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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 @@
#include "CpuNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "openmm/CustomGBForce.h"
#include "openmm/internal/vectorize.h"
#include <map>
#include <set>
#include <vector>
......@@ -40,8 +41,8 @@ private:
bool cutoff;
bool periodic;
const CpuNeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
float periodicBoxSize[3];
float cutoffDistance;
CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
......@@ -59,20 +60,20 @@ private:
std::vector<int> particleValueIndex;
int xindex, yindex, zindex, rindex;
// Workspace vectors
std::vector<std::vector<RealOpenMM> > values, dEdV;
std::vector<RealOpenMM> dVdR1, dVdR2, dVdX, dVdY, dVdZ;
std::vector<std::vector<float> > values, dEdV;
std::vector<float> dVdR1, dVdR2, dVdX, dVdY, dVdZ;
/**
* Calculate a computed value of type SingleParticle
*
* @param index the index of the value to compute
* @param numAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param values the vector to store computed values into
* @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);
/**
......@@ -80,16 +81,16 @@ private:
*
* @param index the index of the value to compute
* @param numAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector to store computed values into
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param useExclusions specifies whether to use exclusions
*/
void calculateParticlePairValue(int index, int numAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values,
const std::vector<std::set<int> >& exclusions, bool useExclusions);
void calculateParticlePairValue(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<float> >& values,
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
......@@ -97,20 +98,20 @@ private:
* @param index the index of the value to compute
* @param atom1 the index of the first 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 values the vector to store computed values into
*/
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values);
void calculateOnePairValue(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<float> >& values, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Calculate an energy term of type SingleParticle
*
* @param index the index of the value to compute
* @param numAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param values the vector containing computed values
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param forces forces on atoms are added to this
......@@ -118,16 +119,16 @@ private:
* @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,
RealOpenMM** atomParameters, std::vector<RealVec>& forces,
RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV);
void calculateSingleParticleEnergyTerm(int index, int numAtoms, float* posq, const std::vector<std::vector<float> >& values,
RealOpenMM** atomParameters, float* forces,
double* totalEnergy, std::vector<std::vector<float> >& dEdV);
/**
* Calculate an energy term that is based on particle pairs
*
* @param index the index of the term to compute
* @param numAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i
......@@ -137,10 +138,11 @@ private:
* @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,
const std::vector<std::vector<RealOpenMM> >& values,
void calculateParticlePairEnergyTerm(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
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
......@@ -148,7 +150,7 @@ private:
* @param index the index of the term to compute
* @param atom1 the index of the first 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 values the vector containing computed values
* @param forces forces on atoms are added to this
......@@ -156,15 +158,16 @@ private:
* @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,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV);
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
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
*
* @param numAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i
......@@ -172,17 +175,18 @@ private:
* @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,
const std::vector<std::vector<RealOpenMM> >& values,
void calculateChainRuleForces(int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
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
*
* @param atom1 the index of the first 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 values the vector containing computed values
* @param forces forces on atoms are added to this
......@@ -190,10 +194,16 @@ private:
* @param isExcluded specifies whether this is an excluded pair
*/
void calculateOnePairChainRule(int atom1, int atom2, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV,
bool isExcluded);
void calculateOnePairChainRule(int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
float* forces, std::vector<std::vector<float> >& dEdV,
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:
......@@ -221,7 +231,7 @@ public:
* @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
......@@ -237,7 +247,7 @@ public:
* Calculate custom GB ixn
*
* @param numberOfAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param globalParameters the values of global parameters
......@@ -245,8 +255,8 @@ public:
* @param totalEnergy total energy
*/
void calculateIxn(int numberOfAtoms, std::vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, std::vector<RealVec>& forces, RealOpenMM* totalEnergy);
void calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, float* forces, double* totalEnergy);
};
} // 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
}
double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
RealVec& box = extractBoxSize(context);
......@@ -978,7 +977,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); 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;
}
......
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