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Commit 7fb10336 authored by peastman's avatar peastman
Browse files

Cleaned up lots of formatting to be more consistent with the rest of OpenMM

parent 1d3ffd7b
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Showing with 170 additions and 170 deletions
platforms/reference/include/CpuGBVI.h
View file @ 7fb10336
......@@ -53,7 +53,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
CpuGBVI( GBVIParameters* gbviParameters );
CpuGBVI(GBVIParameters* gbviParameters);
/**---------------------------------------------------------------------------------------
......@@ -61,7 +61,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
~CpuGBVI( );
~CpuGBVI();
/**---------------------------------------------------------------------------------------
......@@ -71,7 +71,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
GBVIParameters* getGBVIParameters( void ) const;
GBVIParameters* getGBVIParameters() const;
/**---------------------------------------------------------------------------------------
......@@ -81,7 +81,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void setGBVIParameters( GBVIParameters* gbviParameters );
void setGBVIParameters(GBVIParameters* gbviParameters);
/**---------------------------------------------------------------------------------------
......@@ -93,7 +93,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void computeBornRadii( const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
/**---------------------------------------------------------------------------------------
......@@ -107,7 +107,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static RealOpenMM getVolume( RealOpenMM r, RealOpenMM R, RealOpenMM S );
static RealOpenMM getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S);
/**---------------------------------------------------------------------------------------
......@@ -121,7 +121,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static RealOpenMM getL( RealOpenMM r, RealOpenMM x, RealOpenMM S );
static RealOpenMM getL(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
......@@ -135,7 +135,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static RealOpenMM dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S );
static RealOpenMM dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
......@@ -149,7 +149,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static RealOpenMM dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S );
static RealOpenMM dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
......@@ -161,7 +161,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static RealOpenMM Sgb( RealOpenMM t );
static RealOpenMM Sgb(RealOpenMM t);
/**---------------------------------------------------------------------------------------
......@@ -174,7 +174,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergy( const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges );
RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges);
/**---------------------------------------------------------------------------------------
......@@ -186,8 +186,8 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void computeBornForces( std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& inputForces );
void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
/**---------------------------------------------------------------------------------------
......@@ -201,7 +201,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static double getVolumeD( double r, double R, double S );
static double getVolumeD(double r, double R, double S);
/**---------------------------------------------------------------------------------------
......@@ -215,7 +215,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static double getLD( double r, double x, double S );
static double getLD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
......@@ -229,7 +229,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static double dL_drD( double r, double x, double S );
static double dL_drD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
......@@ -243,7 +243,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
static double dL_dxD( double r, double x, double S );
static double dL_dxD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
......@@ -254,7 +254,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
RealOpenMMVector& getSwitchDeriviative( void );
RealOpenMMVector& getSwitchDeriviative();
/**---------------------------------------------------------------------------------------
......@@ -268,8 +268,8 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
RealOpenMM* outValue, RealOpenMM* outDerivative );
void quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
RealOpenMM* outValue, RealOpenMM* outDerivative);
/**---------------------------------------------------------------------------------------
......@@ -285,9 +285,9 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, RealOpenMM bornSum,
GBVIParameters* gbviParameters,
RealOpenMM* bornRadius, RealOpenMM* switchDeriviative );
void computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum,
GBVIParameters* gbviParameters,
RealOpenMM* bornRadius, RealOpenMM* switchDeriviative);
/**---------------------------------------------------------------------------------------
......@@ -303,11 +303,11 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void printGbvi( const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log );
void printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log);
};
......
platforms/reference/include/CpuObc.h
View file @ 7fb10336
......@@ -59,7 +59,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
CpuObc( ObcParameters* obcParameters );
CpuObc(ObcParameters* obcParameters);
/**---------------------------------------------------------------------------------------
......@@ -67,7 +67,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
~CpuObc( );
~CpuObc();
/**---------------------------------------------------------------------------------------
......@@ -77,7 +77,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
ObcParameters* getObcParameters( void ) const;
ObcParameters* getObcParameters() const;
/**---------------------------------------------------------------------------------------
......@@ -87,7 +87,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void setObcParameters( ObcParameters* obcParameters );
void setObcParameters(ObcParameters* obcParameters);
/**---------------------------------------------------------------------------------------
......@@ -97,7 +97,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
int includeAceApproximation( void ) const;
int includeAceApproximation() const;
/**---------------------------------------------------------------------------------------
......@@ -107,7 +107,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void setIncludeAceApproximation( int includeAceApproximation );
void setIncludeAceApproximation(int includeAceApproximation);
/**---------------------------------------------------------------------------------------
......@@ -117,7 +117,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
RealOpenMMVector& getObcChain( void );
RealOpenMMVector& getObcChain();
/**---------------------------------------------------------------------------------------
......@@ -128,7 +128,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void computeBornRadii( const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
/**---------------------------------------------------------------------------------------
......@@ -142,8 +142,8 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void computeAceNonPolarForce( const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii,
RealOpenMM* energy, RealOpenMMVector& forces ) const;
void computeAceNonPolarForce(const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii,
RealOpenMM* energy, RealOpenMMVector& forces) const;
/**---------------------------------------------------------------------------------------
......@@ -155,8 +155,8 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergyForces( const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces );
RealOpenMM computeBornEnergyForces(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces);
/**---------------------------------------------------------------------------------------
......@@ -172,12 +172,12 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void printObc( const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log );
void printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log);
};
......
platforms/reference/include/GBVIParameters.h
View file @ 7fb10336
......@@ -82,7 +82,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
GBVIParameters( int numberOfAtoms );
GBVIParameters(int numberOfAtoms);
/**---------------------------------------------------------------------------------------
......@@ -90,7 +90,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
~GBVIParameters( );
~GBVIParameters();
/**---------------------------------------------------------------------------------------
......@@ -100,7 +100,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms( void ) const;
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
......@@ -110,7 +110,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getElectricConstant( void ) const;
RealOpenMM getElectricConstant() const;
/**---------------------------------------------------------------------------------------
......@@ -120,7 +120,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSolventDielectric( void ) const;
RealOpenMM getSolventDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -130,7 +130,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setSolventDielectric( RealOpenMM solventDielectric );
void setSolventDielectric(RealOpenMM solventDielectric);
/**---------------------------------------------------------------------------------------
......@@ -140,7 +140,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSoluteDielectric( void ) const;
RealOpenMM getSoluteDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -150,7 +150,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setSoluteDielectric( RealOpenMM soluteDielectric );
void setSoluteDielectric(RealOpenMM soluteDielectric);
/**---------------------------------------------------------------------------------------
......@@ -160,7 +160,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadii( void ) const;
const RealOpenMMVector& getScaledRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -170,7 +170,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadii( const RealOpenMMVector& scaledRadii );
void setScaledRadii(const RealOpenMMVector& scaledRadii);
/**---------------------------------------------------------------------------------------
......@@ -180,7 +180,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii( void ) const;
const RealOpenMMVector& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -190,7 +190,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
void setAtomicRadii(const RealOpenMMVector& atomicRadii);
/**---------------------------------------------------------------------------------------
......@@ -200,7 +200,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getGammaParameters( void ) const;
const RealOpenMMVector& getGammaParameters() const;
/**---------------------------------------------------------------------------------------
......@@ -210,7 +210,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setGammaParameters( const RealOpenMMVector& gammaParameters );
void setGammaParameters(const RealOpenMMVector& gammaParameters);
/**---------------------------------------------------------------------------------------
......@@ -220,7 +220,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance );
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......@@ -274,7 +274,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getTau( void ) const;
RealOpenMM getTau() const;
/**---------------------------------------------------------------------------------------
......@@ -284,7 +284,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
int getBornRadiusScalingMethod( void ) const;
int getBornRadiusScalingMethod() const;
/**---------------------------------------------------------------------------------------
......@@ -294,7 +294,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setBornRadiusScalingMethod( int bornRadiusScalingMethod );
void setBornRadiusScalingMethod(int bornRadiusScalingMethod);
/**---------------------------------------------------------------------------------------
......@@ -304,7 +304,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticLowerLimitFactor( void ) const;
RealOpenMM getQuinticLowerLimitFactor() const;
/**---------------------------------------------------------------------------------------
......@@ -314,7 +314,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFactor );
void setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor);
/**---------------------------------------------------------------------------------------
......@@ -324,7 +324,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticUpperBornRadiusLimit( void ) const;
RealOpenMM getQuinticUpperBornRadiusLimit() const;
/**---------------------------------------------------------------------------------------
......@@ -334,7 +334,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setQuinticUpperBornRadiusLimit( RealOpenMM quinticUpperSplineLimit );
void setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperSplineLimit);
};
......
platforms/reference/include/ObcParameters.h
View file @ 7fb10336
......@@ -75,7 +75,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setDielectricOffset( RealOpenMM dielectricOffset );
void setDielectricOffset(RealOpenMM dielectricOffset);
public:
......@@ -87,7 +87,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII );
ObcParameters(int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII);
/**---------------------------------------------------------------------------------------
......@@ -95,7 +95,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
~ObcParameters( );
~ObcParameters();
/**---------------------------------------------------------------------------------------
......@@ -105,7 +105,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms( void ) const;
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
......@@ -115,7 +115,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getElectricConstant( void ) const;
RealOpenMM getElectricConstant() const;
/**---------------------------------------------------------------------------------------
......@@ -125,7 +125,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getProbeRadius( void ) const;
RealOpenMM getProbeRadius() const;
/**---------------------------------------------------------------------------------------
......@@ -135,7 +135,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setProbeRadius( RealOpenMM probeRadius );
void setProbeRadius(RealOpenMM probeRadius);
/**---------------------------------------------------------------------------------------
......@@ -146,7 +146,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getPi4Asolv( void ) const;
RealOpenMM getPi4Asolv() const;
/**---------------------------------------------------------------------------------------
......@@ -154,7 +154,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setPi4Asolv( RealOpenMM pi4Asolv );
void setPi4Asolv(RealOpenMM pi4Asolv);
/**---------------------------------------------------------------------------------------
......@@ -164,7 +164,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSolventDielectric( void ) const;
RealOpenMM getSolventDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -174,7 +174,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setSolventDielectric( RealOpenMM solventDielectric );
void setSolventDielectric(RealOpenMM solventDielectric);
/**---------------------------------------------------------------------------------------
......@@ -184,7 +184,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSoluteDielectric( void ) const;
RealOpenMM getSoluteDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -194,7 +194,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setSoluteDielectric( RealOpenMM soluteDielectric );
void setSoluteDielectric(RealOpenMM soluteDielectric);
/**---------------------------------------------------------------------------------------
......@@ -204,7 +204,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
ObcParameters::ObcType getObcType( void ) const;
ObcParameters::ObcType getObcType() const;
/**---------------------------------------------------------------------------------------
......@@ -214,7 +214,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setObcTypeParameters( ObcParameters::ObcType obcType );
void setObcTypeParameters(ObcParameters::ObcType obcType);
/**---------------------------------------------------------------------------------------
......@@ -224,7 +224,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getAlphaObc( void ) const;
RealOpenMM getAlphaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -234,7 +234,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getBetaObc( void ) const;
RealOpenMM getBetaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -244,7 +244,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getGammaObc( void ) const;
RealOpenMM getGammaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -254,7 +254,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getDielectricOffset( void ) const;
RealOpenMM getDielectricOffset() const;
/**---------------------------------------------------------------------------------------
......@@ -264,7 +264,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadiusFactors( void ) const;
const RealOpenMMVector& getScaledRadiusFactors() const;
/**---------------------------------------------------------------------------------------
......@@ -274,7 +274,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
void setScaledRadiusFactors(const RealOpenMMVector& scaledRadiusFactors);
/**---------------------------------------------------------------------------------------
......@@ -284,7 +284,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii( void ) const;
const RealOpenMMVector& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -294,7 +294,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
void setAtomicRadii(const RealOpenMMVector& atomicRadii);
/**---------------------------------------------------------------------------------------
......@@ -305,7 +305,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance );
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceAndersenThermostat.h
View file @ 7fb10336
......@@ -42,7 +42,7 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
ReferenceAndersenThermostat( );
ReferenceAndersenThermostat();
/**---------------------------------------------------------------------------------------
......@@ -50,7 +50,7 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
~ReferenceAndersenThermostat( );
~ReferenceAndersenThermostat();
/**---------------------------------------------------------------------------------------
......@@ -65,8 +65,8 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
void applyThermostat( const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const;
void applyThermostat(const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const;
};
......
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 7fb10336
......@@ -41,7 +41,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn( );
ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -49,7 +49,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceAngleBondIxn( );
~ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -63,8 +63,8 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm ) const;
void getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm) const;
/**---------------------------------------------------------------------------------------
......@@ -79,9 +79,9 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
......
platforms/reference/include/ReferenceBondForce.h
View file @ 7fb10336
......@@ -42,7 +42,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
ReferenceBondForce( );
ReferenceBondForce();
/**---------------------------------------------------------------------------------------
......@@ -50,7 +50,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
~ReferenceBondForce( );
~ReferenceBondForce();
/**---------------------------------------------------------------------------------------
......@@ -67,10 +67,10 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
void calculateForce( int numberOfBonds, int** atomIndices,
void calculateForce(int numberOfBonds, int** atomIndices,
std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn);
};
......
platforms/reference/include/ReferenceBondIxn.h
View file @ 7fb10336
......@@ -43,7 +43,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceBondIxn( );
ReferenceBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceBondIxn( );
~ReferenceBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -65,9 +65,9 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
virtual void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
/**---------------------------------------------------------------------------------------
......@@ -82,7 +82,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry );
static RealOpenMM getNormedDotProduct(RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry);
/**---------------------------------------------------------------------------------------
......@@ -98,8 +98,8 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry );
static RealOpenMM getAngleBetweenTwoVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry);
/**---------------------------------------------------------------------------------------
......@@ -119,10 +119,10 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry );
static RealOpenMM getDihedralAngleBetweenThreeVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry);
};
......
platforms/reference/include/ReferenceBrownianDynamics.h
View file @ 7fb10336
......@@ -50,7 +50,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature );
ReferenceBrownianDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature);
/**---------------------------------------------------------------------------------------
......@@ -58,7 +58,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
~ReferenceBrownianDynamics( );
~ReferenceBrownianDynamics();
/**---------------------------------------------------------------------------------------
......@@ -68,7 +68,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getFriction( void ) const;
RealOpenMM getFriction() const;
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCCMAAlgorithm.h
View file @ 7fb10336
......@@ -69,22 +69,22 @@ public:
*/
ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles);
~ReferenceCCMAAlgorithm( );
~ReferenceCCMAAlgorithm();
/**
* Get the number of constraints.
*/
int getNumberOfConstraints( void ) const;
int getNumberOfConstraints() const;
/**
* Get the maximum number of iterations to perform.
*/
int getMaximumNumberOfIterations( void ) const;
int getMaximumNumberOfIterations() const;
/**
* Set the maximum number of iterations to perform.
*/
void setMaximumNumberOfIterations( int maximumNumberOfIterations );
void setMaximumNumberOfIterations(int maximumNumberOfIterations);
/**
* Apply the constraint algorithm.
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 7fb10336
......@@ -57,7 +57,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomAngleIxn( );
~ReferenceCustomAngleIxn();
/**---------------------------------------------------------------------------------------
......@@ -71,7 +71,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 7fb10336
......@@ -58,7 +58,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomBondIxn( );
~ReferenceCustomBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -72,9 +72,9 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
......
platforms/reference/include/ReferenceCustomExternalIxn.h
View file @ 7fb10336
......@@ -65,7 +65,7 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomExternalIxn( );
~ReferenceCustomExternalIxn();
/**---------------------------------------------------------------------------------------
......@@ -79,8 +79,8 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */
void calculateForce( int atomIndex, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* energy ) const;
void calculateForce(int atomIndex, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* energy) const;
};
......
platforms/reference/include/ReferenceCustomGBIxn.h
View file @ 7fb10336
......@@ -244,7 +244,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomGBIxn( );
~ReferenceCustomGBIxn();
/**---------------------------------------------------------------------------------------
......@@ -255,7 +255,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors );
void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ 7fb10336
......@@ -68,8 +68,8 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
public:
......@@ -89,7 +89,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomNonbondedIxn( );
~ReferenceCustomNonbondedIxn();
/**---------------------------------------------------------------------------------------
......@@ -100,7 +100,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors );
void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors);
/**---------------------------------------------------------------------------------------
......@@ -121,7 +121,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void setUseSwitchingFunction( RealOpenMM distance );
void setUseSwitchingFunction(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......@@ -152,10 +152,10 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 7fb10336
......@@ -57,7 +57,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceCustomTorsionIxn( );
~ReferenceCustomTorsionIxn();
/**---------------------------------------------------------------------------------------
......@@ -71,9 +71,9 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
......
platforms/reference/include/ReferenceDynamics.h
View file @ 7fb10336
......@@ -68,7 +68,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceDynamics( int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature );
ReferenceDynamics(int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature);
/**---------------------------------------------------------------------------------------
......@@ -76,7 +76,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual ~ReferenceDynamics( );
virtual ~ReferenceDynamics();
/**---------------------------------------------------------------------------------------
......@@ -86,7 +86,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms( void ) const;
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
......@@ -96,7 +96,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
int getTimeStep( void ) const;
int getTimeStep() const;
/**---------------------------------------------------------------------------------------
......@@ -106,7 +106,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
int incrementTimeStep( void );
int incrementTimeStep();
/**---------------------------------------------------------------------------------------
......@@ -116,7 +116,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getDeltaT( void ) const;
RealOpenMM getDeltaT() const;
/**---------------------------------------------------------------------------------------
......@@ -124,7 +124,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void setDeltaT( RealOpenMM deltaT );
void setDeltaT(RealOpenMM deltaT);
/**---------------------------------------------------------------------------------------
......@@ -134,7 +134,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getTemperature( void ) const;
RealOpenMM getTemperature() const;
/**---------------------------------------------------------------------------------------
......@@ -160,7 +160,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm( void ) const;
ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm() const;
/**---------------------------------------------------------------------------------------
......@@ -170,7 +170,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint );
void setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint);
};
} // namespace OpenMM
......
platforms/reference/include/ReferenceForce.h
View file @ 7fb10336
......@@ -44,7 +44,7 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */
ReferenceForce( );
ReferenceForce();
/**---------------------------------------------------------------------------------------
......@@ -52,7 +52,7 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */
~ReferenceForce( );
~ReferenceForce();
/**---------------------------------------------------------------------------------------
......@@ -80,8 +80,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */
static void getDeltaR( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
RealOpenMM* deltaR );
static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
......@@ -95,8 +95,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */
static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR );
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
......@@ -110,8 +110,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */
static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR );
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR);
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ 7fb10336
......@@ -41,7 +41,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn( );
ReferenceHarmonicBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -49,7 +49,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceHarmonicBondIxn( );
~ReferenceHarmonicBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -64,9 +64,9 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
......
platforms/reference/include/ReferenceLJCoulomb14.h
View file @ 7fb10336
......@@ -40,7 +40,7 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceLJCoulomb14( );
ReferenceLJCoulomb14();
/**---------------------------------------------------------------------------------------
......@@ -48,7 +48,7 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceLJCoulomb14( );
~ReferenceLJCoulomb14();
/**---------------------------------------------------------------------------------------
......@@ -62,9 +62,9 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
......
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