmeGridDimension.size() > 2) {
gridDimension[0] = pmeGridDimension[0]; gridDimension[0] = pmeGridDimension[0];
gridDimension[1] = pmeGridDimension[1]; gridDimension[1] = pmeGridDimension[1];
gridDimension[2] = pmeGridDimension[2]; gridDimension[2] = pmeGridDimension[2];
...@@ -95,7 +95,7 @@ void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ...@@ -95,7 +95,7 @@ void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension
return; return;
} }
void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDimension ) { void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
pmeGridDimension.resize(3); pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0]; pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1]; pmeGridDimension[1] = gridDimension[1];
...@@ -107,7 +107,7 @@ int AmoebaMultipoleForce::getMutualInducedMaxIterations() const { ...@@ -107,7 +107,7 @@ int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
return mutualInducedMaxIterations; return mutualInducedMaxIterations;
} }
void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInducedMaxIterations ) { void AmoebaMultipoleForce::setMutualInducedMaxIterations(int inputMutualInducedMaxIterations) {
mutualInducedMaxIterations = inputMutualInducedMaxIterations; mutualInducedMaxIterations = inputMutualInducedMaxIterations;
} }
...@@ -115,7 +115,7 @@ double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const { ...@@ -115,7 +115,7 @@ double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const {
return mutualInducedTargetEpsilon; return mutualInducedTargetEpsilon;
} }
void AmoebaMultipoleForce::setMutualInducedTargetEpsilon( double inputMutualInducedTargetEpsilon ) { void AmoebaMultipoleForce::setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon) {
mutualInducedTargetEpsilon = inputMutualInducedTargetEpsilon; mutualInducedTargetEpsilon = inputMutualInducedTargetEpsilon;
} }
...@@ -127,22 +127,22 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) { ...@@ -127,22 +127,22 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = 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) { 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; return multipoles.size()-1;
} }
void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, 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; charge = multipoles[index].charge;
molecularDipole.resize( 3 ); molecularDipole.resize(3);
molecularDipole[0] = multipoles[index].molecularDipole[0]; molecularDipole[0] = multipoles[index].molecularDipole[0];
molecularDipole[1] = multipoles[index].molecularDipole[1]; molecularDipole[1] = multipoles[index].molecularDipole[1];
molecularDipole[2] = multipoles[index].molecularDipole[2]; molecularDipole[2] = multipoles[index].molecularDipole[2];
molecularQuadrupole.resize( 9 ); molecularQuadrupole.resize(9);
molecularQuadrupole[0] = multipoles[index].molecularQuadrupole[0]; molecularQuadrupole[0] = multipoles[index].molecularQuadrupole[0];
molecularQuadrupole[1] = multipoles[index].molecularQuadrupole[1]; molecularQuadrupole[1] = multipoles[index].molecularQuadrupole[1];
molecularQuadrupole[2] = multipoles[index].molecularQuadrupole[2]; molecularQuadrupole[2] = multipoles[index].molecularQuadrupole[2];
...@@ -164,7 +164,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std ...@@ -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, 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; multipoles[index].charge = charge;
...@@ -192,34 +192,34 @@ void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, cons ...@@ -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]; std::vector<int>& covalentList = multipoles[index].covalentInfo[typeId];
covalentList.resize( covalentAtoms.size() ); covalentList.resize(covalentAtoms.size());
for( unsigned int ii = 0; ii < covalentAtoms.size(); ii++ ){ for (unsigned int ii = 0; ii < covalentAtoms.size(); ii++) {
covalentList[ii] = covalentAtoms[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 // load covalent atom index entries for atomId==index and covalentId==typeId into covalentAtoms
std::vector<int> covalentList = multipoles[index].covalentInfo[typeId]; std::vector<int> covalentList = multipoles[index].covalentInfo[typeId];
covalentAtoms.resize( covalentList.size() ); covalentAtoms.resize(covalentList.size());
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){ for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
covalentAtoms[ii] = covalentList[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 ); covalentLists.resize(CovalentEnd);
for( unsigned int jj = 0; jj < CovalentEnd; jj++ ){ for (unsigned int jj = 0; jj < CovalentEnd; jj++) {
std::vector<int> covalentList = multipoles[index].covalentInfo[jj]; std::vector<int> covalentList = multipoles[index].covalentInfo[jj];
std::vector<int> covalentAtoms; std::vector<int> covalentAtoms;
covalentAtoms.resize( covalentList.size() ); covalentAtoms.resize(covalentList.size());
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){ for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
covalentAtoms[ii] = covalentList[ii]; covalentAtoms[ii] = covalentList[ii];
} }
covalentLists[jj] = covalentAtoms; covalentLists[jj] = covalentAtoms;
...@@ -230,11 +230,11 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip ...@@ -230,11 +230,11 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles); 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); 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); dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getSystemMultipoleMoments(getContextImpl(context), outputMultipoleMoments);
} }
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ f11bafd9
...@@ -64,26 +64,26 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) { ...@@ -64,26 +64,26 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
} }
double quadrupoleValidationTolerance = 1.0e-05; 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; int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity ; double charge, thole, dampingFactor, polarity ;
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole; std::vector<double> molecularQuadrupole;
owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, owner.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity ); thole, dampingFactor, polarity);
// check quadrupole is traceless and symmetric // check quadrupole is traceless and symmetric
double trace = fabs( molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8] ); double trace = fabs(molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8]);
if( trace > quadrupoleValidationTolerance ){ if (trace > quadrupoleValidationTolerance) {
std::stringstream buffer; std::stringstream buffer;
buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii; buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii;
buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole."; buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole.";
throw OpenMMException(buffer.str()); throw OpenMMException(buffer.str());
} }
if( fabs( molecularQuadrupole[1] - molecularQuadrupole[3] ) > quadrupoleValidationTolerance ){ if (fabs(molecularQuadrupole[1] - molecularQuadrupole[3]) > quadrupoleValidationTolerance ) {
std::stringstream buffer; std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii; buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];"; buffer << " are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];";
...@@ -91,7 +91,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) { ...@@ -91,7 +91,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
throw OpenMMException(buffer.str()); throw OpenMMException(buffer.str());
} }
if( fabs( molecularQuadrupole[2] - molecularQuadrupole[6] ) > quadrupoleValidationTolerance ){ if (fabs(molecularQuadrupole[2] - molecularQuadrupole[6]) > quadrupoleValidationTolerance ) {
std::stringstream buffer; std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii; buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];"; buffer << " are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];";
...@@ -99,7 +99,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) { ...@@ -99,7 +99,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
throw OpenMMException(buffer.str()); throw OpenMMException(buffer.str());
} }
if( fabs( molecularQuadrupole[5] - molecularQuadrupole[7] ) > quadrupoleValidationTolerance ){ if (fabs(molecularQuadrupole[5] - molecularQuadrupole[7]) > quadrupoleValidationTolerance ) {
std::stringstream buffer; std::stringstream buffer;
buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii; buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];"; buffer << " are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];";
...@@ -109,9 +109,9 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) { ...@@ -109,9 +109,9 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
// only 'Z-then-X', 'Bisector', Z-Bisect, ThreeFold currently handled // 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::ZBisect && axisType != AmoebaMultipoleForce::ThreeFold &&
axisType != AmoebaMultipoleForce::ZOnly && axisType != AmoebaMultipoleForce::NoAxisType ) { axisType != AmoebaMultipoleForce::ZOnly && axisType != AmoebaMultipoleForce::NoAxisType) {
std::stringstream buffer; std::stringstream buffer;
buffer << "AmoebaMultipoleForce: axis type=" << axisType; buffer << "AmoebaMultipoleForce: axis type=" << axisType;
buffer << " not currently handled - only axisTypes[ "; buffer << " not currently handled - only axisTypes[ ";
...@@ -139,7 +139,7 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() { ...@@ -139,7 +139,7 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
} }
const int* AmoebaMultipoleForceImpl::getCovalentDegrees() { const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
if( !initializedCovalentDegrees ){ if (!initializedCovalentDegrees) {
initializedCovalentDegrees = true; initializedCovalentDegrees = true;
CovalentDegrees[AmoebaMultipoleForce::Covalent12] = 1; CovalentDegrees[AmoebaMultipoleForce::Covalent12] = 1;
CovalentDegrees[AmoebaMultipoleForce::Covalent13] = 2; CovalentDegrees[AmoebaMultipoleForce::Covalent13] = 2;
...@@ -153,20 +153,20 @@ const int* AmoebaMultipoleForceImpl::getCovalentDegrees() { ...@@ -153,20 +153,20 @@ const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
return CovalentDegrees; return CovalentDegrees;
} }
void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists, void AmoebaMultipoleForceImpl::getCovalentRange(const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
int* minCovalentIndex, int* maxCovalentIndex ){ int* minCovalentIndex, int* maxCovalentIndex) {
*minCovalentIndex = 999999999; *minCovalentIndex = 999999999;
*maxCovalentIndex = -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]; AmoebaMultipoleForce::CovalentType jj = lists[kk];
std::vector<int> covalentList; std::vector<int> covalentList;
force.getCovalentMap( atomIndex, jj, covalentList ); force.getCovalentMap(atomIndex, jj, covalentList);
for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){ for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
if( *minCovalentIndex > covalentList[ii] ){ if (*minCovalentIndex > covalentList[ii]) {
*minCovalentIndex = covalentList[ii]; *minCovalentIndex = covalentList[ii];
} }
if( *maxCovalentIndex < covalentList[ii] ){ if (*maxCovalentIndex < covalentList[ii]) {
*maxCovalentIndex = covalentList[ii]; *maxCovalentIndex = covalentList[ii];
} }
} }
...@@ -174,10 +174,10 @@ void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& for ...@@ -174,10 +174,10 @@ void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& for
return; return;
} }
void AmoebaMultipoleForceImpl::getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree ){ void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree) {
covalentDegree.resize( AmoebaMultipoleForce::CovalentEnd ); covalentDegree.resize(AmoebaMultipoleForce::CovalentEnd);
const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees(); 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]; covalentDegree[kk] = CovalentDegrees[kk];
} }
return; return;
...@@ -187,12 +187,12 @@ void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Ve ...@@ -187,12 +187,12 @@ void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Ve
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles); kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles);
} }
void AmoebaMultipoleForceImpl::getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid, void AmoebaMultipoleForceImpl::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ){ std::vector< double >& outputElectrostaticPotential) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, 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); kernel.getAs<CalcAmoebaMultipoleForceKernel>().getSystemMultipoleMoments(context, outputMultipoleMoments);
} }
......
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp
View file @ f11bafd9
...@@ -48,7 +48,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const { ...@@ -48,7 +48,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
return _globalCubicK; return _globalCubicK;
} }
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK ) { void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK) {
_globalCubicK = cubicK; _globalCubicK = cubicK;
} }
...@@ -56,7 +56,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const { ...@@ -56,7 +56,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
return _globalQuarticK; return _globalQuarticK;
} }
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK ) { void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK) {
_globalQuarticK = quarticK; _globalQuarticK = quarticK;
} }
...@@ -64,7 +64,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const { ...@@ -64,7 +64,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
return _globalPenticK; return _globalPenticK;
} }
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK ) { void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK) {
_globalPenticK = penticK; _globalPenticK = penticK;
} }
...@@ -72,7 +72,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const { ...@@ -72,7 +72,7 @@ double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const {
return _globalSexticK; return _globalSexticK;
} }
void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK ) { void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK) {
_globalSexticK = sexticK; _globalSexticK = sexticK;
} }
...@@ -82,7 +82,7 @@ int AmoebaOutOfPlaneBendForce::addOutOfPlaneBend(int particle1, int particle2, i ...@@ -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, void AmoebaOutOfPlaneBendForce::getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
double& k ) const { double& k) const {
particle1 = outOfPlaneBends[index].particle1; particle1 = outOfPlaneBends[index].particle1;
particle2 = outOfPlaneBends[index].particle2; particle2 = outOfPlaneBends[index].particle2;
particle3 = outOfPlaneBends[index].particle3; particle3 = outOfPlaneBends[index].particle3;
......
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