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Commit 54e47d2d authored by peastman's avatar peastman
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Converted lots of ExpressionPrograms to CompiledExpressions

parent 8b3bfc92
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Showing with 285 additions and 170 deletions
openmmapi/include/openmm/internal/CustomNonbondedForceImpl.h
View file @ 54e47d2d
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -35,7 +35,7 @@
#include "ForceImpl.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/Kernel.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
#include <utility>
#include <map>
#include <string>
......@@ -68,7 +68,7 @@ public:
static double calcLongRangeCorrection(const CustomNonbondedForce& force, const Context& context);
private:
class TabulatedFunction;
static double integrateInteraction(const Lepton::ExpressionProgram& expression, const std::vector<double>& params1, const std::vector<double>& params2,
static double integrateInteraction(Lepton::CompiledExpression& expression, const std::vector<double>& params1, const std::vector<double>& params2,
const CustomNonbondedForce& force, const Context& context);
const CustomNonbondedForce& owner;
Kernel kernel;
......
openmmapi/src/CustomNonbondedForceImpl.cpp
View file @ 54e47d2d
......@@ -182,7 +182,7 @@ double CustomNonbondedForceImpl::calcLongRangeCorrection(const CustomNonbondedFo
force.getFunctionParameters(i, name, values, min, max);
functions[name] = new TabulatedFunction(min, max, values);
}
Lepton::ExpressionProgram expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize().createProgram();
Lepton::CompiledExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).createCompiledExpression();
// Identify all particle classes (defined by parameters), and record the class of each particle.
......@@ -251,25 +251,35 @@ double CustomNonbondedForceImpl::calcLongRangeCorrection(const CustomNonbondedFo
return 2*M_PI*numParticles*numParticles*sum;
}
double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionProgram& expression, const vector<double>& params1, const vector<double>& params2,
double CustomNonbondedForceImpl::integrateInteraction(Lepton::CompiledExpression& expression, const vector<double>& params1, const vector<double>& params2,
const CustomNonbondedForce& force, const Context& context) {
map<std::string, double> variables;
const set<string>& variables = expression.getVariables();
for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
stringstream name1, name2;
name1 << force.getPerParticleParameterName(i) << 1;
name2 << force.getPerParticleParameterName(i) << 2;
variables[name1.str()] = params1[i];
variables[name2.str()] = params2[i];
if (variables.find(name1.str()) != variables.end())
expression.getVariableReference(name1.str()) = params1[i];
if (variables.find(name2.str()) != variables.end())
expression.getVariableReference(name2.str()) = params2[i];
}
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
variables[name] = context.getParameter(name);
if (variables.find(name) != variables.end())
expression.getVariableReference(name) = context.getParameter(name);
}
// To integrate from r_cutoff to infinity, make the change of variables x=r_cutoff/r and integrate from 0 to 1.
// This introduces another r^2 into the integral, which along with the r^2 in the formula for the correction
// means we multiply the function by r^4. Use the midpoint method.
double* rPointer;
try {
rPointer = &expression.getVariableReference("r");
}
catch (exception& ex) {
throw OpenMMException("CustomNonbondedForce: Cannot use long range correction with a force that does not depend on r.");
}
double cutoff = force.getCutoffDistance();
double sum = 0;
int numPoints = 1;
......@@ -281,9 +291,9 @@ double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionPr
continue;
double x = (i+0.5)/numPoints;
double r = cutoff/x;
variables["r"] = r;
*rPointer = r;
double r2 = r*r;
newSum += expression.evaluate(variables)*r2*r2;
newSum += expression.evaluate()*r2*r2;
}
sum = newSum/numPoints + oldSum/3;
if (iteration > 2 && (fabs((sum-oldSum)/sum) < 1e-5 || sum == 0))
......@@ -309,8 +319,8 @@ double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionPr
double x = (i+0.5)/numPoints;
double r = rswitch+x*(cutoff-rswitch);
double switchValue = x*x*x*(10+x*(-15+x*6));
variables["r"] = r;
newSum += switchValue*expression.evaluate(variables)*r*r;
*rPointer = r;
newSum += switchValue*expression.evaluate()*r*r;
}
sum2 = newSum/numPoints + oldSum/3;
if (iteration > 2 && (fabs((sum2-oldSum)/sum2) < 1e-5 || sum2 == 0))
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 54e47d2d
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,17 +25,20 @@
#define __ReferenceCustomAngleIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomAngleIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
int numParameters;
public:
......@@ -45,7 +48,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -26,17 +26,20 @@
#define __ReferenceCustomBondIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomBondIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyR;
double* forceR;
int numParameters;
public:
......@@ -46,7 +49,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomExternalIxn.h
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -26,19 +26,26 @@
#define __ReferenceCustomExternalIxn_H__
#include "ReferenceCustomExternalIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomExternalIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpressionX;
Lepton::ExpressionProgram forceExpressionY;
Lepton::ExpressionProgram forceExpressionZ;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpressionX;
Lepton::CompiledExpression forceExpressionY;
Lepton::CompiledExpression forceExpressionZ;
std::vector<double*> energyParams;
std::vector<double*> forceXParams;
std::vector<double*> forceYParams;
std::vector<double*> forceZParams;
double *energyX, *energyY, *energyZ;
double *forceXX, *forceXY, *forceXZ;
double *forceYX, *forceYY, *forceYZ;
double *forceZX, *forceZY, *forceZZ;
int numParameters;
public:
......@@ -48,8 +55,8 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpressionX,
const Lepton::ExpressionProgram& forceExpressionY, const Lepton::ExpressionProgram& forceExpressionZ,
ReferenceCustomExternalIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpressionX,
const Lepton::CompiledExpression& forceExpressionY, const Lepton::CompiledExpression& forceExpressionZ,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -27,7 +27,7 @@
#include "ReferencePairIxn.h"
#include "ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
#include <map>
#include <set>
#include <utility>
......@@ -45,10 +45,13 @@ class ReferenceCustomNonbondedIxn {
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance, switchingDistance;
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<std::string> paramNames;
std::vector<std::string> particleParamNames;
std::vector<double*> energyParticleParams;
std::vector<double*> forceParticleParams;
double* energyR;
double* forceR;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
/**---------------------------------------------------------------------------------------
......@@ -65,9 +68,8 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
public:
......@@ -78,7 +80,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames);
/**---------------------------------------------------------------------------------------
......@@ -153,7 +155,7 @@ class ReferenceCustomNonbondedIxn {
void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 54e47d2d
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,17 +25,20 @@
#define __ReferenceCustomTorsionIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
int numParameters;
public:
......@@ -45,7 +48,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceForce.h
View file @ 54e47d2d
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,6 +24,7 @@
#ifndef __ReferenceForce_H__
#define __ReferenceForce_H__
#include "lepton/CompiledExpression.h"
#include "openmm/internal/windowsExport.h"
// ---------------------------------------------------------------------------------------
......@@ -109,6 +109,18 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
RealOpenMM* deltaR );
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
* does not use the specified variable, return NULL.
*/
static double* getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name);
/**
* Set the value of a variable in a CompiledExpression, using the pointer that was returned by getVariablePointer().
*/
static void setVariable(double* pointer, double value);
};
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceKernels.h
View file @ 54e47d2d
......@@ -36,6 +36,7 @@
#include "openmm/kernels.h"
#include "SimTKOpenMMRealType.h"
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "lepton/ExpressionProgram.h"
class CpuObc;
......@@ -316,7 +317,7 @@ private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -392,7 +393,7 @@ private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -534,7 +535,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -621,7 +622,7 @@ private:
CustomNonbondedForce* forceCopy;
std::map<std::string, double> globalParamValues;
std::vector<std::set<int> > exclusions;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
NonbondedMethod nonbondedMethod;
......@@ -781,7 +782,7 @@ private:
int numParticles;
std::vector<int> particles;
RealOpenMM **particleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
std::vector<std::string> parameterNames, globalParameterNames;
};
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 54e47d2d
......@@ -420,8 +420,8 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const
// Parse the expression used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
energyExpression = expression.createProgram();
forceExpression = expression.differentiate("r").optimize().createProgram();
energyExpression = expression.createCompiledExpression();
forceExpression = expression.differentiate("r").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerBondParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
......@@ -534,8 +534,8 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const
// Parse the expression used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
energyExpression = expression.createProgram();
forceExpression = expression.differentiate("theta").optimize().createProgram();
energyExpression = expression.createCompiledExpression();
forceExpression = expression.differentiate("theta").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerAngleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
......@@ -744,8 +744,8 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con
// Parse the expression used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
energyExpression = expression.createProgram();
forceExpression = expression.differentiate("theta").optimize().createProgram();
energyExpression = expression.createCompiledExpression();
forceExpression = expression.differentiate("theta").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerTorsionParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
......@@ -1028,8 +1028,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
// Parse the various expressions used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
energyExpression = expression.createProgram();
forceExpression = expression.differentiate("r").optimize().createProgram();
energyExpression = expression.createCompiledExpression();
forceExpression = expression.differentiate("r").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
......@@ -1426,10 +1426,10 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
// Parse the expression used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
energyExpression = expression.createProgram();
forceExpressionX = expression.differentiate("x").optimize().createProgram();
forceExpressionY = expression.differentiate("y").optimize().createProgram();
forceExpressionZ = expression.differentiate("z").optimize().createProgram();
energyExpression = expression.createCompiledExpression();
forceExpressionX = expression.differentiate("x").createCompiledExpression();
forceExpressionY = expression.differentiate("y").createCompiledExpression();
forceExpressionZ = expression.differentiate("z").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,16 +39,21 @@ using namespace std;
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::ExpressionProgram& energyExpression,
const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames), globalParameters(globalParameters) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomAngleIxn::ReferenceCustomAngleIxn";
// ---------------------------------------------------------------------------------------
ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression) {
energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpression, iter->first), iter->second);
}
}
/**---------------------------------------------------------------------------------------
......@@ -91,9 +96,10 @@ void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
static const RealOpenMM one = 1.0;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); ++i)
variables[paramNames[i]] = parameters[i];
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
ReferenceForce::setVariable(forceParams[i], parameters[i]);
}
// ---------------------------------------------------------------------------------------
......@@ -118,12 +124,13 @@ void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
angle = PI_M;
else
angle = ACOS(cosine);
variables["theta"] = angle;
ReferenceForce::setVariable(energyTheta, angle);
ReferenceForce::setVariable(forceTheta, angle);
// Compute the force and energy, and apply them to the atoms.
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate(variables);
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
RealOpenMM termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -40,16 +40,20 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::ExpressionProgram& energyExpression,
const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames), globalParameters(globalParameters) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomBondIxn::ReferenceCustomBondIxn";
// ---------------------------------------------------------------------------------------
ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression) {
energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpression, iter->first), iter->second);
}
}
/**---------------------------------------------------------------------------------------
......@@ -95,9 +99,10 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
static const RealOpenMM half = 0.5;
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); ++i)
variables[paramNames[i]] = parameters[i];
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
ReferenceForce::setVariable(forceParams[i], parameters[i]);
}
// ---------------------------------------------------------------------------------------
......@@ -106,8 +111,10 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR );
variables["r"] = deltaR[ReferenceForce::RIndex];
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate(variables);
ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
dEdR = deltaR[ReferenceForce::RIndex] > zero ? (dEdR/deltaR[ReferenceForce::RIndex]) : zero;
forces[atomAIndex][0] += dEdR*deltaR[ReferenceForce::XIndex];
......@@ -119,5 +126,5 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -40,18 +40,37 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::ExpressionProgram& energyExpression,
const Lepton::ExpressionProgram& forceExpressionX, const Lepton::ExpressionProgram& forceExpressionY,
const Lepton::ExpressionProgram& forceExpressionZ, const vector<string>& parameterNames, map<string, double> globalParameters) :
ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpressionX, const Lepton::CompiledExpression& forceExpressionY,
const Lepton::CompiledExpression& forceExpressionZ, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpressionX(forceExpressionX), forceExpressionY(forceExpressionY),
forceExpressionZ(forceExpressionZ), paramNames(parameterNames), globalParameters(globalParameters) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomExternalIxn::ReferenceCustomExternalIxn";
// ---------------------------------------------------------------------------------------
forceExpressionZ(forceExpressionZ) {
energyX = ReferenceForce::getVariablePointer(this->energyExpression, "x");
energyY = ReferenceForce::getVariablePointer(this->energyExpression, "y");
energyZ = ReferenceForce::getVariablePointer(this->energyExpression, "z");
forceXX = ReferenceForce::getVariablePointer(this->forceExpressionX, "x");
forceXY = ReferenceForce::getVariablePointer(this->forceExpressionX, "y");
forceXZ = ReferenceForce::getVariablePointer(this->forceExpressionX, "z");
forceYX = ReferenceForce::getVariablePointer(this->forceExpressionY, "x");
forceYY = ReferenceForce::getVariablePointer(this->forceExpressionY, "y");
forceYZ = ReferenceForce::getVariablePointer(this->forceExpressionY, "z");
forceZX = ReferenceForce::getVariablePointer(this->forceExpressionZ, "x");
forceZY = ReferenceForce::getVariablePointer(this->forceExpressionZ, "y");
forceZZ = ReferenceForce::getVariablePointer(this->forceExpressionZ, "z");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceXParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionX, parameterNames[i]));
forceYParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionY, parameterNames[i]));
forceZParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionZ, parameterNames[i]));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionX, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionY, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionZ, iter->first), iter->second);
}
}
/**---------------------------------------------------------------------------------------
......@@ -90,18 +109,30 @@ void ReferenceCustomExternalIxn::calculateForce( int atomIndex,
static const std::string methodName = "\nReferenceCustomExternalIxn::calculateBondIxn";
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); ++i)
variables[paramNames[i]] = parameters[i];
variables["x"] = atomCoordinates[atomIndex][0];
variables["y"] = atomCoordinates[atomIndex][1];
variables["z"] = atomCoordinates[atomIndex][2];
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
ReferenceForce::setVariable(forceXParams[i], parameters[i]);
ReferenceForce::setVariable(forceYParams[i], parameters[i]);
ReferenceForce::setVariable(forceZParams[i], parameters[i]);
}
ReferenceForce::setVariable(energyX, atomCoordinates[atomIndex][0]);
ReferenceForce::setVariable(energyY, atomCoordinates[atomIndex][1]);
ReferenceForce::setVariable(energyZ, atomCoordinates[atomIndex][2]);
ReferenceForce::setVariable(forceXX, atomCoordinates[atomIndex][0]);
ReferenceForce::setVariable(forceXY, atomCoordinates[atomIndex][1]);
ReferenceForce::setVariable(forceXZ, atomCoordinates[atomIndex][2]);
ReferenceForce::setVariable(forceYX, atomCoordinates[atomIndex][0]);
ReferenceForce::setVariable(forceYY, atomCoordinates[atomIndex][1]);
ReferenceForce::setVariable(forceYZ, atomCoordinates[atomIndex][2]);
ReferenceForce::setVariable(forceZX, atomCoordinates[atomIndex][0]);
ReferenceForce::setVariable(forceZY, atomCoordinates[atomIndex][1]);
ReferenceForce::setVariable(forceZZ, atomCoordinates[atomIndex][2]);
// ---------------------------------------------------------------------------------------
forces[atomIndex][0] -= (RealOpenMM) forceExpressionX.evaluate(variables);
forces[atomIndex][1] -= (RealOpenMM) forceExpressionY.evaluate(variables);
forces[atomIndex][2] -= (RealOpenMM) forceExpressionZ.evaluate(variables);
forces[atomIndex][0] -= (RealOpenMM) forceExpressionX.evaluate();
forces[atomIndex][1] -= (RealOpenMM) forceExpressionY.evaluate();
forces[atomIndex][2] -= (RealOpenMM) forceExpressionZ.evaluate();
if (energy != NULL)
*energy += (RealOpenMM) energyExpression.evaluate(variables);
*energy += (RealOpenMM) energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -45,8 +45,8 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression,
const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames) :
ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames) :
cutoff(false), useSwitch(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames) {
// ---------------------------------------------------------------------------------------
......@@ -55,11 +55,14 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::Expressio
// ---------------------------------------------------------------------------------------
energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
for (int i = 0; i < (int) paramNames.size(); i++) {
for (int j = 1; j < 3; j++) {
stringstream name;
name << paramNames[i] << j;
particleParamNames.push_back(name.str());
energyParticleParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, name.str()));
forceParticleParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, name.str()));
}
}
}
......@@ -166,9 +169,12 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance )
void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) {
map<string, double> variables = globalParameters;
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(forceExpression, iter->first), iter->second);
}
if (interactionGroups.size() > 0) {
// The user has specified interaction groups, so compute only the requested interactions.
......@@ -182,10 +188,12 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
continue; // Both atoms are in both sets, so skip duplicate interactions.
for (int j = 0; j < (int) paramNames.size(); j++) {
variables[particleParamNames[j*2]] = atomParameters[*atom1][j];
variables[particleParamNames[j*2+1]] = atomParameters[*atom2][j];
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[*atom2][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[*atom2][j]);
}
calculateOneIxn(*atom1, *atom2, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
calculateOneIxn(*atom1, *atom2, atomCoordinates, forces, energyByAtom, totalEnergy);
}
}
}
......@@ -196,10 +204,12 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (int j = 0; j < (int) paramNames.size(); j++) {
variables[particleParamNames[j*2]] = atomParameters[pair.first][j];
variables[particleParamNames[j*2+1]] = atomParameters[pair.second][j];
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[pair.first][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[pair.second][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[pair.first][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[pair.second][j]);
}
calculateOneIxn(pair.first, pair.second, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
calculateOneIxn(pair.first, pair.second, atomCoordinates, forces, energyByAtom, totalEnergy);
}
}
else {
......@@ -209,10 +219,12 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
for (int jj = ii+1; jj < numberOfAtoms; jj++) {
if (exclusions[jj].find(ii) == exclusions[jj].end()) {
for (int j = 0; j < (int) paramNames.size(); j++) {
variables[particleParamNames[j*2]] = atomParameters[ii][j];
variables[particleParamNames[j*2+1]] = atomParameters[jj][j];
ReferenceForce::setVariable(energyParticleParams[j*2], atomParameters[ii][j]);
ReferenceForce::setVariable(energyParticleParams[j*2+1], atomParameters[jj][j]);
ReferenceForce::setVariable(forceParticleParams[j*2], atomParameters[ii][j]);
ReferenceForce::setVariable(forceParticleParams[j*2+1], atomParameters[jj][j]);
}
calculateOneIxn(ii, jj, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
calculateOneIxn(ii, jj, atomCoordinates, forces, energyByAtom, totalEnergy);
}
}
}
......@@ -233,9 +245,8 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates,
map<string, double>& variables, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) {
// ---------------------------------------------------------------------------------------
......@@ -266,9 +277,10 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVe
// accumulate forces
variables["r"] = r;
RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate(variables)/(deltaR[ReferenceForce::RIndex]));
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
ReferenceForce::setVariable(energyR, r);
ReferenceForce::setVariable(forceR, r);
RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate()/(deltaR[ReferenceForce::RIndex]));
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
if (useSwitch) {
if (r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,16 +39,21 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::ExpressionProgram& energyExpression,
const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames), globalParameters(globalParameters) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn";
// ---------------------------------------------------------------------------------------
ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression) {
energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpression, iter->first), iter->second);
}
}
/**---------------------------------------------------------------------------------------
......@@ -91,9 +96,10 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
static const RealOpenMM one = 1.0;
RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
map<string, double> variables = globalParameters;
for (int i = 0; i < (int) paramNames.size(); ++i)
variables[paramNames[i]] = parameters[i];
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
ReferenceForce::setVariable(forceParams[i], parameters[i]);
}
// ---------------------------------------------------------------------------------------
......@@ -118,13 +124,13 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
variables["theta"] = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
crossProduct, &dotDihedral, deltaR[0],
&signOfAngle, 1);
RealOpenMM angle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2], crossProduct, &dotDihedral, deltaR[0], &signOfAngle, 1);
ReferenceForce::setVariable(energyTheta, angle);
ReferenceForce::setVariable(forceTheta, angle);
// evaluate delta angle, dE/d(angle)
RealOpenMM dEdAngle = (RealOpenMM) forceExpression.evaluate(variables);
RealOpenMM dEdAngle = (RealOpenMM) forceExpression.evaluate();
// compute force
......@@ -166,6 +172,6 @@ void ReferenceCustomTorsionIxn::calculateBondIxn( int* atomIndices,
// accumulate energies
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 54e47d2d
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -161,3 +161,14 @@ void ReferenceForce::getDeltaROnly( const RealOpenMM* atomCoordinatesI,
deltaR[YIndex] = atomCoordinatesJ[1] - atomCoordinatesI[1];
deltaR[ZIndex] = atomCoordinatesJ[2] - atomCoordinatesI[2];
}
double* ReferenceForce::getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name) {
if (expression.getVariables().find(name) == expression.getVariables().end())
return NULL;
return &expression.getVariableReference(name);
}
void ReferenceForce::setVariable(double* pointer, double value) {
if (pointer != NULL)
*pointer = value;
}
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