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Commit 7fb10336 authored by peastman's avatar peastman
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Cleaned up lots of formatting to be more consistent with the rest of OpenMM

parent 1d3ffd7b
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Showing with 180 additions and 180 deletions
platforms/reference/include/ReferenceLJCoulombIxn.h
View file @ 7fb10336
...@@ -67,9 +67,9 @@ class ReferenceLJCoulombIxn { ...@@ -67,9 +67,9 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const; RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const;
public: public:
...@@ -80,7 +80,7 @@ class ReferenceLJCoulombIxn { ...@@ -80,7 +80,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLJCoulombIxn( ); ReferenceLJCoulombIxn();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -88,7 +88,7 @@ class ReferenceLJCoulombIxn { ...@@ -88,7 +88,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceLJCoulombIxn( ); ~ReferenceLJCoulombIxn();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -100,7 +100,7 @@ class ReferenceLJCoulombIxn { ...@@ -100,7 +100,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric ); void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -110,7 +110,7 @@ class ReferenceLJCoulombIxn { ...@@ -110,7 +110,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseSwitchingFunction( RealOpenMM distance ); void setUseSwitchingFunction(RealOpenMM distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceLincsAlgorithm.h
View file @ 7fb10336
...@@ -92,7 +92,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -92,7 +92,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceLincsAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance ); ReferenceLincsAlgorithm(int numberOfConstraints, int** atomIndices, RealOpenMM* distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -102,7 +102,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -102,7 +102,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int getNumberOfConstraints( void ) const; int getNumberOfConstraints() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -112,7 +112,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -112,7 +112,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int getNumTerms( void ) const; int getNumTerms() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -120,7 +120,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -120,7 +120,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setNumTerms( int terms ); void setNumTerms(int terms);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -136,8 +136,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -136,8 +136,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, int apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses ); std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceNeighborList.h
View file @ 7fb10336
...@@ -27,7 +27,7 @@ void OPENMM_EXPORT computeNeighborListNaive( ...@@ -27,7 +27,7 @@ void OPENMM_EXPORT computeNeighborListNaive(
double maxDistance, double maxDistance,
double minDistance = 0.0, double minDistance = 0.0,
bool reportSymmetricPairs = false bool reportSymmetricPairs = false
); );
// O(n) neighbor list method using voxel hash data structure // O(n) neighbor list method using voxel hash data structure
// parameter neighborList is automatically clear()ed before // parameter neighborList is automatically clear()ed before
...@@ -42,7 +42,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash( ...@@ -42,7 +42,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
double maxDistance, double maxDistance,
double minDistance = 0.0, double minDistance = 0.0,
bool reportSymmetricPairs = false bool reportSymmetricPairs = false
); );
} // namespace OpenMM } // namespace OpenMM
......
platforms/reference/include/ReferencePairIxn.h
View file @ 7fb10336
...@@ -42,7 +42,7 @@ class OPENMM_EXPORT ReferencePairIxn { ...@@ -42,7 +42,7 @@ class OPENMM_EXPORT ReferencePairIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferencePairIxn( ); ReferencePairIxn();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -50,7 +50,7 @@ class OPENMM_EXPORT ReferencePairIxn { ...@@ -50,7 +50,7 @@ class OPENMM_EXPORT ReferencePairIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferencePairIxn( ); ~ReferencePairIxn();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -67,10 +67,10 @@ class OPENMM_EXPORT ReferencePairIxn { ...@@ -67,10 +67,10 @@ class OPENMM_EXPORT ReferencePairIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions, RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const = 0; RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const = 0;
}; };
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ 7fb10336
...@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond( ); ReferenceProperDihedralBond();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceProperDihedralBond( ); ~ReferenceProperDihedralBond();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -65,9 +65,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -65,9 +65,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : 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* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const; RealOpenMM* totalEnergy) const;
}; };
......
platforms/reference/include/ReferenceRbDihedralBond.h
View file @ 7fb10336
...@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn { ...@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond( ); ReferenceRbDihedralBond();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn { ...@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceRbDihedralBond( ); ~ReferenceRbDihedralBond();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -63,9 +63,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn { ...@@ -63,9 +63,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : 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* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const; RealOpenMM* totalEnergy) const;
}; };
......
platforms/reference/include/ReferenceStochasticDynamics.h
View file @ 7fb10336
...@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature ); ReferenceStochasticDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -59,7 +59,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -59,7 +59,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceStochasticDynamics( ); ~ReferenceStochasticDynamics();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -69,7 +69,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -69,7 +69,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getTau( void ) const; RealOpenMM getTau() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -100,8 +100,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -100,8 +100,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime ); std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -115,8 +115,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -115,8 +115,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime ); std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
}; };
......
platforms/reference/include/ReferenceVariableStochasticDynamics.h
View file @ 7fb10336
...@@ -50,7 +50,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -50,7 +50,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceVariableStochasticDynamics( int numberOfAtoms, RealOpenMM tau, RealOpenMM temperature, RealOpenMM accuracy ); ReferenceVariableStochasticDynamics(int numberOfAtoms, RealOpenMM tau, RealOpenMM temperature, RealOpenMM accuracy);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -58,7 +58,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -58,7 +58,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceVariableStochasticDynamics( ); ~ReferenceVariableStochasticDynamics();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -68,7 +68,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -68,7 +68,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getTau( void ) const; RealOpenMM getTau() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -78,7 +78,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -78,7 +78,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getAccuracy( void ) const; RealOpenMM getAccuracy() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -86,7 +86,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -86,7 +86,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setAccuracy( RealOpenMM accuracy ); void setAccuracy(RealOpenMM accuracy);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -120,9 +120,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -120,9 +120,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, std::vector<RealOpenMM>& inverseMasses,
std::vector<OpenMM::RealVec>& xPrime, RealOpenMM maxStepSize ); std::vector<OpenMM::RealVec>& xPrime, RealOpenMM maxStepSize);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -136,9 +136,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -136,9 +136,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses,
std::vector<OpenMM::RealVec>& xPrime ); std::vector<OpenMM::RealVec>& xPrime);
}; };
......
platforms/reference/include/ReferenceVariableVerletDynamics.h
View file @ 7fb10336
...@@ -48,7 +48,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics { ...@@ -48,7 +48,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceVariableVerletDynamics( int numberOfAtoms, RealOpenMM accuracy ); ReferenceVariableVerletDynamics(int numberOfAtoms, RealOpenMM accuracy);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -56,7 +56,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics { ...@@ -56,7 +56,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceVariableVerletDynamics( ); ~ReferenceVariableVerletDynamics();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -66,7 +66,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics { ...@@ -66,7 +66,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getAccuracy( void ) const; RealOpenMM getAccuracy() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -74,7 +74,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics { ...@@ -74,7 +74,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setAccuracy( RealOpenMM accuracy ); void setAccuracy(RealOpenMM accuracy);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceVerletDynamics.h
View file @ 7fb10336
...@@ -49,7 +49,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics { ...@@ -49,7 +49,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceVerletDynamics( int numberOfAtoms, RealOpenMM deltaT ); ReferenceVerletDynamics(int numberOfAtoms, RealOpenMM deltaT);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -57,7 +57,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics { ...@@ -57,7 +57,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceVerletDynamics( ); ~ReferenceVerletDynamics();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/SimTKOpenMMUtilities.h
View file @ 7fb10336
...@@ -56,8 +56,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -56,8 +56,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
// dummy constructor/destructor // dummy constructor/destructor
SimTKOpenMMUtilities(){}; SimTKOpenMMUtilities() {};
~SimTKOpenMMUtilities(){}; ~SimTKOpenMMUtilities() {};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -75,9 +75,9 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -75,9 +75,9 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM* allocateOneDRealOpenMMArray( int iSize, RealOpenMM* array1D, int initialize, static RealOpenMM* allocateOneDRealOpenMMArray(int iSize, RealOpenMM* array1D, int initialize,
RealOpenMM initialValue, RealOpenMM initialValue,
const std::string& idString = std::string( "1DArray" ) ); const std::string& idString = std::string("1DArray"));
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -96,10 +96,10 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -96,10 +96,10 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM** allocateTwoDRealOpenMMArray( int iSize, int jSize, static RealOpenMM** allocateTwoDRealOpenMMArray(int iSize, int jSize,
RealOpenMM** array2D, int initialize, RealOpenMM** array2D, int initialize,
RealOpenMM initialValue, RealOpenMM initialValue,
const std::string& idString = std::string( "2DArray" ) ); const std::string& idString = std::string("2DArray"));
/* --------------------------------------------------------------------------------------- /* ---------------------------------------------------------------------------------------
...@@ -112,8 +112,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -112,8 +112,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void freeOneDRealOpenMMArray( RealOpenMM* array1D, static void freeOneDRealOpenMMArray(RealOpenMM* array1D,
const std::string& idString = std::string( "1DArray" ) ); const std::string& idString = std::string("1DArray"));
/* --------------------------------------------------------------------------------------- /* ---------------------------------------------------------------------------------------
...@@ -126,8 +126,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -126,8 +126,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void freeTwoDRealOpenMMArray( RealOpenMM** array2D, static void freeTwoDRealOpenMMArray(RealOpenMM** array2D,
const std::string& idString = std::string( "2DArray" ) ); const std::string& idString = std::string("2DArray"));
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -142,8 +142,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -142,8 +142,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void initialize2DRealOpenMMArray( int iSize, int jSize, static void initialize2DRealOpenMMArray(int iSize, int jSize,
RealOpenMM** array2D, RealOpenMM initialValue ); RealOpenMM** array2D, RealOpenMM initialValue);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -159,7 +159,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -159,7 +159,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void crossProductVector3( RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ ); static void crossProductVector3(RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -169,7 +169,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -169,7 +169,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM getNormallyDistributedRandomNumber( void ); static RealOpenMM getNormallyDistributedRandomNumber();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -179,7 +179,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -179,7 +179,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM getUniformlyDistributedRandomNumber( void ); static RealOpenMM getUniformlyDistributedRandomNumber();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -189,7 +189,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -189,7 +189,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static uint32_t getRandomNumberSeed( void ); static uint32_t getRandomNumberSeed();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -199,7 +199,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities { ...@@ -199,7 +199,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void setRandomNumberSeed( uint32_t seed ); static void setRandomNumberSeed(uint32_t seed);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ 7fb10336
...@@ -100,5 +100,5 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla ...@@ -100,5 +100,5 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceApplyMonteCarloBarostatKernel(name, platform); return new ReferenceApplyMonteCarloBarostatKernel(name, platform);
if (name == RemoveCMMotionKernel::Name()) if (name == RemoveCMMotionKernel::Name())
return new ReferenceRemoveCMMotionKernel(name, platform, data); return new ReferenceRemoveCMMotionKernel(name, platform, data);
throw OpenMMException( (std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str() ); throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
} }
platforms/reference/src/ReferenceKernels.cpp
View file @ 7fb10336
...@@ -1105,8 +1105,8 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS ...@@ -1105,8 +1105,8 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
ObcParameters* obcParameters = new ObcParameters(numParticles, ObcParameters::ObcTypeII); ObcParameters* obcParameters = new ObcParameters(numParticles, ObcParameters::ObcTypeII);
obcParameters->setAtomicRadii(atomicRadii); obcParameters->setAtomicRadii(atomicRadii);
obcParameters->setScaledRadiusFactors(scaleFactors); obcParameters->setScaledRadiusFactors(scaleFactors);
obcParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) ); obcParameters->setSolventDielectric(static_cast<RealOpenMM>(force.getSolventDielectric()));
obcParameters->setSoluteDielectric( static_cast<RealOpenMM>(force.getSoluteDielectric()) ); obcParameters->setSoluteDielectric(static_cast<RealOpenMM>(force.getSoluteDielectric()));
obcParameters->setPi4Asolv(4*M_PI*force.getSurfaceAreaEnergy()); obcParameters->setPi4Asolv(4*M_PI*force.getSurfaceAreaEnergy());
if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff) if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff)
obcParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance())); obcParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
...@@ -1152,7 +1152,7 @@ ReferenceCalcGBVIForceKernel::~ReferenceCalcGBVIForceKernel() { ...@@ -1152,7 +1152,7 @@ ReferenceCalcGBVIForceKernel::~ReferenceCalcGBVIForceKernel() {
} }
} }
void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIForce& force, const std::vector<double> & inputScaledRadii ) { void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIForce& force, const std::vector<double> & inputScaledRadii) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
...@@ -1201,7 +1201,7 @@ double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeF ...@@ -1201,7 +1201,7 @@ double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeF
gbvi->computeBornForces(posData, charges, forceData); gbvi->computeBornForces(posData, charges, forceData);
energy = 0.0; energy = 0.0;
} }
if( includeEnergy ){ if (includeEnergy) {
energy = gbvi->computeBornEnergy(posData, charges); energy = gbvi->computeBornEnergy(posData, charges);
} }
return static_cast<double>(energy); return static_cast<double>(energy);
...@@ -1710,7 +1710,7 @@ void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const Ver ...@@ -1710,7 +1710,7 @@ void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const Ver
if (dynamics) if (dynamics)
delete dynamics; delete dynamics;
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) ); dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize));
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context)); dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevStepSize = stepSize; prevStepSize = stepSize;
} }
...@@ -1748,12 +1748,12 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L ...@@ -1748,12 +1748,12 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
if (dynamics) if (dynamics)
delete dynamics; delete dynamics;
RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction ); RealOpenMM tau = static_cast<RealOpenMM>(friction == 0.0 ? 0.0 : 1.0/friction);
dynamics = new ReferenceStochasticDynamics( dynamics = new ReferenceStochasticDynamics(
context.getSystem().getNumParticles(), context.getSystem().getNumParticles(),
static_cast<RealOpenMM>(stepSize), static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) ); static_cast<RealOpenMM>(temperature));
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context)); dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature; prevTemp = temperature;
prevFriction = friction; prevFriction = friction;
...@@ -1797,7 +1797,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B ...@@ -1797,7 +1797,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
context.getSystem().getNumParticles(), context.getSystem().getNumParticles(),
static_cast<RealOpenMM>(stepSize), static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction), static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) ); static_cast<RealOpenMM>(temperature));
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context)); dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature; prevTemp = temperature;
prevFriction = friction; prevFriction = friction;
...@@ -1837,7 +1837,7 @@ double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& contex ...@@ -1837,7 +1837,7 @@ double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& contex
if (dynamics) if (dynamics)
delete dynamics; delete dynamics;
RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction ); RealOpenMM tau = static_cast<RealOpenMM>(friction == 0.0 ? 0.0 : 1.0/friction);
dynamics = new ReferenceVariableStochasticDynamics(context.getSystem().getNumParticles(), (RealOpenMM) tau, (RealOpenMM) temperature, (RealOpenMM) errorTol); dynamics = new ReferenceVariableStochasticDynamics(context.getSystem().getNumParticles(), (RealOpenMM) tau, (RealOpenMM) temperature, (RealOpenMM) errorTol);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context)); dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature; prevTemp = temperature;
......
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ 7fb10336
...@@ -37,7 +37,7 @@ using namespace OpenMM; ...@@ -37,7 +37,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceAndersenThermostat::ReferenceAndersenThermostat( ) { ReferenceAndersenThermostat::ReferenceAndersenThermostat() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -46,7 +46,7 @@ using namespace OpenMM; ...@@ -46,7 +46,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceAndersenThermostat::~ReferenceAndersenThermostat( ) { ReferenceAndersenThermostat::~ReferenceAndersenThermostat() {
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -61,8 +61,8 @@ using namespace OpenMM; ...@@ -61,8 +61,8 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceAndersenThermostat::applyThermostat( const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses, void ReferenceAndersenThermostat::applyThermostat(const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const { RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const {
const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize); const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize);
for (int i = 0; i < (int) atomGroups.size(); ++i) { for (int i = 0; i < (int) atomGroups.size(); ++i) {
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn::ReferenceAngleBondIxn( ){ ReferenceAngleBondIxn::ReferenceAngleBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceAngleBondIxn::ReferenceAngleBondIxn( ){ ...@@ -55,7 +55,7 @@ ReferenceAngleBondIxn::ReferenceAngleBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn::~ReferenceAngleBondIxn( ){ ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -77,8 +77,8 @@ ReferenceAngleBondIxn::~ReferenceAngleBondIxn( ){ ...@@ -77,8 +77,8 @@ ReferenceAngleBondIxn::~ReferenceAngleBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters, void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm ) const { RealOpenMM* dEdR, RealOpenMM* energyTerm) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -91,9 +91,9 @@ void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Re ...@@ -91,9 +91,9 @@ void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Re
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
RealOpenMM angle; RealOpenMM angle;
if( cosine >= one ){ if (cosine >= one) {
angle = zero; angle = zero;
} else if( cosine <= -one ){ } else if (cosine <= -one) {
angle = PI_M; angle = PI_M;
} else { } else {
angle = ACOS(cosine); angle = ACOS(cosine);
...@@ -119,11 +119,11 @@ void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Re ...@@ -119,11 +119,11 @@ void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Re
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
// constants -- reduce Visual Studio warnings regarding conversions between float & double // constants -- reduce Visual Studio warnings regarding conversions between float & double
...@@ -146,31 +146,31 @@ void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, ...@@ -146,31 +146,31 @@ void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
int atomAIndex = atomIndices[0]; int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2]; int atomCIndex = atomIndices[2];
ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0] ); ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR( atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1] ); ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
RealOpenMM pVector[threeI]; RealOpenMM pVector[threeI];
SimTKOpenMMUtilities::crossProductVector3( deltaR[0], deltaR[1], pVector ); SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
RealOpenMM rp = DOT3( pVector, pVector ); RealOpenMM rp = DOT3(pVector, pVector);
rp = SQRT( rp ); rp = SQRT(rp);
if( rp < 1.0e-06 ){ if (rp < 1.0e-06) {
rp = (RealOpenMM) 1.0e-06; rp = (RealOpenMM) 1.0e-06;
} }
RealOpenMM dot = DOT3( deltaR[0], deltaR[1] ); RealOpenMM dot = DOT3(deltaR[0], deltaR[1]);
RealOpenMM cosine = dot/SQRT( (deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]) ); RealOpenMM cosine = dot/SQRT((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
RealOpenMM dEdR; RealOpenMM dEdR;
RealOpenMM energy; RealOpenMM energy;
getPrefactorsGivenAngleCosine( cosine, parameters, &dEdR, &energy ); getPrefactorsGivenAngleCosine(cosine, parameters, &dEdR, &energy);
RealOpenMM termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp); RealOpenMM termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp); RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
RealOpenMM deltaCrossP[LastAtomIndex][threeI]; RealOpenMM deltaCrossP[LastAtomIndex][threeI];
SimTKOpenMMUtilities::crossProductVector3( deltaR[0], pVector, deltaCrossP[0] ); SimTKOpenMMUtilities::crossProductVector3(deltaR[0], pVector, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3( deltaR[1], pVector, deltaCrossP[2] ); SimTKOpenMMUtilities::crossProductVector3(deltaR[1], pVector, deltaCrossP[2]);
for( int ii = 0; ii < threeI; ii++ ){ for (int ii = 0; ii < threeI; ii++) {
deltaCrossP[0][ii] *= termA; deltaCrossP[0][ii] *= termA;
deltaCrossP[2][ii] *= termC; deltaCrossP[2][ii] *= termC;
deltaCrossP[1][ii] = oneM*(deltaCrossP[0][ii] + deltaCrossP[2][ii]); deltaCrossP[1][ii] = oneM*(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
...@@ -178,8 +178,8 @@ void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, ...@@ -178,8 +178,8 @@ void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
// accumulate forces // accumulate forces
for( int jj = 0; jj < LastAtomIndex; jj++ ){ for (int jj = 0; jj < LastAtomIndex; jj++) {
for( int ii = 0; ii < threeI; ii++ ){ for (int ii = 0; ii < threeI; ii++) {
forces[atomIndices[jj]][ii] += deltaCrossP[jj][ii]; forces[atomIndices[jj]][ii] += deltaCrossP[jj][ii];
} }
} }
......
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ 7fb10336
...@@ -38,7 +38,7 @@ using namespace OpenMM; ...@@ -38,7 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBondForce::ReferenceBondForce( ){ ReferenceBondForce::ReferenceBondForce() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -54,7 +54,7 @@ ReferenceBondForce::ReferenceBondForce( ){ ...@@ -54,7 +54,7 @@ ReferenceBondForce::ReferenceBondForce( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBondForce::~ReferenceBondForce( ){ ReferenceBondForce::~ReferenceBondForce() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -79,12 +79,12 @@ ReferenceBondForce::~ReferenceBondForce( ){ ...@@ -79,12 +79,12 @@ ReferenceBondForce::~ReferenceBondForce( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices, void ReferenceBondForce::calculateForce(int numberOfBonds, int** atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM** parameters, RealOpenMM** parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM *totalEnergy, RealOpenMM *totalEnergy,
ReferenceBondIxn& referenceBondIxn ){ ReferenceBondIxn& referenceBondIxn) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -93,12 +93,12 @@ void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices, ...@@ -93,12 +93,12 @@ void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
for( int ii = 0; ii < numberOfBonds; ii++ ){ for (int ii = 0; ii < numberOfBonds; ii++) {
// calculate bond ixn // calculate bond ixn
referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii], referenceBondIxn.calculateBondIxn(atomIndices[ii], atomCoordinates, parameters[ii],
forces, totalEnergy ); forces, totalEnergy);
} }
} }
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ 7fb10336
...@@ -39,7 +39,7 @@ using namespace OpenMM; ...@@ -39,7 +39,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBondIxn::ReferenceBondIxn( ){ ReferenceBondIxn::ReferenceBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -55,7 +55,7 @@ ReferenceBondIxn::ReferenceBondIxn( ){ ...@@ -55,7 +55,7 @@ ReferenceBondIxn::ReferenceBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBondIxn::~ReferenceBondIxn( ){ ReferenceBondIxn::~ReferenceBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -77,9 +77,9 @@ ReferenceBondIxn::~ReferenceBondIxn( ){ ...@@ -77,9 +77,9 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceBondIxn::calculateBondIxn( int* atomIndices, vector<RealVec>& atomCoordinates, void ReferenceBondIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn"; // static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn";
...@@ -103,8 +103,8 @@ ReferenceBondIxn::~ReferenceBondIxn( ){ ...@@ -103,8 +103,8 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, RealOpenMM ReferenceBondIxn::getNormedDotProduct(RealOpenMM* vector1, RealOpenMM* vector2,
int hasREntry = 0 ) { int hasREntry = 0) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -123,35 +123,35 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM ...@@ -123,35 +123,35 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM
#if defined USE_DOUBLE_FOR_NORMED_DOT_PRODUCT #if defined USE_DOUBLE_FOR_NORMED_DOT_PRODUCT
double v1D[3]; double v1D[3];
double v2D[3]; double v2D[3];
v1D[0] = static_cast<double>( vector1[0] ); v1D[0] = static_cast<double>(vector1[0]);
v1D[1] = static_cast<double>( vector1[1] ); v1D[1] = static_cast<double>(vector1[1]);
v1D[2] = static_cast<double>( vector1[2] ); v1D[2] = static_cast<double>(vector1[2]);
v2D[0] = static_cast<double>( vector2[0] ); v2D[0] = static_cast<double>(vector2[0]);
v2D[1] = static_cast<double>( vector2[1] ); v2D[1] = static_cast<double>(vector2[1]);
v2D[2] = static_cast<double>( vector2[2] ); v2D[2] = static_cast<double>(vector2[2]);
double dotProductD = DOT3( v1D, v2D ); double dotProductD = DOT3(v1D, v2D);
if( dotProductD != 0.0 ){ if (dotProductD != 0.0) {
if( hasREntry ){ if (hasREntry) {
dotProductD /= ( static_cast<double>(vector1[ReferenceForce::RIndex])*static_cast<double>(vector2[ReferenceForce::RIndex]) ); dotProductD /= (static_cast<double>(vector1[ReferenceForce::RIndex])*static_cast<double>(vector2[ReferenceForce::RIndex]));
} else { } else {
double norm1 = DOT3( v1D, v1D ); double norm1 = DOT3(v1D, v1D);
double norm2 = DOT3( v2D, v2D); double norm2 = DOT3(v2D, v2D);
dotProductD /= sqrt( norm1*norm2 ); dotProductD /= sqrt(norm1*norm2);
} }
} }
RealOpenMM dotProduct = static_cast<RealOpenMM>(dotProductD); RealOpenMM dotProduct = static_cast<RealOpenMM>(dotProductD);
#else #else
RealOpenMM dotProduct = DOT3( vector1, vector2 ); RealOpenMM dotProduct = DOT3(vector1, vector2);
if( dotProduct != zero ){ if (dotProduct != zero) {
if( hasREntry ){ if (hasREntry) {
dotProduct /= ( vector1[ReferenceForce::RIndex]*vector2[ReferenceForce::RIndex] ); dotProduct /= (vector1[ReferenceForce::RIndex]*vector2[ReferenceForce::RIndex]);
} else { } else {
RealOpenMM norm1 = DOT3( vector1, vector1 ); RealOpenMM norm1 = DOT3(vector1, vector1);
RealOpenMM norm2 = DOT3( vector2, vector2 ); RealOpenMM norm2 = DOT3(vector2, vector2);
dotProduct /= SQRT( norm1*norm2 ); dotProduct /= SQRT(norm1*norm2);
} }
} }
...@@ -160,9 +160,9 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM ...@@ -160,9 +160,9 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM
// clamp dot product to [-1,1] // clamp dot product to [-1,1]
if( dotProduct > one ){ if (dotProduct > one) {
dotProduct = one; dotProduct = one;
} else if( dotProduct < -one ){ } else if (dotProduct < -one) {
dotProduct = -one; dotProduct = -one;
} }
...@@ -184,9 +184,9 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM ...@@ -184,9 +184,9 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2, RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct = NULL, RealOpenMM* outputDotProduct = NULL,
int hasREntry = 0 ) { int hasREntry = 0) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -199,7 +199,7 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea ...@@ -199,7 +199,7 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea
// get dot product betweenn vectors and then angle // get dot product betweenn vectors and then angle
RealOpenMM dotProduct = getNormedDotProduct( vector1, vector2, hasREntry ); RealOpenMM dotProduct = getNormedDotProduct(vector1, vector2, hasREntry);
RealOpenMM angle; RealOpenMM angle;
if (dotProduct > (RealOpenMM) 0.99 || dotProduct < (RealOpenMM) -0.99) { if (dotProduct > (RealOpenMM) 0.99 || dotProduct < (RealOpenMM) -0.99) {
...@@ -215,7 +215,7 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea ...@@ -215,7 +215,7 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea
angle = ACOS(dotProduct); angle = ACOS(dotProduct);
} }
if( outputDotProduct ){ if (outputDotProduct) {
*outputDotProduct = dotProduct; *outputDotProduct = dotProduct;
} }
...@@ -241,14 +241,14 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea ...@@ -241,14 +241,14 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(RealOpenMM* vector1,
RealOpenMM* vector2, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM* vector3,
RealOpenMM** outputCrossProduct = NULL, RealOpenMM** outputCrossProduct = NULL,
RealOpenMM* cosineOfAngle = NULL, RealOpenMM* cosineOfAngle = NULL,
RealOpenMM* signVector = NULL, RealOpenMM* signVector = NULL,
RealOpenMM* signOfAngle = NULL, RealOpenMM* signOfAngle = NULL,
int hasREntry = 0 ) { int hasREntry = 0) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -264,7 +264,7 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* v ...@@ -264,7 +264,7 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* v
// get cross products between vectors and then angle between cross product vectors // get cross products between vectors and then angle between cross product vectors
RealOpenMM* crossProduct[2]; RealOpenMM* crossProduct[2];
if( outputCrossProduct ){ if (outputCrossProduct) {
crossProduct[0] = outputCrossProduct[0]; crossProduct[0] = outputCrossProduct[0];
crossProduct[1] = outputCrossProduct[1]; crossProduct[1] = outputCrossProduct[1];
} else { } else {
...@@ -272,17 +272,17 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* v ...@@ -272,17 +272,17 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* v
crossProduct[1] = tempVectors + 3; crossProduct[1] = tempVectors + 3;
} }
SimTKOpenMMUtilities::crossProductVector3( vector1, vector2, crossProduct[0] ); SimTKOpenMMUtilities::crossProductVector3(vector1, vector2, crossProduct[0]);
SimTKOpenMMUtilities::crossProductVector3( vector2, vector3, crossProduct[1] ); SimTKOpenMMUtilities::crossProductVector3(vector2, vector3, crossProduct[1]);
RealOpenMM angle = getAngleBetweenTwoVectors( crossProduct[0], crossProduct[1], cosineOfAngle, 0 ); RealOpenMM angle = getAngleBetweenTwoVectors(crossProduct[0], crossProduct[1], cosineOfAngle, 0);
// take care of sign of angle // take care of sign of angle
if( signVector ){ if (signVector) {
RealOpenMM dotProduct = DOT3( signVector, crossProduct[1] ); RealOpenMM dotProduct = DOT3(signVector, crossProduct[1]);
RealOpenMM sign = dotProduct < zero ? -one : one; RealOpenMM sign = dotProduct < zero ? -one : one;
if( signOfAngle ){ if (signOfAngle) {
*signOfAngle = sign; *signOfAngle = sign;
} }
angle *= sign; angle *= sign;
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 7fb10336
...@@ -47,10 +47,10 @@ using namespace OpenMM; ...@@ -47,10 +47,10 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms, ReferenceBrownianDynamics::ReferenceBrownianDynamics(int numberOfAtoms,
RealOpenMM deltaT, RealOpenMM friction, RealOpenMM deltaT, RealOpenMM friction,
RealOpenMM temperature ) : RealOpenMM temperature) :
ReferenceDynamics( numberOfAtoms, deltaT, temperature ), friction( friction ) { ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
if (friction <= 0) { if (friction <= 0) {
std::stringstream message; std::stringstream message;
...@@ -67,7 +67,7 @@ ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms, ...@@ -67,7 +67,7 @@ ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms,
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics::~ReferenceBrownianDynamics( ){ ReferenceBrownianDynamics::~ReferenceBrownianDynamics() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -85,7 +85,7 @@ ReferenceBrownianDynamics::~ReferenceBrownianDynamics( ){ ...@@ -85,7 +85,7 @@ ReferenceBrownianDynamics::~ReferenceBrownianDynamics( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const { RealOpenMM ReferenceBrownianDynamics::getFriction() const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -125,10 +125,10 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real ...@@ -125,10 +125,10 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
// first-time-through initialization // first-time-through initialization
int numberOfAtoms = system.getNumParticles(); int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){ if (getTimeStep() == 0) {
// invert masses // invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){ for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == zero) if (masses[ii] == zero)
inverseMasses[ii] = zero; inverseMasses[ii] = zero;
else else
...@@ -138,7 +138,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real ...@@ -138,7 +138,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
// Perform the integration. // Perform the integration.
const RealOpenMM noiseAmplitude = static_cast<RealOpenMM>( sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction()) ); const RealOpenMM noiseAmplitude = static_cast<RealOpenMM>(sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction()));
const RealOpenMM forceScale = getDeltaT()/getFriction(); const RealOpenMM forceScale = getDeltaT()/getFriction();
for (int i = 0; i < numberOfAtoms; ++i) { for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero) if (masses[i] != zero)
...@@ -152,7 +152,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real ...@@ -152,7 +152,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
// Update the positions and velocities. // Update the positions and velocities.
RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/getDeltaT() ); RealOpenMM velocityScale = static_cast<RealOpenMM>(1.0/getDeltaT());
for (int i = 0; i < numberOfAtoms; ++i) { for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero) if (masses[i] != zero)
for (int j = 0; j < 3; ++j) { for (int j = 0; j < 3; ++j) {
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 7fb10336
...@@ -61,7 +61,7 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio ...@@ -61,7 +61,7 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn( ){ ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -83,11 +83,11 @@ ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn( ){ ...@@ -83,11 +83,11 @@ ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices, void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn"; static const std::string methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn";
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 7fb10336
...@@ -61,7 +61,7 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& ...@@ -61,7 +61,7 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn::~ReferenceCustomBondIxn( ){ ReferenceCustomBondIxn::~ReferenceCustomBondIxn() {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -83,11 +83,11 @@ ReferenceCustomBondIxn::~ReferenceCustomBondIxn( ){ ...@@ -83,11 +83,11 @@ ReferenceCustomBondIxn::~ReferenceCustomBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices, void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
vector<RealVec>& forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy) const {
static const std::string methodName = "\nReferenceCustomBondIxn::calculateBondIxn"; static const std::string methodName = "\nReferenceCustomBondIxn::calculateBondIxn";
...@@ -109,7 +109,7 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices, ...@@ -109,7 +109,7 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
int atomAIndex = atomIndices[0]; int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1]; int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR ); ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]); ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]); ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);
......
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