Skip to content

GitLab

Commit 0b1f03db authored by peastman's avatar peastman
Browse files

Use CompiledExpressionSet for reference CustomGBForce

parent f54a0079
Expand all Show whitespace changes
Inline Side-by-side
Showing with 183 additions and 192 deletions
platforms/reference/include/ReferenceCustomGBIxn.h
View file @ 0b1f03db
......@@ -26,7 +26,7 @@
#define __ReferenceCustomGBIxn_H__
#include "ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "openmm/CustomGBForce.h"
#include <map>
#include <set>
......@@ -43,18 +43,20 @@ class ReferenceCustomGBIxn {
const OpenMM::NeighborList* neighborList;
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance;
std::vector<Lepton::ExpressionProgram> valueExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
std::vector<std::string> valueNames;
CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
std::vector<Lepton::ExpressionProgram> energyExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
std::vector<std::string> paramNames;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
std::vector<std::string> particleParamNames;
std::vector<std::string> particleValueNames;
std::vector<int> paramIndex;
std::vector<int> valueIndex;
std::vector<int> particleParamIndex;
std::vector<int> particleValueIndex;
int rIndex, xIndex, yIndex, zIndex;
/**---------------------------------------------------------------------------------------
......@@ -64,13 +66,12 @@ class ReferenceCustomGBIxn {
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param values the vector to store computed values into
@param globalParameters the values of global parameters
@param atomParameters atomParameters[atomIndex][paramterIndex]
--------------------------------------------------------------------------------------- */
void calculateSingleParticleValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters, RealOpenMM** atomParameters) const;
RealOpenMM** atomParameters);
/**---------------------------------------------------------------------------------------
......@@ -81,7 +82,6 @@ class ReferenceCustomGBIxn {
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector to store computed values into
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param useExclusions specifies whether to use exclusions
......@@ -89,8 +89,7 @@ class ReferenceCustomGBIxn {
void calculateParticlePairValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions) const;
const std::vector<std::set<int> >& exclusions, bool useExclusions);
/**---------------------------------------------------------------------------------------
......@@ -101,14 +100,12 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector to store computed values into
--------------------------------------------------------------------------------------- */
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
std::vector<std::vector<RealOpenMM> >& values) const;
std::vector<std::vector<RealOpenMM> >& values);
/**---------------------------------------------------------------------------------------
......@@ -118,7 +115,6 @@ class ReferenceCustomGBIxn {
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param forces forces on atoms are added to this
@param totalEnergy the energy contribution is added to this
......@@ -127,8 +123,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters, RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV);
/**---------------------------------------------------------------------------------------
......@@ -139,7 +135,6 @@ class ReferenceCustomGBIxn {
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param useExclusions specifies whether to use exclusions
@param forces forces on atoms are added to this
......@@ -150,9 +145,8 @@ class ReferenceCustomGBIxn {
void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV);
/**---------------------------------------------------------------------------------------
......@@ -163,7 +157,6 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector containing computed values
@param forces forces on atoms are added to this
@param totalEnergy the energy contribution is added to this
......@@ -172,9 +165,8 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV);
/**---------------------------------------------------------------------------------------
......@@ -184,7 +176,6 @@ class ReferenceCustomGBIxn {
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param forces forces on atoms are added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
......@@ -193,9 +184,8 @@ class ReferenceCustomGBIxn {
void calculateChainRuleForces(int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions,
std::vector<OpenMM::RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV) const;
std::vector<OpenMM::RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV);
/**---------------------------------------------------------------------------------------
......@@ -205,7 +195,6 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector containing computed values
@param forces forces on atoms are added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
......@@ -214,10 +203,9 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void calculateOnePairChainRule(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<OpenMM::RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV,
bool isExcluded) const;
bool isExcluded);
public:
......@@ -227,14 +215,14 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn(const std::vector<Lepton::ExpressionProgram>& valueExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions,
ReferenceCustomGBIxn(const std::vector<Lepton::CompiledExpression>& valueExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions,
const std::vector<std::string>& valueNames,
const std::vector<OpenMM::CustomGBForce::ComputationType>& valueTypes,
const std::vector<Lepton::ExpressionProgram>& energyExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions,
const std::vector<Lepton::CompiledExpression>& energyExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions,
const std::vector<OpenMM::CustomGBForce::ComputationType>& energyTypes,
const std::vector<std::string>& parameterNames);
......@@ -284,7 +272,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void calculateIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
std::map<std::string, double>& globalParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy);
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceKernels.h
View file @ 0b1f03db
......@@ -38,7 +38,6 @@
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionProgram.h"
namespace OpenMM {
......@@ -739,13 +738,13 @@ private:
RealOpenMM nonbondedCutoff;
std::vector<std::set<int> > exclusions;
std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
std::vector<Lepton::ExpressionProgram> valueExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
std::vector<Lepton::ExpressionProgram> energyExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 0b1f03db
......@@ -1376,19 +1376,19 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
CustomGBForce::ComputationType type;
force.getComputedValueParameters(i, name, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
valueExpressions.push_back(ex.createProgram());
valueExpressions.push_back(ex.createCompiledExpression());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0) {
valueDerivExpressions[i].push_back(ex.differentiate("r").optimize().createProgram());
valueDerivExpressions[i].push_back(ex.differentiate("r").optimize().createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("x").optimize().createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("y").optimize().createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("z").optimize().createCompiledExpression());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createProgram());
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
particleVariables.insert(name);
......@@ -1405,21 +1405,21 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
CustomGBForce::ComputationType type;
force.getEnergyTermParameters(i, expression, type);
Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
energyExpressions.push_back(ex.createProgram());
energyExpressions.push_back(ex.createCompiledExpression());
energyTypes.push_back(type);
if (type != CustomGBForce::SingleParticle)
energyDerivExpressions[i].push_back(ex.differentiate("r").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate("r").optimize().createCompiledExpression());
for (int j = 0; j < force.getNumComputedValues(); j++) {
if (type == CustomGBForce::SingleParticle) {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("x").optimize().createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("y").optimize().createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("z").optimize().createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").optimize().createCompiledExpression());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").optimize().createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment