Merge remote-tracking branch 'upstream/master'

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h

@@ -71,28 +71,28 @@ public:
      * 
      * @param cubicK        the cubic force constant for the bond
      */
-    void setAmoebaGlobalBondCubic( double cubicK );
+    void setAmoebaGlobalBondCubic(double cubicK);
 
     /**
      * Get the global cubic term
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalBondCubic( void ) const;
+    double getAmoebaGlobalBondCubic() const;
 
     /**
      * Set the global quartic term
      * 
      * @param quarticK       the quartic force constant for the bond
      */
-    void setAmoebaGlobalBondQuartic( double quarticK );
+    void setAmoebaGlobalBondQuartic(double quarticK);
 
     /**
      * Get the global quartic term
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalBondQuartic( void ) const;
+    double getAmoebaGlobalBondQuartic() const;
 
     /**
      * Add a bond term to the force field.
@@ -104,7 +104,7 @@ public:
      * @return the index of the bond that was added
      */
 
-    int addBond(int particle1, int particle2, double length, double quadraticK );
+    int addBond(int particle1, int particle2, double length, double quadraticK);
 
     /**
      * Get the force field parameters for a bond term.
@@ -116,7 +116,7 @@ public:
      * @param quadratic k   the quadratic force constant for the bond
      */
 
-    void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
+    void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK) const;
 
     /**
      * Set the force field parameters for a bond term.
@@ -127,7 +127,7 @@ public:
      * @param length    the equilibrium length of the bond, measured in nm
      * @param k         the quadratic force constant for the bond
      */
-    void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
+    void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK);
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
@@ -167,7 +167,7 @@ public:
         particle1 = particle2    = -1;
         length    = quadraticK   = 0.0;
     }
-    BondInfo(int particle1, int particle2, double length, double  quadraticK ) :
+    BondInfo(int particle1, int particle2, double length, double  quadraticK) :
         particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
     }
 };

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -127,7 +127,7 @@ public:
     /**
      * Get the flag signaling whether the cavity term should be included
      */
-    int getIncludeCavityTerm( ) const;
+    int getIncludeCavityTerm() const;
 
     /**
      * Set the flag signaling whether the cavity term should be included
@@ -152,7 +152,7 @@ public:
     /**
      * Set the surface area factor kJ/(nm*nm) used in SASA contribution
      */
-    void setSurfaceAreaFactor( double surfaceAreaFactor );
+    void setSurfaceAreaFactor(double surfaceAreaFactor);
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h

@@ -70,56 +70,56 @@ public:
      * 
      * @param cubicK        the cubic force constant for the angle
      */
-    void setAmoebaGlobalInPlaneAngleCubic( double cubicK );
+    void setAmoebaGlobalInPlaneAngleCubic(double cubicK);
 
     /**
      * Get the global cubic term
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalInPlaneAngleCubic( void ) const;
+    double getAmoebaGlobalInPlaneAngleCubic() const;
 
     /**
      * Set the global quartic term
      * 
      * @param quarticK the quartic force constant for the angle
      */
-    void setAmoebaGlobalInPlaneAngleQuartic( double quarticK );
+    void setAmoebaGlobalInPlaneAngleQuartic(double quarticK);
 
     /**
      * Get the global quartic term
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalInPlaneAngleQuartic( void ) const;
+    double getAmoebaGlobalInPlaneAngleQuartic() const;
 
     /**
      * Set the global pentic term
      * 
      * @param penticK the pentic force constant for the angle
      */
-    void setAmoebaGlobalInPlaneAnglePentic( double penticK );
+    void setAmoebaGlobalInPlaneAnglePentic(double penticK);
 
     /**
      * Get the global pentic term
      * 
      * @return global penticK term
      */
-    double getAmoebaGlobalInPlaneAnglePentic( void ) const;
+    double getAmoebaGlobalInPlaneAnglePentic() const;
 
     /**
      * Set the global sextic term
      * 
      * @param sexticK       the sextic force constant for the angle
      */
-    void setAmoebaGlobalInPlaneAngleSextic( double sexticK );
+    void setAmoebaGlobalInPlaneAngleSextic(double sexticK);
 
     /**
      * Get the global sextic term
      * 
      * @return global  sextic term
      */
-    double getAmoebaGlobalInPlaneAngleSextic( void ) const;
+    double getAmoebaGlobalInPlaneAngleSextic() const;
 
     /**
      * Add an angle term to the force field.
@@ -133,7 +133,7 @@ public:
      * @return the index of the angle that was added
      */
     int addAngle(int particle1, int particle2, int particle3, int particle4, double length, 
-                 double quadraticK );
+                 double quadraticK);
 
     /**
      * Get the force field parameters for an angle term.
@@ -147,7 +147,7 @@ public:
      * @param quadratic k   the quadratic force constant for the angle measured in kJ/mol/radian^2
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& length,
-                            double& quadraticK ) const;
+                            double& quadraticK) const;
 
     /**
      * Set the force field parameters for an angle term.
@@ -160,7 +160,7 @@ public:
      * @param length        the equilibrium angle, measured in radians
      * @param quadratic k   the quadratic force constant for the angle, measured in kJ/mol/radian^2
      */
-    void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK );
+    void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK);
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
@@ -200,7 +200,7 @@ public:
         particle1 = particle2  = particle3 = particle4 = -1;
         length    = quadraticK = 0.0;
     }
-    AngleInfo(int particle1, int particle2, int particle3, int particle4, double length, double  quadraticK ) :
+    AngleInfo(int particle1, int particle2, int particle3, int particle4, double length, double  quadraticK) :
         particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4),
         length(length), quadraticK(quadraticK) {
     }

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -148,7 +148,7 @@ public:
         lengthAB  = lengthCB   = angle     = k1 = k2 = 0.0;
     }
     StretchBendInfo(int particle1, int particle2, int particle3, 
-                    double lengthAB,  double lengthCB, double angle, double k1, double k2 ) :
+                    double lengthAB,  double lengthCB, double angle, double k1, double k2) :
                     particle1(particle1), particle2(particle2), particle3(particle3), 
                     lengthAB(lengthAB), lengthCB(lengthCB), angle(angle), k1(k1), k2(k2) {
     }

plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h

@@ -350,10 +350,10 @@ public:
 
     virtual void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles) = 0;
 
-    virtual void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
-                                            std::vector< double >& outputElectrostaticPotential ) = 0;
+    virtual void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
+                                           std::vector< double >& outputElectrostaticPotential) = 0;
 
-    virtual void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments ) = 0;
+    virtual void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) = 0;
     /**
      * Copy changed parameters over to a context.
      *

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h

@@ -70,9 +70,9 @@ public:
      * @param minCovalentIndex     minimum covalent index
      * @param maxCovalentIndex     maximum covalent index
      */
-    static void getCovalentRange( const AmoebaMultipoleForce& force, int index,
-                                  const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
-                                  int* minCovalentIndex, int* maxCovalentIndex );
+    static void getCovalentRange(const AmoebaMultipoleForce& force, int index,
+                                 const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
+                                 int* minCovalentIndex, int* maxCovalentIndex);
 
     /**
      * Get the covalent degree for the  CovalentEnd lists
@@ -80,14 +80,14 @@ public:
      * @param force                AmoebaMultipoleForce force reference
      * @param covalentDegree      covalent degrees for the CovalentEnd lists
      */
-    static void getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree );
+    static void getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree);
 
     void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
 
-    void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
-                                    std::vector< double >& outputElectrostaticPotential );
+    void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
+                                   std::vector< double >& outputElectrostaticPotential);
 
-    void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments );
+    void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
     void updateParametersInContext(ContextImpl& context);
  
 
@@ -97,7 +97,7 @@ private:
 
     static int CovalentDegrees[AmoebaMultipoleForce::CovalentEnd];
     static bool initializedCovalentDegrees;
-    static const int* getCovalentDegrees( void );
+    static const int* getCovalentDegrees();
 };
 
 } // namespace OpenMM

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h

@@ -61,7 +61,7 @@ public:
     }
     std::vector<std::string> getKernelNames();
 
-    OPENMM_EXPORT_AMOEBA static void reorderGrid( const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid );
+    OPENMM_EXPORT_AMOEBA static void reorderGrid(const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid);
 
 private:
     const AmoebaTorsionTorsionForce& owner;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaWcaDispersionForceImpl.h

@@ -69,7 +69,7 @@ public:
      * @param particleIndex       the particle index
      * @param maxDispersionEnergy maximum dispersion energy
      */
-    static void getMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy );
+    static void getMaximumDispersionEnergy(const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy);
 
     /** 
      * Get the total maximum dispersion energy
@@ -78,7 +78,7 @@ public:
      *
      * @return total maximum dispersion energy for the system
      */
-    static double getTotalMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force);
+    static double getTotalMaximumDispersionEnergy(const AmoebaWcaDispersionForce& force);
     void updateParametersInContext(ContextImpl& context);
 
 private:

plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp

@@ -46,7 +46,7 @@ int AmoebaAngleForce::addAngle(int particle1, int particle2, int particle3,  dou
 }
 
 void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3,
-                                                  double& length, double&  quadraticK ) const {
+                                                  double& length, double&  quadraticK) const {
     particle1       = angles[index].particle1;
     particle2       = angles[index].particle2;
     particle3       = angles[index].particle3;
@@ -55,7 +55,7 @@ void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& partic
 }
 
 void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, 
-                                                  double length, double quadraticK ) {
+                                                  double length, double quadraticK) {
     angles[index].particle1  = particle1;
     angles[index].particle2  = particle2;
     angles[index].particle3  = particle3;
@@ -63,35 +63,35 @@ void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle
     angles[index].quadraticK = quadraticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleCubic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
     return _globalCubicK;
 }
 
-void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
+void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK) {
     _globalCubicK           = cubicK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleQuartic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
     return _globalQuarticK;
 }
 
-void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
+void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAnglePentic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
     return _globalPenticK;
 }
 
-void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
+void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK) {
     _globalPenticK           = penticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleSextic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const {
     return _globalSexticK;
 }
 
-void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK ) {
+void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK) {
     _globalSexticK         = sexticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp

@@ -41,37 +41,37 @@ AmoebaBondForce::AmoebaBondForce() {
 }
 
 int AmoebaBondForce::addBond(int particle1, int particle2, double length, double quadraticK) {
-    bonds.push_back(BondInfo(particle1, particle2, length, quadraticK ));
+    bonds.push_back(BondInfo(particle1, particle2, length, quadraticK));
     return bonds.size()-1;
 }
 
-void AmoebaBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double&  quadraticK ) const {
+void AmoebaBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double&  quadraticK) const {
     particle1       = bonds[index].particle1;
     particle2       = bonds[index].particle2;
     length          = bonds[index].length;
     quadraticK      = bonds[index].quadraticK;
 }
 
-void AmoebaBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK ) {
+void AmoebaBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK) {
     bonds[index].particle1  = particle1;
     bonds[index].particle2  = particle2;
     bonds[index].length     = length;
     bonds[index].quadraticK = quadraticK;
 }
 
-void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK ) {
+void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK) {
     _globalCubicK           = cubicK;
 }
 
-void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) {
+void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaBondForce::getAmoebaGlobalBondCubic( void ) const {
+double AmoebaBondForce::getAmoebaGlobalBondCubic() const {
     return _globalCubicK;
 }
 
-double AmoebaBondForce::getAmoebaGlobalBondQuartic( void ) const {
+double AmoebaBondForce::getAmoebaGlobalBondQuartic() const {
     return _globalQuarticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp

@@ -62,7 +62,7 @@ double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
     return dielectricOffset;
 }
 
-void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset ) {
+void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset) {
     dielectricOffset = inputDielectricOffset;
 } */
 
@@ -70,7 +70,7 @@ int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const {
     return includeCavityTerm;
 }
 
-void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm ) {
+void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm) {
     includeCavityTerm = inputIncludeCavityTerm;
 }
 
@@ -78,7 +78,7 @@ double AmoebaGeneralizedKirkwoodForce::getProbeRadius() const {
     return probeRadius;
 }
 
-void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius ) {
+void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius) {
     probeRadius = inputProbeRadius;
 }
 
@@ -86,7 +86,7 @@ double AmoebaGeneralizedKirkwoodForce::getSurfaceAreaFactor() const {
     return surfaceAreaFactor;
 }
 
-void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor ) {
+void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor) {
     surfaceAreaFactor = inputSurfaceAreaFactor;
 }
 

plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp

@@ -40,13 +40,13 @@ AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
     _globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
 }
 
-int AmoebaInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4,  double length, double quadraticK ) {
-    angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK ));
+int AmoebaInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4,  double length, double quadraticK) {
+    angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK));
     return angles.size()-1;
 }
 
 void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
-                                                  double& length, double&  quadraticK ) const {
+                                                  double& length, double&  quadraticK) const {
     particle1       = angles[index].particle1;
     particle2       = angles[index].particle2;
     particle3       = angles[index].particle3;
@@ -56,7 +56,7 @@ void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int&
 }
 
 void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4,
-                                                    double length, double quadraticK ) {
+                                                    double length, double quadraticK) {
     angles[index].particle1  = particle1;
     angles[index].particle2  = particle2;
     angles[index].particle3  = particle3;
@@ -65,35 +65,35 @@ void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int p
     angles[index].quadraticK = quadraticK;
 }
 
-void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK ) {
+void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK) {
     _globalCubicK           = cubicK;
 }
 
-void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK ) {
+void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic() const {
     return _globalCubicK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic() const {
     return _globalQuarticK;
 }
 
-void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK ) {
+void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK) {
     _globalPenticK           = cubicK;
 }
 
-void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK ) {
+void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK) {
     _globalSexticK         = quarticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic() const {
     return _globalPenticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic() const {
     return _globalSexticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -45,19 +45,19 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
     pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
 }
 
-AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
+AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
     return nonbondedMethod;
 }
 
-void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMethod method) {
+void AmoebaMultipoleForce::setNonbondedMethod(AmoebaMultipoleForce::NonbondedMethod method) {
     nonbondedMethod = method;
 }
 
-AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
+AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType() const {
     return polarizationType;
 }
 
-void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::PolarizationType type ) {
+void AmoebaMultipoleForce::setPolarizationType(AmoebaMultipoleForce::PolarizationType type) {
     polarizationType = type;
 }
 
@@ -73,19 +73,19 @@ double AmoebaMultipoleForce::getAEwald() const {
     return aewald; 
 } 
  
-void AmoebaMultipoleForce::setAEwald(double inputAewald ) { 
+void AmoebaMultipoleForce::setAEwald(double inputAewald) { 
     aewald = inputAewald; 
 } 
  
-int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const { 
+int AmoebaMultipoleForce::getPmeBSplineOrder() const { 
     return pmeBSplineOrder; 
 } 
  
-void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension ) const { 
-    if( gridDimension.size() < 3 ){
+void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const { 
+    if (gridDimension.size() < 3) {
         gridDimension.resize(3);
     }
-    if( pmeGridDimension.size() > 2 ){
+    if (pmeGridDimension.size() > 2) {
         gridDimension[0] = pmeGridDimension[0];
         gridDimension[1] = pmeGridDimension[1];
         gridDimension[2] = pmeGridDimension[2];
@@ -95,7 +95,7 @@ void AmoebaMultipoleForce::getPmeGridDimensions( std::vector<int>& gridDimension
     return;
 } 
  
-void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDimension ) {
+void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
     pmeGridDimension.resize(3);
     pmeGridDimension[0] = gridDimension[0];
     pmeGridDimension[1] = gridDimension[1];
@@ -103,19 +103,19 @@ void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDim
     return;
 } 
 
-int AmoebaMultipoleForce::getMutualInducedMaxIterations( void ) const {
+int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
     return mutualInducedMaxIterations;
 }
 
-void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInducedMaxIterations ) {
+void AmoebaMultipoleForce::setMutualInducedMaxIterations(int inputMutualInducedMaxIterations) {
     mutualInducedMaxIterations = inputMutualInducedMaxIterations;
 }
 
-double AmoebaMultipoleForce::getMutualInducedTargetEpsilon( void ) const {
+double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const {
     return mutualInducedTargetEpsilon;
 }
 
-void AmoebaMultipoleForce::setMutualInducedTargetEpsilon( double inputMutualInducedTargetEpsilon ) {
+void AmoebaMultipoleForce::setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon) {
     mutualInducedTargetEpsilon = inputMutualInducedTargetEpsilon;
 }
 
@@ -127,22 +127,22 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
     ewaldErrorTol = tol;
 }
 
-int AmoebaMultipoleForce::addMultipole( double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType, 
+int AmoebaMultipoleForce::addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType, 
                                        int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
-    multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole,  axisType, multipoleAtomZ,  multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
+    multipoles.push_back(MultipoleInfo(charge, molecularDipole, molecularQuadrupole,  axisType, multipoleAtomZ,  multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
     return multipoles.size()-1;
 }
 
 void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, 
-                                                  int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity ) const {
+                                                  int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const {
     charge                      = multipoles[index].charge;
 
-    molecularDipole.resize( 3 );
+    molecularDipole.resize(3);
     molecularDipole[0]          = multipoles[index].molecularDipole[0];
     molecularDipole[1]          = multipoles[index].molecularDipole[1];
     molecularDipole[2]          = multipoles[index].molecularDipole[2];
 
-    molecularQuadrupole.resize( 9 );
+    molecularQuadrupole.resize(9);
     molecularQuadrupole[0]      = multipoles[index].molecularQuadrupole[0];
     molecularQuadrupole[1]      = multipoles[index].molecularQuadrupole[1];
     molecularQuadrupole[2]      = multipoles[index].molecularQuadrupole[2];
@@ -164,7 +164,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
 }
 
 void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, 
-                                                  int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity ) {
+                                                  int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
 
     multipoles[index].charge                      = charge;
 
@@ -192,34 +192,34 @@ void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, cons
 
 }
 
-void AmoebaMultipoleForce::setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms ) {
+void AmoebaMultipoleForce::setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms) {
 
     std::vector<int>& covalentList = multipoles[index].covalentInfo[typeId];
-    covalentList.resize( covalentAtoms.size() );
-    for( unsigned int ii = 0; ii < covalentAtoms.size(); ii++ ){
+    covalentList.resize(covalentAtoms.size());
+    for (unsigned int ii = 0; ii < covalentAtoms.size(); ii++) {
        covalentList[ii] = covalentAtoms[ii];
     }
 }
 
-void AmoebaMultipoleForce::getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms ) const {
+void AmoebaMultipoleForce::getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms) const {
 
     // load covalent atom index entries for atomId==index and covalentId==typeId into covalentAtoms
 
     std::vector<int> covalentList = multipoles[index].covalentInfo[typeId];
-    covalentAtoms.resize( covalentList.size() );
-    for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
+    covalentAtoms.resize(covalentList.size());
+    for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
        covalentAtoms[ii] = covalentList[ii];
     }
 }
 
-void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<int> >& covalentLists ) const {
+void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<int> >& covalentLists) const {
 
-    covalentLists.resize( CovalentEnd );
-    for( unsigned int jj = 0; jj < CovalentEnd; jj++ ){
+    covalentLists.resize(CovalentEnd);
+    for (unsigned int jj = 0; jj < CovalentEnd; jj++) {
         std::vector<int> covalentList = multipoles[index].covalentInfo[jj];
         std::vector<int> covalentAtoms;
-        covalentAtoms.resize( covalentList.size() );
-        for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
+        covalentAtoms.resize(covalentList.size());
+        for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
            covalentAtoms[ii] = covalentList[ii];
         }
         covalentLists[jj] = covalentAtoms;
@@ -230,11 +230,11 @@ void AmoebaMultipoleForce::getInducedDipoles(Context& context, vector<Vec3>& dip
     dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getInducedDipoles(getContextImpl(context), dipoles);
 }
 
-void AmoebaMultipoleForce::getElectrostaticPotential( const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential ){
+void AmoebaMultipoleForce::getElectrostaticPotential(const std::vector< Vec3 >& inputGrid, Context& context, std::vector< double >& outputElectrostaticPotential) {
     dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
 }
 
-void AmoebaMultipoleForce::getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments ){
+void AmoebaMultipoleForce::getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments) {
     dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getSystemMultipoleMoments(getContextImpl(context), outputMultipoleMoments);
 }
 

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -64,26 +64,26 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
     }   
 
     double quadrupoleValidationTolerance = 1.0e-05;
-    for( int ii = 0; ii < system.getNumParticles(); ii++ ){
+    for (int ii = 0; ii < system.getNumParticles(); ii++) {
 
         int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
         double charge, thole, dampingFactor, polarity ;
         std::vector<double> molecularDipole;
         std::vector<double> molecularQuadrupole;
 
-        owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
-                                      thole, dampingFactor, polarity );
+        owner.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
+                                     thole, dampingFactor, polarity);
 
        // check quadrupole is traceless and symmetric
 
-       double trace = fabs( molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8] );
-       if( trace > quadrupoleValidationTolerance ){
+       double trace = fabs(molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8]);
+       if (trace > quadrupoleValidationTolerance) {
              std::stringstream buffer;
              buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii;
              buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole.";
              throw OpenMMException(buffer.str());
        }
-       if( fabs( molecularQuadrupole[1] - molecularQuadrupole[3] ) > quadrupoleValidationTolerance  ){
+       if (fabs(molecularQuadrupole[1] - molecularQuadrupole[3]) > quadrupoleValidationTolerance ) {
              std::stringstream buffer;
              buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii;
              buffer << "  are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];";
@@ -91,7 +91,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
              throw OpenMMException(buffer.str());
        }
 
-       if( fabs( molecularQuadrupole[2] - molecularQuadrupole[6] ) > quadrupoleValidationTolerance  ){
+       if (fabs(molecularQuadrupole[2] - molecularQuadrupole[6]) > quadrupoleValidationTolerance ) {
              std::stringstream buffer;
              buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii;
              buffer << "  are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];";
@@ -99,7 +99,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
              throw OpenMMException(buffer.str());
        }
 
-       if( fabs( molecularQuadrupole[5] - molecularQuadrupole[7] ) > quadrupoleValidationTolerance  ){
+       if (fabs(molecularQuadrupole[5] - molecularQuadrupole[7]) > quadrupoleValidationTolerance ) {
              std::stringstream buffer;
              buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii;
              buffer << "  are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];";
@@ -109,9 +109,9 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
 
        // only 'Z-then-X', 'Bisector', Z-Bisect, ThreeFold  currently handled
 
-        if( axisType != AmoebaMultipoleForce::ZThenX     && axisType != AmoebaMultipoleForce::Bisector &&
+        if (axisType != AmoebaMultipoleForce::ZThenX     && axisType != AmoebaMultipoleForce::Bisector &&
             axisType != AmoebaMultipoleForce::ZBisect    && axisType != AmoebaMultipoleForce::ThreeFold &&
-            axisType != AmoebaMultipoleForce::ZOnly      && axisType != AmoebaMultipoleForce::NoAxisType ) {
+            axisType != AmoebaMultipoleForce::ZOnly      && axisType != AmoebaMultipoleForce::NoAxisType) {
              std::stringstream buffer;
              buffer << "AmoebaMultipoleForce: axis type=" << axisType;
              buffer << " not currently handled - only axisTypes[ ";
@@ -138,8 +138,8 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
     return names;
 }
 
-const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
-    if( !initializedCovalentDegrees ){
+const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
+    if (!initializedCovalentDegrees) {
         initializedCovalentDegrees                                      = true;
         CovalentDegrees[AmoebaMultipoleForce::Covalent12]               = 1;
         CovalentDegrees[AmoebaMultipoleForce::Covalent13]               = 2;
@@ -153,20 +153,20 @@ const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
     return CovalentDegrees;
 }
 
-void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
-                                                 int* minCovalentIndex, int* maxCovalentIndex ){
+void AmoebaMultipoleForceImpl::getCovalentRange(const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
+                                                int* minCovalentIndex, int* maxCovalentIndex) {
 
     *minCovalentIndex =  999999999;
     *maxCovalentIndex = -999999999;
-    for( unsigned int kk = 0; kk < lists.size(); kk++ ){
+    for (unsigned int kk = 0; kk < lists.size(); kk++) {
         AmoebaMultipoleForce::CovalentType jj = lists[kk];
         std::vector<int> covalentList;
-        force.getCovalentMap( atomIndex, jj, covalentList );
-        for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
-            if( *minCovalentIndex > covalentList[ii] ){
+        force.getCovalentMap(atomIndex, jj, covalentList);
+        for (unsigned int ii = 0; ii < covalentList.size(); ii++) {
+            if (*minCovalentIndex > covalentList[ii]) {
                *minCovalentIndex = covalentList[ii];
             }
-            if( *maxCovalentIndex < covalentList[ii] ){
+            if (*maxCovalentIndex < covalentList[ii]) {
                *maxCovalentIndex = covalentList[ii];
             }
         }
@@ -174,10 +174,10 @@ void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& for
     return;
 }
 
-void AmoebaMultipoleForceImpl::getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree ){
-    covalentDegree.resize( AmoebaMultipoleForce::CovalentEnd );
+void AmoebaMultipoleForceImpl::getCovalentDegree(const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree) {
+    covalentDegree.resize(AmoebaMultipoleForce::CovalentEnd);
     const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees();
-    for( unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++ ){
+    for (unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++) {
         covalentDegree[kk] = CovalentDegrees[kk];
     }   
     return;
@@ -187,12 +187,12 @@ void AmoebaMultipoleForceImpl::getInducedDipoles(ContextImpl& context, vector<Ve
     kernel.getAs<CalcAmoebaMultipoleForceKernel>().getInducedDipoles(context, dipoles);
 }
 
-void AmoebaMultipoleForceImpl::getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
-                                                          std::vector< double >& outputElectrostaticPotential ){
+void AmoebaMultipoleForceImpl::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
+                                                         std::vector< double >& outputElectrostaticPotential) {
     kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, outputElectrostaticPotential);
 }
 
-void AmoebaMultipoleForceImpl::getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMoments ){
+void AmoebaMultipoleForceImpl::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) {
     kernel.getAs<CalcAmoebaMultipoleForceKernel>().getSystemMultipoleMoments(context, outputMultipoleMoments);
 }
 

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp

@@ -44,35 +44,35 @@ AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
 
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
     return _globalCubicK;
 }
 
-void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK ) {
+void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK) {
     _globalCubicK           = cubicK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
     return _globalQuarticK;
 }
 
-void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK ) {
+void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
     return _globalPenticK;
 }
 
-void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK ) {
+void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penticK) {
     _globalPenticK           = penticK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const {
     return _globalSexticK;
 }
 
-void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK ) {
+void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendSextic(double sexticK) {
     _globalSexticK         = sexticK;
 }
 
@@ -82,7 +82,7 @@ int AmoebaOutOfPlaneBendForce::addOutOfPlaneBend(int particle1, int particle2, i
 }
 
 void AmoebaOutOfPlaneBendForce::getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
-                                                            double& k ) const {
+                                                            double& k) const {
     particle1       = outOfPlaneBends[index].particle1;
     particle2       = outOfPlaneBends[index].particle2;
     particle3       = outOfPlaneBends[index].particle3;

plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp

@@ -44,7 +44,7 @@ int AmoebaPiTorsionForce::addPiTorsion(int particle1, int particle2, int particl
     return piTorsions.size()-1;
 }
 
-void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k ) const {
+void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k) const {
     particle1       = piTorsions[index].particle1;
     particle2       = piTorsions[index].particle2;
     particle3       = piTorsions[index].particle3;
@@ -54,7 +54,7 @@ void AmoebaPiTorsionForce::getPiTorsionParameters(int index, int& particle1, int
     k               = piTorsions[index].k;
 }
 
-void AmoebaPiTorsionForce::setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6,  double k ) {
+void AmoebaPiTorsionForce::setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6,  double k) {
     piTorsions[index].particle1  = particle1;
     piTorsions[index].particle2  = particle2;
     piTorsions[index].particle3  = particle3;

plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp

@@ -46,7 +46,7 @@ int AmoebaStretchBendForce::addStretchBend(int particle1, int particle2, int par
 }
 
 void AmoebaStretchBendForce::getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3,
-                                                      double& lengthAB, double& lengthCB, double& angle, double& k1, double& k2 ) const {
+                                                      double& lengthAB, double& lengthCB, double& angle, double& k1, double& k2) const {
     particle1       = stretchBends[index].particle1;
     particle2       = stretchBends[index].particle2;
     particle3       = stretchBends[index].particle3;

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp

@@ -70,13 +70,13 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionParameters(int index, int parti
     torsionTorsions[index].gridIndex              = gridIndex;
 }
 
-const TorsionTorsionGrid& AmoebaTorsionTorsionForce::getTorsionTorsionGrid(int index ) const {
+const TorsionTorsionGrid& AmoebaTorsionTorsionForce::getTorsionTorsionGrid(int index) const {
    return torsionTorsionGrids[index].getTorsionTorsionGrid();
 }
 
-void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTorsionGrid& grid ) {
-   if( index >= static_cast<int>(torsionTorsionGrids.size()) ){
-      torsionTorsionGrids.resize( index + 1);
+void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTorsionGrid& grid) {
+   if (index >= static_cast<int>(torsionTorsionGrids.size())) {
+      torsionTorsionGrids.resize(index + 1);
    }
    torsionTorsionGrids[index] = grid;
 }

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForceImpl.cpp

@@ -70,12 +70,11 @@ typedef std::map< double, Map_Double_IntPair > Map_Double_MapDoubleIntPair;
 typedef Map_Double_MapDoubleIntPair::iterator Map_Double_MapDoubleIntPairI;
 typedef Map_Double_MapDoubleIntPair::const_iterator Map_Double_MapDoubleIntPairCI;
 
-void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid ){
+void AmoebaTorsionTorsionForceImpl::reorderGrid(const TorsionTorsionGrid& grid, TorsionTorsionGrid& reorderedGrid) {
 
-    reorderedGrid.resize( grid.size() );
-    std::vector<Map_Double_IntPair> map_Double_IntPair_Vector( grid.size() );
+    reorderedGrid.resize(grid.size());
+    std::vector<Map_Double_IntPair> map_Double_IntPair_Vector(grid.size());
     Map_Double_MapDoubleIntPair mapAngles;
-    //(void) fprintf( stderr, "AmoebaTorsionTorsionForceImpl::reorder grid\n" );
 
     // (1) set dimensions for reorderd grid
     // (2) build map:
@@ -84,27 +83,27 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
 
     for (unsigned int ii = 0; ii < grid.size(); ii++) {
     
-        reorderedGrid[ii].resize( grid[ii].size() );
+        reorderedGrid[ii].resize(grid[ii].size());
         for (unsigned int jj = 0; jj < grid[ii].size(); jj++) {
-            reorderedGrid[ii][jj].resize( grid[ii][jj].size() );
+            reorderedGrid[ii][jj].resize(grid[ii][jj].size());
 
             double angleX =  grid[ii][jj][0]; 
             double angleY =  grid[ii][jj][1]; 
 
-            if( mapAngles.find( angleX ) == mapAngles.end() ){
-                if( map_Double_IntPair_Vector[ii].size() > 0 ){
+            if (mapAngles.find(angleX) == mapAngles.end()) {
+                if (map_Double_IntPair_Vector[ii].size() > 0) {
                     char buffer[1024];
-                    (void) sprintf( buffer, "TorsionTorsion grid reorder: x-angle not set correctly: x=%15.7e y=%15.7e size=%u should be zero; ii/jj indies=%u %u.\n",
-                                    angleX, angleY, static_cast<unsigned int>(map_Double_IntPair_Vector[ii].size()), ii, jj );
+                    (void) sprintf(buffer, "TorsionTorsion grid reorder: x-angle not set correctly: x=%15.7e y=%15.7e size=%u should be zero; ii/jj indies=%u %u.\n",
+                                    angleX, angleY, static_cast<unsigned int>(map_Double_IntPair_Vector[ii].size()), ii, jj);
                     throw OpenMMException(buffer);
                  }
                  mapAngles[angleX] = map_Double_IntPair_Vector[ii];
             }
 
             Map_Double_IntPair& map_Double_IntPair  = mapAngles[angleX];
-            if( map_Double_IntPair.find( angleY ) != map_Double_IntPair.end() ){
+            if (map_Double_IntPair.find(angleY) != map_Double_IntPair.end()) {
                 char buffer[1024];
-                (void) sprintf( buffer, "TorsionTorsion grid reorder: angle pair found twice: %15.7e %15.7e %u\n", angleX, angleY, static_cast<unsigned int>(map_Double_IntPair.size()) );
+                (void) sprintf(buffer, "TorsionTorsion grid reorder: angle pair found twice: %15.7e %15.7e %u\n", angleX, angleY, static_cast<unsigned int>(map_Double_IntPair.size()));
                 throw OpenMMException(buffer);
             }
             struct IntPair pair; 
@@ -114,24 +113,6 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
         }
     }
 
-#if 0
-     (void) fprintf( stderr, "TorsionTorsion grid reorder map\n" );
-     for( Map_Double_MapDoubleIntPairCI ii = mapAngles.begin(); ii != mapAngles.end(); ii++ ){
-         double angleX                          = ii->first;
-         Map_Double_IntPair map_Double_IntPair  = ii->second;
-         (void) fprintf( stderr, "   %15.7e %u \n", angleX, static_cast<unsigned int>(map_Double_IntPair.size()) );
-      }
-      for( Map_Double_MapDoubleIntPairCI ii = mapAngles.begin(); ii != mapAngles.end(); ii++ ){
-          double angleX                          = ii->first;
-          Map_Double_IntPair map_Double_IntPair  = ii->second;
-          for( Map_Double_IntPairCI jj = map_Double_IntPair.begin(); jj != map_Double_IntPair.end(); jj++ ){
-              double angle         = jj->first;
-              struct IntPair pair  = jj->second;
-              (void) fprintf( stderr, "   %15.7e %15.7e %d %d\n", angleX, angle, pair.index1, pair.index2 );
-          }
-            }
-#endif
-
     // load reordered entries
 
     Map_Double_MapDoubleIntPairCI mapII    = mapAngles.begin();
@@ -144,7 +125,6 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
             struct IntPair pair  = mapJJ->second;
             int index1           = pair.index1;
             int index2           = pair.index2;
-            //(void) fprintf( stderr, "   %3d %3d %15.7e %15.7e %3d %3d zzz\n", ii, jj, mapII->first, mapJJ->first, index1, index2 );
 
             for (unsigned int kk = 0; kk < grid[ii][jj].size(); kk++) {
                 reorderedGrid[ii][jj][kk] = static_cast<float>(grid[index1][index2][kk]);
@@ -153,12 +133,12 @@ void AmoebaTorsionTorsionForceImpl::reorderGrid( const TorsionTorsionGrid& grid,
             // increment map iterators
 
             mapJJ++;
-            if( mapJJ == map_Double_IntPair.end() ){
+            if (mapJJ == map_Double_IntPair.end()) {
                 mapII++;
-                if( mapII == mapAngles.end() ){
-                    if( (jj != (grid[ii].size()-1)) && (ii != (grid.size()-1)) ){
+                if (mapII == mapAngles.end()) {
+                    if ((jj != (grid[ii].size()-1)) && (ii != (grid.size()-1))) {
                         char buffer[1024];
-                        (void) sprintf( buffer, "AmoebaTorsionTorsionForceImpl::reorderGrid: error detected with map iterators.\n" );
+                        (void) sprintf(buffer, "AmoebaTorsionTorsionForceImpl::reorderGrid: error detected with map iterators.\n");
                         throw OpenMMException(buffer);
                     }
                 } else {

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -41,13 +41,13 @@ using std::vector;
 AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), cutoff(1.0e+10), useDispersionCorrection(true) {
 }
 
-int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor ) {
+int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor) {
     parameters.push_back(VdwInfo(parentIndex, sigma, epsilon, reductionFactor));
     return parameters.size()-1;
 }
 
 void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
-                                           double& sigma, double& epsilon, double& reductionFactor ) const {
+                                           double& sigma, double& epsilon, double& reductionFactor) const {
     parentIndex     = parameters[particleIndex].parentIndex;
     sigma           = parameters[particleIndex].sigma;
     epsilon         = parameters[particleIndex].epsilon;
@@ -55,54 +55,54 @@ void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
 }
 
 void AmoebaVdwForce::setParticleParameters(int particleIndex, int parentIndex,
-                                           double sigma, double epsilon, double reductionFactor ) {
+                                           double sigma, double epsilon, double reductionFactor) {
     parameters[particleIndex].parentIndex     = parentIndex;
     parameters[particleIndex].sigma           = sigma;
     parameters[particleIndex].epsilon         = epsilon;
     parameters[particleIndex].reductionFactor = reductionFactor;
 }
 
-void AmoebaVdwForce::setSigmaCombiningRule( const std::string& inputSigmaCombiningRule ) {
+void AmoebaVdwForce::setSigmaCombiningRule(const std::string& inputSigmaCombiningRule) {
     sigmaCombiningRule = inputSigmaCombiningRule;
 }
 
-const std::string& AmoebaVdwForce::getSigmaCombiningRule( void ) const {
+const std::string& AmoebaVdwForce::getSigmaCombiningRule() const {
     return sigmaCombiningRule;
 }
 
-void AmoebaVdwForce::setEpsilonCombiningRule( const std::string& inputEpsilonCombiningRule ) {
+void AmoebaVdwForce::setEpsilonCombiningRule(const std::string& inputEpsilonCombiningRule) {
     epsilonCombiningRule = inputEpsilonCombiningRule;
 }
 
-const std::string& AmoebaVdwForce::getEpsilonCombiningRule( void ) const {
+const std::string& AmoebaVdwForce::getEpsilonCombiningRule() const {
     return epsilonCombiningRule;
 }
 
-void AmoebaVdwForce::setParticleExclusions( int particleIndex, const std::vector< int >& inputExclusions ) {
+void AmoebaVdwForce::setParticleExclusions(int particleIndex, const std::vector< int >& inputExclusions) {
 
-   if( exclusions.size() < parameters.size() ){
-       exclusions.resize( parameters.size() );
+   if (exclusions.size() < parameters.size()) {
+       exclusions.resize(parameters.size());
    }
-   if(  static_cast<int>(exclusions.size()) < particleIndex ){
-       exclusions.resize( particleIndex + 10 );
+   if (static_cast<int>(exclusions.size()) < particleIndex) {
+       exclusions.resize(particleIndex + 10);
    }
-   for( unsigned int ii = 0; ii < inputExclusions.size(); ii++ ){
-       exclusions[particleIndex].push_back( inputExclusions[ii] );
+   for (unsigned int ii = 0; ii < inputExclusions.size(); ii++) {
+       exclusions[particleIndex].push_back(inputExclusions[ii]);
    }
 }
 
-void AmoebaVdwForce::getParticleExclusions( int particleIndex, std::vector< int >& outputExclusions ) const {
+void AmoebaVdwForce::getParticleExclusions(int particleIndex, std::vector< int >& outputExclusions) const {
 
-   if( particleIndex < static_cast<int>(exclusions.size()) ){
-       outputExclusions.resize( exclusions[particleIndex].size() );
-       for( unsigned int ii = 0; ii < exclusions[particleIndex].size(); ii++ ){
+   if (particleIndex < static_cast<int>(exclusions.size())) {
+       outputExclusions.resize(exclusions[particleIndex].size());
+       for (unsigned int ii = 0; ii < exclusions[particleIndex].size(); ii++) {
            outputExclusions[ii] = exclusions[particleIndex][ii];
        }
    }
 
 }
 
-void AmoebaVdwForce::setCutoff( double inputCutoff ){
+void AmoebaVdwForce::setCutoff(double inputCutoff) {
     cutoff = inputCutoff;
 }