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Commit bb70341a authored by peastman's avatar peastman
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Further optimizations to CustomGBForce

parent 83a0b613
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Showing with 160 additions and 146 deletions
platforms/cpu/include/CpuCustomGBForce.h
View file @ bb70341a
...@@ -29,6 +29,7 @@ ...@@ -29,6 +29,7 @@
#include "CpuNeighborList.h" #include "CpuNeighborList.h"
#include "lepton/CompiledExpression.h" #include "lepton/CompiledExpression.h"
#include "openmm/CustomGBForce.h" #include "openmm/CustomGBForce.h"
#include "openmm/internal/vectorize.h"
#include <map> #include <map>
#include <set> #include <set>
#include <vector> #include <vector>
...@@ -40,8 +41,8 @@ private: ...@@ -40,8 +41,8 @@ private:
bool cutoff; bool cutoff;
bool periodic; bool periodic;
const CpuNeighborList* neighborList; const CpuNeighborList* neighborList;
RealOpenMM periodicBoxSize[3]; float periodicBoxSize[3];
RealOpenMM cutoffDistance; float 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;
...@@ -59,20 +60,20 @@ private: ...@@ -59,20 +60,20 @@ private:
std::vector<int> particleValueIndex; std::vector<int> particleValueIndex;
int xindex, yindex, zindex, rindex; int xindex, yindex, zindex, rindex;
// Workspace vectors // Workspace vectors
std::vector<std::vector<RealOpenMM> > values, dEdV; std::vector<std::vector<float> > values, dEdV;
std::vector<RealOpenMM> dVdR1, dVdR2, dVdX, dVdY, dVdZ; std::vector<float> dVdR1, dVdR2, dVdX, dVdY, dVdZ;
/** /**
* Calculate a computed value of type SingleParticle * Calculate a computed value of type SingleParticle
* *
* @param index the index of the value to compute * @param index the index of the value to compute
* @param numAtoms number of atoms * @param numAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param values the vector to store computed values into * @param values the vector to store computed values into
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
*/ */
void calculateSingleParticleValue(int index, int numAtoms, std::vector<RealVec>& atomCoordinates, std::vector<std::vector<RealOpenMM> >& values, void calculateSingleParticleValue(int index, int numAtoms, float* posq, std::vector<std::vector<float> >& values,
RealOpenMM** atomParameters); RealOpenMM** atomParameters);
/** /**
...@@ -80,16 +81,16 @@ private: ...@@ -80,16 +81,16 @@ private:
* *
* @param index the index of the value to compute * @param index the index of the value to compute
* @param numAtoms number of atoms * @param numAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector to store computed values into * @param values the vector to store computed values into
* @param exclusions exclusions[i] is the set of excluded indices for atom i * @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param useExclusions specifies whether to use exclusions * @param useExclusions specifies whether to use exclusions
*/ */
void calculateParticlePairValue(int index, int numAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateParticlePairValue(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values, std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions, bool useExclusions); const std::vector<std::set<int> >& exclusions, bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Evaluate a single atom pair as part of calculating a computed value * Evaluate a single atom pair as part of calculating a computed value
...@@ -97,20 +98,20 @@ private: ...@@ -97,20 +98,20 @@ private:
* @param index the index of the value to compute * @param index the index of the value to compute
* @param atom1 the index of the first atom in the pair * @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair * @param atom2 the index of the second atom in the pair
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector to store computed values into * @param values the vector to store computed values into
*/ */
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateOnePairValue(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values); std::vector<std::vector<float> >& values, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Calculate an energy term of type SingleParticle * Calculate an energy term of type SingleParticle
* *
* @param index the index of the value to compute * @param index the index of the value to compute
* @param numAtoms number of atoms * @param numAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param values the vector containing computed values * @param values the vector containing computed values
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param forces forces on atoms are added to this * @param forces forces on atoms are added to this
...@@ -118,16 +119,16 @@ private: ...@@ -118,16 +119,16 @@ private:
* @param dEdV the derivative of energy with respect to computed values is stored in this * @param dEdV the derivative of energy with respect to computed values is stored in this
*/ */
void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<RealVec>& atomCoordinates, const std::vector<std::vector<RealOpenMM> >& values, void calculateSingleParticleEnergyTerm(int index, int numAtoms, float* posq, const std::vector<std::vector<float> >& values,
RealOpenMM** atomParameters, std::vector<RealVec>& forces, RealOpenMM** atomParameters, float* forces,
RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV); double* totalEnergy, std::vector<std::vector<float> >& dEdV);
/** /**
* Calculate an energy term that is based on particle pairs * Calculate an energy term that is based on particle pairs
* *
* @param index the index of the term to compute * @param index the index of the term to compute
* @param numAtoms number of atoms * @param numAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values * @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i * @param exclusions exclusions[i] is the set of excluded indices for atom i
...@@ -137,10 +138,11 @@ private: ...@@ -137,10 +138,11 @@ private:
* @param dEdV the derivative of energy with respect to computed values is stored in this * @param dEdV the derivative of energy with respect to computed values is stored in this
*/ */
void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateParticlePairEnergyTerm(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values, const std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions, bool useExclusions, const std::vector<std::set<int> >& exclusions, bool useExclusions,
std::vector<RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV); float* forces, double* totalEnergy, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Evaluate a single atom pair as part of calculating an energy term * Evaluate a single atom pair as part of calculating an energy term
...@@ -148,7 +150,7 @@ private: ...@@ -148,7 +150,7 @@ private:
* @param index the index of the term to compute * @param index the index of the term to compute
* @param atom1 the index of the first atom in the pair * @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair * @param atom2 the index of the second atom in the pair
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values * @param values the vector containing computed values
* @param forces forces on atoms are added to this * @param forces forces on atoms are added to this
...@@ -156,15 +158,16 @@ private: ...@@ -156,15 +158,16 @@ private:
* @param dEdV the derivative of energy with respect to computed values is stored in this * @param dEdV the derivative of energy with respect to computed values is stored in this
*/ */
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateOnePairEnergyTerm(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values, const std::vector<std::vector<float> >& values,
std::vector<RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV); float* forces, double* totalEnergy, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Apply the chain rule to compute forces on atoms * Apply the chain rule to compute forces on atoms
* *
* @param numAtoms number of atoms * @param numAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values * @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i * @param exclusions exclusions[i] is the set of excluded indices for atom i
...@@ -172,17 +175,18 @@ private: ...@@ -172,17 +175,18 @@ private:
* @param dEdV the derivative of energy with respect to computed values is stored in this * @param dEdV the derivative of energy with respect to computed values is stored in this
*/ */
void calculateChainRuleForces(int numAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateChainRuleForces(int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values, const std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions, const std::vector<std::set<int> >& exclusions,
std::vector<RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV); float* forces, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Evaluate a single atom pair as part of applying the chain rule * Evaluate a single atom pair as part of applying the chain rule
* *
* @param atom1 the index of the first atom in the pair * @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair * @param atom2 the index of the second atom in the pair
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values * @param values the vector containing computed values
* @param forces forces on atoms are added to this * @param forces forces on atoms are added to this
...@@ -190,10 +194,16 @@ private: ...@@ -190,10 +194,16 @@ private:
* @param isExcluded specifies whether this is an excluded pair * @param isExcluded specifies whether this is an excluded pair
*/ */
void calculateOnePairChainRule(int atom1, int atom2, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, void calculateOnePairChainRule(int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values, const std::vector<std::vector<float> >& values,
std::vector<RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV, float* forces, std::vector<std::vector<float> >& dEdV,
bool isExcluded); bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between two points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
public: public:
...@@ -221,7 +231,7 @@ public: ...@@ -221,7 +231,7 @@ public:
* @param neighbors the neighbor list to use * @param neighbors the neighbor list to use
*/ */
void setUseCutoff(RealOpenMM distance, const CpuNeighborList& neighbors); void setUseCutoff(float distance, const CpuNeighborList& neighbors);
/** /**
* Set the force to use periodic boundary conditions. This requires that a cutoff has * Set the force to use periodic boundary conditions. This requires that a cutoff has
...@@ -237,7 +247,7 @@ public: ...@@ -237,7 +247,7 @@ public:
* Calculate custom GB ixn * Calculate custom GB ixn
* *
* @param numberOfAtoms number of atoms * @param numberOfAtoms number of atoms
* @param atomCoordinates atom coordinates * @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex] * @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param exclusions exclusions[i] is the set of excluded indices for atom i * @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param globalParameters the values of global parameters * @param globalParameters the values of global parameters
...@@ -245,8 +255,8 @@ public: ...@@ -245,8 +255,8 @@ public:
* @param totalEnergy total energy * @param totalEnergy total energy
*/ */
void calculateIxn(int numberOfAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions, void calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, std::vector<RealVec>& forces, RealOpenMM* totalEnergy); std::map<std::string, double>& globalParameters, float* forces, double* totalEnergy);
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ bb70341a
This diff is collapsed.
platforms/cpu/src/CpuKernels.cpp
View file @ bb70341a
...@@ -963,7 +963,6 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB ...@@ -963,7 +963,6 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
} }
double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0; RealOpenMM energy = 0;
RealVec& box = extractBoxSize(context); RealVec& box = extractBoxSize(context);
...@@ -978,7 +977,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor ...@@ -978,7 +977,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
map<string, double> globalParameters; map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]); globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ixn->calculateIxn(numParticles, posData, particleParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL); ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, exclusions, globalParameters, &data.threadForce[0][0], includeEnergy ? &energy : NULL);
return energy; return energy;
} }
......
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