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Commit a783b996 authored by peastman's avatar peastman
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Eliminated RealOpenMM type

parent 9500f3af
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Showing with 236 additions and 237 deletions
platforms/reference/include/ReferenceCustomExternalIxn.h
View file @ a783b996
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __ReferenceCustomExternalIxn_H__ #define __ReferenceCustomExternalIxn_H__
#include "ReferenceCustomExternalIxn.h" #include "ReferenceCustomExternalIxn.h"
#include "openmm/Vec3.h"
#include "lepton/CompiledExpression.h" #include "lepton/CompiledExpression.h"
namespace OpenMM { namespace OpenMM {
...@@ -79,8 +80,8 @@ class ReferenceCustomExternalIxn { ...@@ -79,8 +80,8 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateForce(int atomIndex, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateForce(int atomIndex, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* energy) const; double* parameters, std::vector<OpenMM::Vec3>& forces, double* energy) const;
}; };
......
platforms/reference/include/ReferenceCustomGBIxn.h
View file @ a783b996
...@@ -41,8 +41,8 @@ class ReferenceCustomGBIxn { ...@@ -41,8 +41,8 @@ class ReferenceCustomGBIxn {
bool cutoff; bool cutoff;
bool periodic; bool periodic;
const OpenMM::NeighborList* neighborList; const OpenMM::NeighborList* neighborList;
OpenMM::RealVec periodicBoxVectors[3]; OpenMM::Vec3 periodicBoxVectors[3];
RealOpenMM cutoffDistance; double cutoffDistance;
CompiledExpressionSet expressionSet; CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions; std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions; std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
...@@ -59,8 +59,8 @@ class ReferenceCustomGBIxn { ...@@ -59,8 +59,8 @@ class ReferenceCustomGBIxn {
std::vector<int> particleParamIndex; std::vector<int> particleParamIndex;
std::vector<int> particleValueIndex; std::vector<int> particleValueIndex;
int rIndex, xIndex, yIndex, zIndex; int rIndex, xIndex, yIndex, zIndex;
std::vector<std::vector<RealOpenMM> > values, dEdV; std::vector<std::vector<double> > values, dEdV;
std::vector<std::vector<std::vector<RealOpenMM> > > dValuedParam; std::vector<std::vector<std::vector<double> > > dValuedParam;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -73,7 +73,7 @@ class ReferenceCustomGBIxn { ...@@ -73,7 +73,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateSingleParticleValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters); void calculateSingleParticleValue(int index, int numAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -88,7 +88,7 @@ class ReferenceCustomGBIxn { ...@@ -88,7 +88,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateParticlePairValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateParticlePairValue(int index, int numAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions); const std::vector<std::set<int> >& exclusions, bool useExclusions);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -103,7 +103,7 @@ class ReferenceCustomGBIxn { ...@@ -103,7 +103,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters); void calculateOnePairValue(int index, int atom1, int atom2, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -118,8 +118,8 @@ class ReferenceCustomGBIxn { ...@@ -118,8 +118,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs); double** atomParameters, std::vector<OpenMM::Vec3>& forces, double* totalEnergy, double* energyParamDerivs);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -136,9 +136,9 @@ class ReferenceCustomGBIxn { ...@@ -136,9 +136,9 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions, const std::vector<std::set<int> >& exclusions, bool useExclusions,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs); std::vector<OpenMM::Vec3>& forces, double* totalEnergy, double* energyParamDerivs);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -154,8 +154,8 @@ class ReferenceCustomGBIxn { ...@@ -154,8 +154,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs); std::vector<OpenMM::Vec3>& forces, double* totalEnergy, double* energyParamDerivs);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -169,8 +169,8 @@ class ReferenceCustomGBIxn { ...@@ -169,8 +169,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateChainRuleForces(int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateChainRuleForces(int numAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
const std::vector<std::set<int> >& exclusions, std::vector<OpenMM::RealVec>& forces, double* energyParamDerivs); const std::vector<std::set<int> >& exclusions, std::vector<OpenMM::Vec3>& forces, double* energyParamDerivs);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -185,8 +185,8 @@ class ReferenceCustomGBIxn { ...@@ -185,8 +185,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOnePairChainRule(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateOnePairChainRule(int atom1, int atom2, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters,
std::vector<OpenMM::RealVec>& forces, bool isExcluded); std::vector<OpenMM::Vec3>& forces, bool isExcluded);
public: public:
...@@ -226,7 +226,7 @@ class ReferenceCustomGBIxn { ...@@ -226,7 +226,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors); void setUseCutoff(double distance, const OpenMM::NeighborList& neighbors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -238,7 +238,7 @@ class ReferenceCustomGBIxn { ...@@ -238,7 +238,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -254,8 +254,8 @@ class ReferenceCustomGBIxn { ...@@ -254,8 +254,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions, void calculateIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, double** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs); std::map<std::string, double>& globalParameters, std::vector<OpenMM::Vec3>& forces, double* totalEnergy, double* energyParamDerivs);
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomHbondIxn.h
View file @ a783b996
...@@ -43,8 +43,8 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn { ...@@ -43,8 +43,8 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
class DihedralTermInfo; class DihedralTermInfo;
bool cutoff; bool cutoff;
bool periodic; bool periodic;
OpenMM::RealVec periodicBoxVectors[3]; OpenMM::Vec3 periodicBoxVectors[3];
RealOpenMM cutoffDistance; double cutoffDistance;
std::vector<std::vector<int> > donorAtoms, acceptorAtoms; std::vector<std::vector<int> > donorAtoms, acceptorAtoms;
Lepton::ExpressionProgram energyExpression; Lepton::ExpressionProgram energyExpression;
std::vector<std::string> donorParamNames, acceptorParamNames; std::vector<std::string> donorParamNames, acceptorParamNames;
...@@ -65,13 +65,13 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn { ...@@ -65,13 +65,13 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn(int donor, int acceptor, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateOneIxn(int donor, int acceptor, std::vector<OpenMM::Vec3>& atomCoordinates,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces, std::map<std::string, double>& variables, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy) const; double* totalEnergy) const;
void computeDelta(int atom1, int atom2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& atomCoordinates) const; void computeDelta(int atom1, int atom2, double* delta, std::vector<OpenMM::Vec3>& atomCoordinates) const;
static RealOpenMM computeAngle(RealOpenMM* vec1, RealOpenMM* vec2); static double computeAngle(double* vec1, double* vec2);
public: public:
...@@ -103,7 +103,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn { ...@@ -103,7 +103,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance); void setUseCutoff(double distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -115,7 +115,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn { ...@@ -115,7 +115,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -152,9 +152,9 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn { ...@@ -152,9 +152,9 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** donorParameters, RealOpenMM** acceptorParameters, void calculatePairIxn(std::vector<OpenMM::Vec3>& atomCoordinates, double** donorParameters, double** acceptorParameters,
std::vector<std::set<int> >& exclusions, const std::map<std::string, double>& globalParameters, std::vector<std::set<int> >& exclusions, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const; std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -165,7 +165,7 @@ public: ...@@ -165,7 +165,7 @@ public:
std::string name; std::string name;
int p1, p2; int p1, p2;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex]; mutable double delta[ReferenceForce::LastDeltaRIndex];
DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) {
} }
...@@ -176,8 +176,8 @@ public: ...@@ -176,8 +176,8 @@ public:
std::string name; std::string name;
int p1, p2, p3; int p1, p2, p3;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable double delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex]; mutable double delta2[ReferenceForce::LastDeltaRIndex];
AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) {
} }
...@@ -188,11 +188,11 @@ public: ...@@ -188,11 +188,11 @@ public:
std::string name; std::string name;
int p1, p2, p3, p4; int p1, p2, p3, p4;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable double delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex]; mutable double delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex]; mutable double delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3]; mutable double cross1[3];
mutable RealOpenMM cross2[3]; mutable double cross2[3];
DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) {
} }
......
platforms/reference/include/ReferenceCustomManyParticleIxn.h
View file @ a783b996
...@@ -45,8 +45,8 @@ class ReferenceCustomManyParticleIxn { ...@@ -45,8 +45,8 @@ class ReferenceCustomManyParticleIxn {
class DihedralTermInfo; class DihedralTermInfo;
int numParticlesPerSet, numPerParticleParameters, numTypes; int numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, centralParticleMode; bool useCutoff, usePeriodic, centralParticleMode;
RealOpenMM cutoffDistance; double cutoffDistance;
OpenMM::RealVec periodicBoxVectors[3]; OpenMM::Vec3 periodicBoxVectors[3];
Lepton::ExpressionProgram energyExpression; Lepton::ExpressionProgram energyExpression;
std::vector<std::vector<std::string> > particleParamNames; std::vector<std::vector<std::string> > particleParamNames;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
...@@ -58,9 +58,9 @@ class ReferenceCustomManyParticleIxn { ...@@ -58,9 +58,9 @@ class ReferenceCustomManyParticleIxn {
std::vector<AngleTermInfo> angleTerms; std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms; std::vector<DihedralTermInfo> dihedralTerms;
void loopOverInteractions(std::vector<int>& particles, int loopIndex, std::vector<OpenMM::RealVec>& atomCoordinates, void loopOverInteractions(std::vector<int>& particles, int loopIndex, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** particleParameters, std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces, double** particleParameters, std::map<std::string, double>& variables, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy) const; double* totalEnergy) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -75,13 +75,13 @@ class ReferenceCustomManyParticleIxn { ...@@ -75,13 +75,13 @@ class ReferenceCustomManyParticleIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn(const std::vector<int>& particles, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateOneIxn(const std::vector<int>& particles, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** particleParameters, std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces, double** particleParameters, std::map<std::string, double>& variables, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy) const; double* totalEnergy) const;
void computeDelta(int atom1, int atom2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& atomCoordinates) const; void computeDelta(int atom1, int atom2, double* delta, std::vector<OpenMM::Vec3>& atomCoordinates) const;
static RealOpenMM computeAngle(RealOpenMM* vec1, RealOpenMM* vec2); static double computeAngle(double* vec1, double* vec2);
public: public:
...@@ -110,7 +110,7 @@ class ReferenceCustomManyParticleIxn { ...@@ -110,7 +110,7 @@ class ReferenceCustomManyParticleIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance); void setUseCutoff(double distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -122,7 +122,7 @@ class ReferenceCustomManyParticleIxn { ...@@ -122,7 +122,7 @@ class ReferenceCustomManyParticleIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -136,12 +136,9 @@ class ReferenceCustomManyParticleIxn { ...@@ -136,12 +136,9 @@ class ReferenceCustomManyParticleIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** particleParameters, void calculateIxn(std::vector<OpenMM::Vec3>& atomCoordinates, double** particleParameters,
const std::map<std::string, double>& globalParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const; std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;
// ---------------------------------------------------------------------------------------
}; };
class ReferenceCustomManyParticleIxn::ParticleTermInfo { class ReferenceCustomManyParticleIxn::ParticleTermInfo {
...@@ -159,7 +156,7 @@ public: ...@@ -159,7 +156,7 @@ public:
std::string name; std::string name;
int p1, p2; int p1, p2;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex]; mutable double delta[ReferenceForce::LastDeltaRIndex];
DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) {
} }
...@@ -170,8 +167,8 @@ public: ...@@ -170,8 +167,8 @@ public:
std::string name; std::string name;
int p1, p2, p3; int p1, p2, p3;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable double delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex]; mutable double delta2[ReferenceForce::LastDeltaRIndex];
AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) {
} }
...@@ -182,11 +179,11 @@ public: ...@@ -182,11 +179,11 @@ public:
std::string name; std::string name;
int p1, p2, p3, p4; int p1, p2, p3, p4;
Lepton::ExpressionProgram forceExpression; Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable double delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex]; mutable double delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex]; mutable double delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3]; mutable double cross1[3];
mutable RealOpenMM cross2[3]; mutable double cross2[3];
DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) : DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) { name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) {
} }
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ a783b996
...@@ -43,8 +43,8 @@ class ReferenceCustomNonbondedIxn { ...@@ -43,8 +43,8 @@ class ReferenceCustomNonbondedIxn {
bool useSwitch; bool useSwitch;
bool periodic; bool periodic;
const OpenMM::NeighborList* neighborList; const OpenMM::NeighborList* neighborList;
OpenMM::RealVec periodicBoxVectors[3]; OpenMM::Vec3 periodicBoxVectors[3];
RealOpenMM cutoffDistance, switchingDistance; double cutoffDistance, switchingDistance;
Lepton::CompiledExpression energyExpression; Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression; Lepton::CompiledExpression forceExpression;
std::vector<std::string> paramNames; std::vector<std::string> paramNames;
...@@ -68,8 +68,8 @@ class ReferenceCustomNonbondedIxn { ...@@ -68,8 +68,8 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces, void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs); double* energyByAtom, double* totalEnergy, double* energyParamDerivs);
public: public:
...@@ -100,7 +100,7 @@ class ReferenceCustomNonbondedIxn { ...@@ -100,7 +100,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors); void setUseCutoff(double distance, const OpenMM::NeighborList& neighbors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -121,7 +121,7 @@ class ReferenceCustomNonbondedIxn { ...@@ -121,7 +121,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseSwitchingFunction(RealOpenMM distance); void setUseSwitchingFunction(double distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -133,7 +133,7 @@ class ReferenceCustomNonbondedIxn { ...@@ -133,7 +133,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -152,10 +152,10 @@ class ReferenceCustomNonbondedIxn { ...@@ -152,10 +152,10 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions, double** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters, double* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, std::vector<OpenMM::Vec3>& forces, double* energyByAtom, double* totalEnergy,
double* energyParamDerivs); double* energyParamDerivs);
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ a783b996
...@@ -40,7 +40,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn { ...@@ -40,7 +40,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
int thetaIndex; int thetaIndex;
int numParameters; int numParameters;
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; Vec3 boxVectors[3];
public: public:
...@@ -70,7 +70,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn { ...@@ -70,7 +70,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -84,9 +84,9 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn { ...@@ -84,9 +84,9 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, double* parameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs); double* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceDynamics.h
View file @ a783b996
...@@ -49,8 +49,8 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -49,8 +49,8 @@ class OPENMM_EXPORT ReferenceDynamics {
int _numberOfAtoms; int _numberOfAtoms;
int _timeStep; int _timeStep;
RealOpenMM _deltaT; double _deltaT;
RealOpenMM _temperature; double _temperature;
int _ownReferenceConstraint; int _ownReferenceConstraint;
ReferenceConstraintAlgorithm* _referenceConstraint; ReferenceConstraintAlgorithm* _referenceConstraint;
...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceDynamics(int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature); ReferenceDynamics(int numberOfAtoms, double _deltaT, double temperature);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -115,7 +115,7 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -115,7 +115,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getDeltaT() const; double getDeltaT() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -123,7 +123,7 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -123,7 +123,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setDeltaT(RealOpenMM deltaT); void setDeltaT(double deltaT);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -133,7 +133,7 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -133,7 +133,7 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getTemperature() const; double getTemperature() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -148,8 +148,8 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -148,8 +148,8 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates, virtual void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM tolerance); std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceForce.h
View file @ a783b996
...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
#ifndef __ReferenceForce_H__ #ifndef __ReferenceForce_H__
#define __ReferenceForce_H__ #define __ReferenceForce_H__
#include "RealVec.h" #include "openmm/Vec3.h"
#include "lepton/CompiledExpression.h" #include "lepton/CompiledExpression.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
...@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceForce {
private: private:
static RealOpenMM periodicDifference(RealOpenMM val1, RealOpenMM val2, RealOpenMM period); static double periodicDifference(double val1, double val2, double period);
public: public:
...@@ -80,8 +80,8 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -80,8 +80,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ, static void getDeltaR(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
RealOpenMM* deltaR); double* deltaR);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealVec getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ); static Vec3 getDeltaR(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -108,8 +108,8 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -108,8 +108,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ, static void getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR); const double* boxSize, double* deltaR);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -123,8 +123,8 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -123,8 +123,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ, static void getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR); const OpenMM::Vec3* boxVectors, double* deltaR);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -138,8 +138,8 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -138,8 +138,8 @@ class OPENMM_EXPORT ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealVec getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ, static Vec3 getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors); const OpenMM::Vec3* boxVectors);
/** /**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression * Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
......
platforms/reference/include/ReferenceGayBerneForce.h
View file @ a783b996
...@@ -33,7 +33,7 @@ ...@@ -33,7 +33,7 @@
#define __ReferenceGayBerneForce_H__ #define __ReferenceGayBerneForce_H__
#include "openmm/GayBerneForce.h" #include "openmm/GayBerneForce.h"
#include "RealVec.h" #include "openmm/Vec3.h"
#include <set> #include <set>
#include <utility> #include <utility>
...@@ -55,7 +55,7 @@ public: ...@@ -55,7 +55,7 @@ public:
* @param boxVectors the periodic box vectors * @param boxVectors the periodic box vectors
* @return the energy of the interaction * @return the energy of the interaction
*/ */
RealOpenMM calculateForce(const std::vector<RealVec>& positions, std::vector<RealVec>& forces, const RealVec* boxVectors); double calculateForce(const std::vector<Vec3>& positions, std::vector<Vec3>& forces, const Vec3* boxVectors);
private: private:
struct ParticleInfo; struct ParticleInfo;
...@@ -64,33 +64,33 @@ private: ...@@ -64,33 +64,33 @@ private:
std::vector<ExceptionInfo> exceptions; std::vector<ExceptionInfo> exceptions;
std::set<std::pair<int, int> > exclusions; std::set<std::pair<int, int> > exclusions;
GayBerneForce::NonbondedMethod nonbondedMethod; GayBerneForce::NonbondedMethod nonbondedMethod;
RealOpenMM cutoffDistance, switchingDistance; double cutoffDistance, switchingDistance;
bool useSwitchingFunction; bool useSwitchingFunction;
std::vector<RealOpenMM> s; std::vector<double> s;
std::vector<Matrix> A, B, G; std::vector<Matrix> A, B, G;
void computeEllipsoidFrames(const std::vector<RealVec>& positions); void computeEllipsoidFrames(const std::vector<Vec3>& positions);
void applyTorques(const std::vector<RealVec>& positions, std::vector<RealVec>& forces, const std::vector<RealVec>& torques); void applyTorques(const std::vector<Vec3>& positions, std::vector<Vec3>& forces, const std::vector<Vec3>& torques);
RealOpenMM computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const std::vector<RealVec>& positions, double computeOneInteraction(int particle1, int particle2, double sigma, double epsilon, const std::vector<Vec3>& positions,
std::vector<RealVec>& forces, std::vector<RealVec>& torques, const RealVec* boxVectors); std::vector<Vec3>& forces, std::vector<Vec3>& torques, const Vec3* boxVectors);
}; };
struct ReferenceGayBerneForce::ParticleInfo { struct ReferenceGayBerneForce::ParticleInfo {
int xparticle, yparticle; int xparticle, yparticle;
RealOpenMM sigma, epsilon, rx, ry, rz, ex, ey, ez; double sigma, epsilon, rx, ry, rz, ex, ey, ez;
}; };
struct ReferenceGayBerneForce::ExceptionInfo { struct ReferenceGayBerneForce::ExceptionInfo {
int particle1, particle2; int particle1, particle2;
RealOpenMM sigma, epsilon; double sigma, epsilon;
}; };
struct ReferenceGayBerneForce::Matrix { struct ReferenceGayBerneForce::Matrix {
RealOpenMM v[3][3]; double v[3][3];
RealVec operator*(const RealVec& r) { Vec3 operator*(const Vec3& r) {
return RealVec(v[0][0]*r[0] + v[0][1]*r[1] + v[0][2]*r[2], return Vec3(v[0][0]*r[0] + v[0][1]*r[1] + v[0][2]*r[2],
v[1][0]*r[0] + v[1][1]*r[1] + v[1][2]*r[2], v[1][0]*r[0] + v[1][1]*r[1] + v[1][2]*r[2],
v[2][0]*r[0] + v[2][1]*r[1] + v[2][2]*r[2]); v[2][0]*r[0] + v[2][1]*r[1] + v[2][2]*r[2]);
} }
...@@ -103,13 +103,13 @@ struct ReferenceGayBerneForce::Matrix { ...@@ -103,13 +103,13 @@ struct ReferenceGayBerneForce::Matrix {
return result; return result;
} }
RealOpenMM determinant() { double determinant() {
return (v[0][0]*v[1][1]*v[2][2] + v[0][1]*v[1][2]*v[2][0] + v[0][2]*v[1][0]*v[2][1] - return (v[0][0]*v[1][1]*v[2][2] + v[0][1]*v[1][2]*v[2][0] + v[0][2]*v[1][0]*v[2][1] -
v[0][0]*v[1][2]*v[2][1] - v[0][1]*v[1][0]*v[2][2] - v[0][2]*v[1][1]*v[2][0]); v[0][0]*v[1][2]*v[2][1] - v[0][1]*v[1][0]*v[2][2] - v[0][2]*v[1][1]*v[2][0]);
} }
Matrix inverse() { Matrix inverse() {
RealOpenMM invDet = 1/determinant(); double invDet = 1/determinant();
Matrix result; Matrix result;
result.v[0][0] = invDet*(v[1][1]*v[2][2] - v[1][2]*v[2][1]); result.v[0][0] = invDet*(v[1][1]*v[2][2] - v[1][2]*v[2][1]);
result.v[1][0] = -invDet*(v[1][0]*v[2][2] - v[1][2]*v[2][0]); result.v[1][0] = -invDet*(v[1][0]*v[2][2] - v[1][2]*v[2][0]);
...@@ -124,10 +124,10 @@ struct ReferenceGayBerneForce::Matrix { ...@@ -124,10 +124,10 @@ struct ReferenceGayBerneForce::Matrix {
} }
}; };
static RealVec operator*(const RealVec& r, ReferenceGayBerneForce::Matrix& m) { static Vec3 operator*(const Vec3& r, ReferenceGayBerneForce::Matrix& m) {
return RealVec(m.v[0][0]*r[0] + m.v[1][0]*r[1] + m.v[2][0]*r[2], return Vec3(m.v[0][0]*r[0] + m.v[1][0]*r[1] + m.v[2][0]*r[2],
m.v[0][1]*r[0] + m.v[1][1]*r[1] + m.v[2][1]*r[2], m.v[0][1]*r[0] + m.v[1][1]*r[1] + m.v[2][1]*r[2],
m.v[0][2]*r[0] + m.v[1][2]*r[1] + m.v[2][2]*r[2]); m.v[0][2]*r[0] + m.v[1][2]*r[1] + m.v[2][2]*r[2]);
} }
} // namespace OpenMM } // namespace OpenMM
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ a783b996
...@@ -34,7 +34,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn { ...@@ -34,7 +34,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
private: private:
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; Vec3 boxVectors[3];
public: public:
...@@ -62,7 +62,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn { ...@@ -62,7 +62,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -77,9 +77,9 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn { ...@@ -77,9 +77,9 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, double* parameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs); double* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceKernels.h
View file @ a783b996
...@@ -98,7 +98,7 @@ public: ...@@ -98,7 +98,7 @@ public:
*/ */
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid); double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
private: private:
std::vector<RealVec> savedForces; std::vector<Vec3> savedForces;
}; };
/** /**
...@@ -226,8 +226,8 @@ public: ...@@ -226,8 +226,8 @@ public:
void applyToVelocities(ContextImpl& context, double tol); void applyToVelocities(ContextImpl& context, double tol);
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
std::vector<RealOpenMM> masses; std::vector<double> masses;
std::vector<RealOpenMM> inverseMasses; std::vector<double> inverseMasses;
}; };
/** /**
...@@ -285,7 +285,7 @@ public: ...@@ -285,7 +285,7 @@ public:
private: private:
int numBonds; int numBonds;
int **bondIndexArray; int **bondIndexArray;
RealOpenMM **bondParamArray; double **bondParamArray;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -323,7 +323,7 @@ public: ...@@ -323,7 +323,7 @@ public:
private: private:
int numBonds; int numBonds;
int **bondIndexArray; int **bondIndexArray;
RealOpenMM **bondParamArray; double **bondParamArray;
Lepton::CompiledExpression energyExpression, forceExpression; Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions; std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames; std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
...@@ -364,7 +364,7 @@ public: ...@@ -364,7 +364,7 @@ public:
private: private:
int numAngles; int numAngles;
int **angleIndexArray; int **angleIndexArray;
RealOpenMM **angleParamArray; double **angleParamArray;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -402,7 +402,7 @@ public: ...@@ -402,7 +402,7 @@ public:
private: private:
int numAngles; int numAngles;
int **angleIndexArray; int **angleIndexArray;
RealOpenMM **angleParamArray; double **angleParamArray;
Lepton::CompiledExpression energyExpression, forceExpression; Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions; std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames; std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
...@@ -443,7 +443,7 @@ public: ...@@ -443,7 +443,7 @@ public:
private: private:
int numTorsions; int numTorsions;
int **torsionIndexArray; int **torsionIndexArray;
RealOpenMM **torsionParamArray; double **torsionParamArray;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -481,7 +481,7 @@ public: ...@@ -481,7 +481,7 @@ public:
private: private:
int numTorsions; int numTorsions;
int **torsionIndexArray; int **torsionIndexArray;
RealOpenMM **torsionParamArray; double **torsionParamArray;
bool usePeriodic; bool usePeriodic;
}; };
...@@ -516,7 +516,7 @@ public: ...@@ -516,7 +516,7 @@ public:
*/ */
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force); void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private: private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff; std::vector<std::vector<std::vector<double> > > coeff;
std::vector<int> torsionMaps; std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices; std::vector<std::vector<int> > torsionIndices;
bool usePeriodic; bool usePeriodic;
...@@ -556,7 +556,7 @@ public: ...@@ -556,7 +556,7 @@ public:
private: private:
int numTorsions; int numTorsions;
int **torsionIndexArray; int **torsionIndexArray;
RealOpenMM **torsionParamArray; double **torsionParamArray;
Lepton::CompiledExpression energyExpression, forceExpression; Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions; std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames; std::vector<std::string> parameterNames, globalParameterNames, energyParamDerivNames;
...@@ -607,8 +607,8 @@ public: ...@@ -607,8 +607,8 @@ public:
private: private:
int numParticles, num14; int numParticles, num14;
int **bonded14IndexArray; int **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray; double **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient; double nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
int kmax[3], gridSize[3]; int kmax[3], gridSize[3];
bool useSwitchingFunction; bool useSwitchingFunction;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
...@@ -649,8 +649,8 @@ public: ...@@ -649,8 +649,8 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force); void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private: private:
int numParticles; int numParticles;
RealOpenMM **particleParamArray; double **particleParamArray;
RealOpenMM nonbondedCutoff, switchingDistance, periodicBoxSize[3], longRangeCoefficient; double nonbondedCutoff, switchingDistance, periodicBoxSize[3], longRangeCoefficient;
bool useSwitchingFunction, hasInitializedLongRangeCorrection; bool useSwitchingFunction, hasInitializedLongRangeCorrection;
CustomNonbondedForce* forceCopy; CustomNonbondedForce* forceCopy;
std::map<std::string, double> globalParamValues; std::map<std::string, double> globalParamValues;
...@@ -697,7 +697,7 @@ public: ...@@ -697,7 +697,7 @@ public:
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force); void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private: private:
ReferenceObc* obc; ReferenceObc* obc;
std::vector<RealOpenMM> charges; std::vector<double> charges;
bool isPeriodic; bool isPeriodic;
}; };
...@@ -735,8 +735,8 @@ public: ...@@ -735,8 +735,8 @@ public:
private: private:
int numParticles; int numParticles;
bool isPeriodic; bool isPeriodic;
RealOpenMM **particleParamArray; double **particleParamArray;
RealOpenMM nonbondedCutoff; double nonbondedCutoff;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
std::vector<std::string> particleParameterNames, globalParameterNames, energyParamDerivNames, valueNames; std::vector<std::string> particleParameterNames, globalParameterNames, energyParamDerivNames, valueNames;
std::vector<Lepton::CompiledExpression> valueExpressions; std::vector<Lepton::CompiledExpression> valueExpressions;
...@@ -788,16 +788,16 @@ private: ...@@ -788,16 +788,16 @@ private:
class PeriodicDistanceFunction; class PeriodicDistanceFunction;
int numParticles; int numParticles;
std::vector<int> particles; std::vector<int> particles;
RealOpenMM **particleParamArray; double **particleParamArray;
Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ; Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
std::vector<std::string> parameterNames, globalParameterNames; std::vector<std::string> parameterNames, globalParameterNames;
RealVec* boxVectors; Vec3* boxVectors;
}; };
class ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction : public Lepton::CustomFunction { class ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction : public Lepton::CustomFunction {
public: public:
RealVec** boxVectorHandle; Vec3** boxVectorHandle;
PeriodicDistanceFunction(RealVec** boxVectorHandle); PeriodicDistanceFunction(Vec3** boxVectorHandle);
int getNumArguments() const; int getNumArguments() const;
double evaluate(const double* arguments) const; double evaluate(const double* arguments) const;
double evaluateDerivative(const double* arguments, const int* derivOrder) const; double evaluateDerivative(const double* arguments, const int* derivOrder) const;
...@@ -838,8 +838,8 @@ public: ...@@ -838,8 +838,8 @@ public:
private: private:
int numDonors, numAcceptors, numParticles; int numDonors, numAcceptors, numParticles;
bool isPeriodic; bool isPeriodic;
RealOpenMM **donorParamArray, **acceptorParamArray; double **donorParamArray, **acceptorParamArray;
RealOpenMM nonbondedCutoff; double nonbondedCutoff;
ReferenceCustomHbondIxn* ixn; ReferenceCustomHbondIxn* ixn;
std::vector<std::set<int> > exclusions; std::vector<std::set<int> > exclusions;
std::vector<std::string> globalParameterNames; std::vector<std::string> globalParameterNames;
...@@ -878,7 +878,7 @@ public: ...@@ -878,7 +878,7 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force); void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
private: private:
int numBonds, numParticles; int numBonds, numParticles;
RealOpenMM **bondParamArray; double **bondParamArray;
ReferenceCustomCentroidBondIxn* ixn; ReferenceCustomCentroidBondIxn* ixn;
std::vector<std::string> globalParameterNames, energyParamDerivNames; std::vector<std::string> globalParameterNames, energyParamDerivNames;
bool usePeriodic; bool usePeriodic;
...@@ -917,7 +917,7 @@ public: ...@@ -917,7 +917,7 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force); void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private: private:
int numBonds; int numBonds;
RealOpenMM **bondParamArray; double **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn; ReferenceCustomCompoundBondIxn* ixn;
std::vector<std::string> globalParameterNames, energyParamDerivNames; std::vector<std::string> globalParameterNames, energyParamDerivNames;
bool usePeriodic; bool usePeriodic;
...@@ -956,8 +956,8 @@ public: ...@@ -956,8 +956,8 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force); void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
private: private:
int numParticles; int numParticles;
RealOpenMM cutoffDistance; double cutoffDistance;
RealOpenMM **particleParamArray; double **particleParamArray;
ReferenceCustomManyParticleIxn* ixn; ReferenceCustomManyParticleIxn* ixn;
std::vector<std::string> globalParameterNames; std::vector<std::string> globalParameterNames;
NonbondedMethod nonbondedMethod; NonbondedMethod nonbondedMethod;
...@@ -1030,7 +1030,7 @@ public: ...@@ -1030,7 +1030,7 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVerletDynamics* dynamics; ReferenceVerletDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevStepSize; double prevStepSize;
}; };
...@@ -1067,7 +1067,7 @@ public: ...@@ -1067,7 +1067,7 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceStochasticDynamics* dynamics; ReferenceStochasticDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevTemp, prevFriction, prevStepSize; double prevTemp, prevFriction, prevStepSize;
}; };
...@@ -1104,7 +1104,7 @@ public: ...@@ -1104,7 +1104,7 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceBrownianDynamics* dynamics; ReferenceBrownianDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevTemp, prevFriction, prevStepSize; double prevTemp, prevFriction, prevStepSize;
}; };
...@@ -1143,7 +1143,7 @@ public: ...@@ -1143,7 +1143,7 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableStochasticDynamics* dynamics; ReferenceVariableStochasticDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevTemp, prevFriction, prevErrorTol; double prevTemp, prevFriction, prevErrorTol;
}; };
...@@ -1182,7 +1182,7 @@ public: ...@@ -1182,7 +1182,7 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableVerletDynamics* dynamics; ReferenceVariableVerletDynamics* dynamics;
std::vector<RealOpenMM> masses; std::vector<double> masses;
double prevErrorTol; double prevErrorTol;
}; };
...@@ -1257,8 +1257,8 @@ public: ...@@ -1257,8 +1257,8 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceCustomDynamics* dynamics; ReferenceCustomDynamics* dynamics;
std::vector<RealOpenMM> masses, globalValues; std::vector<double> masses, globalValues;
std::vector<std::vector<OpenMM::RealVec> > perDofValues; std::vector<std::vector<OpenMM::Vec3> > perDofValues;
}; };
/** /**
...@@ -1285,7 +1285,7 @@ public: ...@@ -1285,7 +1285,7 @@ public:
private: private:
ReferenceAndersenThermostat* thermostat; ReferenceAndersenThermostat* thermostat;
std::vector<std::vector<int> > particleGroups; std::vector<std::vector<int> > particleGroups;
std::vector<RealOpenMM> masses; std::vector<double> masses;
}; };
/** /**
......
platforms/reference/include/ReferenceLJCoulomb14.h
View file @ a783b996
...@@ -62,9 +62,9 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn { ...@@ -62,9 +62,9 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, double* parameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs); double* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceLJCoulombIxn.h
View file @ a783b996
...@@ -40,10 +40,10 @@ class ReferenceLJCoulombIxn { ...@@ -40,10 +40,10 @@ class ReferenceLJCoulombIxn {
bool ewald; bool ewald;
bool pme; bool pme;
const OpenMM::NeighborList* neighborList; const OpenMM::NeighborList* neighborList;
OpenMM::RealVec periodicBoxVectors[3]; OpenMM::Vec3 periodicBoxVectors[3];
RealOpenMM cutoffDistance, switchingDistance; double cutoffDistance, switchingDistance;
RealOpenMM krf, crf; double krf, crf;
RealOpenMM alphaEwald; double alphaEwald;
int numRx, numRy, numRz; int numRx, numRy, numRz;
int meshDim[3]; int meshDim[3];
...@@ -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::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces, double** atomParameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const; double* energyByAtom, double* totalEnergy) const;
public: public:
...@@ -100,7 +100,7 @@ class ReferenceLJCoulombIxn { ...@@ -100,7 +100,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric); void setUseCutoff(double distance, const OpenMM::NeighborList& neighbors, double solventDielectric);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -110,7 +110,7 @@ class ReferenceLJCoulombIxn { ...@@ -110,7 +110,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseSwitchingFunction(RealOpenMM distance); void setUseSwitchingFunction(double distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -122,7 +122,7 @@ class ReferenceLJCoulombIxn { ...@@ -122,7 +122,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -135,7 +135,7 @@ class ReferenceLJCoulombIxn { ...@@ -135,7 +135,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUseEwald(RealOpenMM alpha, int kmaxx, int kmaxy, int kmaxz); void setUseEwald(double alpha, int kmaxx, int kmaxy, int kmaxz);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -147,7 +147,7 @@ class ReferenceLJCoulombIxn { ...@@ -147,7 +147,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setUsePME(RealOpenMM alpha, int meshSize[3]); void setUsePME(double alpha, int meshSize[3]);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -167,10 +167,10 @@ class ReferenceLJCoulombIxn { ...@@ -167,10 +167,10 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions, double** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces, double* fixedParameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const; double* energyByAtom, double* totalEnergy, bool includeDirect, bool includeReciprocal) const;
private: private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -191,10 +191,10 @@ private: ...@@ -191,10 +191,10 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateEwaldIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateEwaldIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions, double** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces, double* fixedParameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const; double* energyByAtom, double* totalEnergy, bool includeDirect, bool includeReciprocal) const;
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/reference/include/ReferenceLincsAlgorithm.h
View file @ a783b996
...@@ -37,16 +37,16 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -37,16 +37,16 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
int _numTerms; int _numTerms;
int _numberOfConstraints; int _numberOfConstraints;
int** _atomIndices; int** _atomIndices;
RealOpenMM* _distance; double* _distance;
bool _hasInitialized; bool _hasInitialized;
std::vector<std::vector<int> > _linkedConstraints; std::vector<std::vector<int> > _linkedConstraints;
std::vector<RealOpenMM> _sMatrix; std::vector<double> _sMatrix;
std::vector<RealOpenMM> _rhs1; std::vector<double> _rhs1;
std::vector<RealOpenMM> _rhs2; std::vector<double> _rhs2;
std::vector<RealOpenMM> _solution; std::vector<double> _solution;
std::vector<std::vector<RealOpenMM> > _couplingMatrix; std::vector<std::vector<double> > _couplingMatrix;
std::vector<OpenMM::RealVec> _constraintDir; std::vector<OpenMM::Vec3> _constraintDir;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -58,7 +58,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -58,7 +58,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void initialize(int numberOfAtoms, std::vector<RealOpenMM>& inverseMasses); void initialize(int numberOfAtoms, std::vector<double>& inverseMasses);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -78,7 +78,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -78,7 +78,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void updateAtomPositions(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& inverseMasses); void updateAtomPositions(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<double>& inverseMasses);
public: public:
...@@ -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, double* distance);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -133,8 +133,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -133,8 +133,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void apply(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses); std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -147,8 +147,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -147,8 +147,8 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses); std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/reference/include/ReferenceMonteCarloBarostat.h
View file @ a783b996
...@@ -25,6 +25,7 @@ ...@@ -25,6 +25,7 @@
#ifndef __ReferenceMonteCarloBarostat_H__ #ifndef __ReferenceMonteCarloBarostat_H__
#define __ReferenceMonteCarloBarostat_H__ #define __ReferenceMonteCarloBarostat_H__
#include "openmm/Vec3.h"
#include <utility> #include <utility>
#include <vector> #include <vector>
...@@ -34,7 +35,7 @@ class ReferenceMonteCarloBarostat { ...@@ -34,7 +35,7 @@ class ReferenceMonteCarloBarostat {
private: private:
std::vector<RealOpenMM> savedAtomPositions[3]; std::vector<double> savedAtomPositions[3];
std::vector<std::vector<int> > molecules; std::vector<std::vector<int> > molecules;
public: public:
...@@ -67,7 +68,7 @@ class ReferenceMonteCarloBarostat { ...@@ -67,7 +68,7 @@ class ReferenceMonteCarloBarostat {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void applyBarostat(std::vector<OpenMM::RealVec>& atomPositions, const OpenMM::RealVec* boxVectors, RealOpenMM scaleX, RealOpenMM scaleY, RealOpenMM scaleZ); void applyBarostat(std::vector<OpenMM::Vec3>& atomPositions, const OpenMM::Vec3* boxVectors, double scaleX, double scaleY, double scaleZ);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -77,7 +78,7 @@ class ReferenceMonteCarloBarostat { ...@@ -77,7 +78,7 @@ class ReferenceMonteCarloBarostat {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void restorePositions(std::vector<OpenMM::RealVec>& atomPositions); void restorePositions(std::vector<OpenMM::Vec3>& atomPositions);
}; };
......
platforms/reference/include/ReferenceNeighborList.h
View file @ a783b996
#ifndef OPENMM_REFERENCE_NEIGHBORLIST_H_ #ifndef OPENMM_REFERENCE_NEIGHBORLIST_H_
#define OPENMM_REFERENCE_NEIGHBORLIST_H_ #define OPENMM_REFERENCE_NEIGHBORLIST_H_
#include "RealVec.h" #include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
#include <set> #include <set>
#include <vector> #include <vector>
namespace OpenMM { namespace OpenMM {
typedef std::vector<RealVec> AtomLocationList; typedef std::vector<Vec3> AtomLocationList;
typedef unsigned int AtomIndex; typedef unsigned int AtomIndex;
typedef std::pair<AtomIndex, AtomIndex> AtomPair; typedef std::pair<AtomIndex, AtomIndex> AtomPair;
typedef std::vector<AtomPair> NeighborList; typedef std::vector<AtomPair> NeighborList;
...@@ -22,7 +22,7 @@ void OPENMM_EXPORT computeNeighborListNaive( ...@@ -22,7 +22,7 @@ void OPENMM_EXPORT computeNeighborListNaive(
int nAtoms, int nAtoms,
const AtomLocationList& atomLocations, const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions, const std::vector<std::set<int> >& exclusions,
const RealVec* periodicBoxVectors, const Vec3* periodicBoxVectors,
bool usePeriodic, bool usePeriodic,
double maxDistance, double maxDistance,
double minDistance = 0.0, double minDistance = 0.0,
...@@ -37,7 +37,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash( ...@@ -37,7 +37,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
int nAtoms, int nAtoms,
const AtomLocationList& atomLocations, const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions, const std::vector<std::set<int> >& exclusions,
const RealVec* periodicBoxVectors, const Vec3* periodicBoxVectors,
bool usePeriodic, bool usePeriodic,
double maxDistance, double maxDistance,
double minDistance = 0.0, double minDistance = 0.0,
......
platforms/reference/include/ReferenceObc.h
View file @ a783b996
...@@ -39,7 +39,7 @@ class ReferenceObc { ...@@ -39,7 +39,7 @@ class ReferenceObc {
// arrays containing OBC chain derivative // arrays containing OBC chain derivative
std::vector<RealOpenMM> _obcChain; std::vector<double> _obcChain;
// flag to signal whether ACE approximation // flag to signal whether ACE approximation
// is to be included // is to be included
...@@ -117,7 +117,7 @@ class ReferenceObc { ...@@ -117,7 +117,7 @@ class ReferenceObc {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getObcChain(); std::vector<double>& getObcChain();
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -128,7 +128,7 @@ class ReferenceObc { ...@@ -128,7 +128,7 @@ class ReferenceObc {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii); void computeBornRadii(const std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<double>& bornRadii);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -142,8 +142,8 @@ class ReferenceObc { ...@@ -142,8 +142,8 @@ class ReferenceObc {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<RealOpenMM>& bornRadii, void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<double>& bornRadii,
RealOpenMM* energy, std::vector<RealOpenMM>& forces) const; double* energy, std::vector<double>& forces) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -155,8 +155,8 @@ class ReferenceObc { ...@@ -155,8 +155,8 @@ class ReferenceObc {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergyForces(const std::vector<OpenMM::RealVec>& atomCoordinates, double computeBornEnergyForces(const std::vector<OpenMM::Vec3>& atomCoordinates,
const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& forces); const std::vector<double>& partialCharges, std::vector<OpenMM::Vec3>& forces);
}; };
......
platforms/reference/include/ReferencePME.h
View file @ a783b996
...@@ -32,13 +32,13 @@ ...@@ -32,13 +32,13 @@
#ifndef __ReferencePME_H__ #ifndef __ReferencePME_H__
#define __ReferencePME_H__ #define __ReferencePME_H__
#include "RealVec.h" #include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
#include <vector> #include <vector>
namespace OpenMM { namespace OpenMM {
typedef RealOpenMM rvec[3]; typedef double rvec[3];
typedef struct pme * typedef struct pme *
...@@ -59,12 +59,12 @@ pme_t; ...@@ -59,12 +59,12 @@ pme_t;
* epsilon_r Dielectric coefficient, typically 1.0. * epsilon_r Dielectric coefficient, typically 1.0.
*/ */
int OPENMM_EXPORT int OPENMM_EXPORT
pme_init(pme_t * ppme, pme_init(pme_t* ppme,
RealOpenMM ewaldcoeff, double ewaldcoeff,
int natoms, int natoms,
const int ngrid[3], const int ngrid[3],
int pme_order, int pme_order,
RealOpenMM epsilon_r); double epsilon_r);
/* /*
* Evaluate reciprocal space PME energy and forces. * Evaluate reciprocal space PME energy and forces.
...@@ -79,12 +79,12 @@ pme_init(pme_t * ppme, ...@@ -79,12 +79,12 @@ pme_init(pme_t * ppme,
* energy Total energy (will be written in units of kJ/mol) * energy Total energy (will be written in units of kJ/mol)
*/ */
int OPENMM_EXPORT int OPENMM_EXPORT
pme_exec(pme_t pme, pme_exec(pme_t pme,
const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::RealVec>& forces, std::vector<OpenMM::Vec3>& forces,
const std::vector<RealOpenMM>& charges, const std::vector<double>& charges,
const OpenMM::RealVec periodicBoxVectors[3], const OpenMM::Vec3 periodicBoxVectors[3],
RealOpenMM * energy); double* energy);
......
platforms/reference/include/ReferencePairIxn.h
View file @ a783b996
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __ReferencePairIxn_H__ #ifndef __ReferencePairIxn_H__
#define __ReferencePairIxn_H__ #define __ReferencePairIxn_H__
#include "RealVec.h" #include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h" #include "openmm/internal/windowsExport.h"
#include <vector> #include <vector>
...@@ -68,10 +68,10 @@ class OPENMM_EXPORT ReferencePairIxn { ...@@ -68,10 +68,10 @@ class OPENMM_EXPORT ReferencePairIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions, double** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces, double* fixedParameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const = 0; double* energyByAtom, double* totalEnergy) const = 0;
}; };
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ a783b996
...@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
private: private:
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; Vec3 boxVectors[3];
public: public:
...@@ -62,7 +62,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -62,7 +62,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors); void setPeriodic(OpenMM::Vec3* vectors);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -78,9 +78,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn { ...@@ -78,9 +78,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, double* parameters, std::vector<OpenMM::Vec3>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs); double* totalEnergy, double* energyParamDerivs);
}; };
......
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