Optimization to CustomNonbondedForce and CustomIntegrator on CPU

platforms/cpu/include/CpuCustomNonbondedForce.h

@@ -183,8 +183,8 @@ public:
     Lepton::CompiledExpression forceExpression;
     std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
     CompiledExpressionSet expressionSet;
-    std::vector<int> particleParamIndex;
-    int rIndex;
+    std::vector<double> particleParam;
+    double r;
     std::vector<RealOpenMM> energyParamDerivs; 
 };
 

platforms/cpu/src/CpuCustomGBForce.cpp

@@ -513,7 +513,8 @@ void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom
     getDeltaR(pos2, pos1, deltaR, r2, periodic, boxSize, invBoxSize);
     if (cutoff && r2 >= cutoffDistance2)
         return;
-    data.r = sqrtf(r2);
+    float r = sqrtf(r2);
+    data.r = r;
 
     // Record variables for evaluating expressions.
 
@@ -531,7 +532,7 @@ void CpuCustomGBForce::calculateOnePairEnergyTerm(int index, int atom1, int atom
     if (includeEnergy)
         totalEnergy += (float) data.energyExpressions[index].evaluate();
     float dEdR = (float) data.energyDerivExpressions[index][0].evaluate();
-    dEdR *= 1/data.r;
+    dEdR *= 1/r;
     fvec4 result = deltaR*dEdR;
     (fvec4(forces+4*atom1)-result).store(forces+4*atom1);
     (fvec4(forces+4*atom2)+result).store(forces+4*atom2);
@@ -634,7 +635,8 @@ void CpuCustomGBForce::calculateOnePairChainRule(int atom1, int atom2, ThreadDat
     getDeltaR(pos2, pos1, deltaR, r2, periodic, boxSize, invBoxSize);
     if (cutoff && r2 >= cutoffDistance2)
         return;
-    data.r = sqrtf(r2);
+    float r = sqrtf(r2);
+    data.r = r;
 
     // Record variables for evaluating expressions.
 
@@ -652,7 +654,7 @@ void CpuCustomGBForce::calculateOnePairChainRule(int atom1, int atom2, ThreadDat
 
     // Evaluate the derivative of each parameter with respect to position and apply forces.
 
-    float rinv = 1/data.r;
+    float rinv = 1/r;
     deltaR *= rinv;
     fvec4 f1(0.0f), f2(0.0f);
     if (!isExcluded || valueTypes[0] != CustomGBForce::ParticlePair) {

platforms/cpu/src/CpuCustomNonbondedForce.cpp

@@ -46,19 +46,25 @@ public:
 CpuCustomNonbondedForce::ThreadData::ThreadData(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
             const vector<string>& parameterNames, const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
             energyExpression(energyExpression), forceExpression(forceExpression), energyParamDerivExpressions(energyParamDerivExpressions) {
-    expressionSet.registerExpression(this->energyExpression);
-    expressionSet.registerExpression(this->forceExpression);
-    for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
-        expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
-    rIndex = expressionSet.getVariableIndex("r");
+    map<string, double*> variableLocations;
+    variableLocations["r"] = &r;
+    particleParam.resize(2*parameterNames.size());
     for (int i = 0; i < (int) parameterNames.size(); i++) {
-        for (int j = 1; j < 3; j++) {
+        for (int j = 0; j < 2; j++) {
             stringstream name;
-            name << parameterNames[i] << j;
-            particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
+            name << parameterNames[i] << (j+1);
+            variableLocations[name.str()] = &particleParam[i*2+j];
         }
     }
     energyParamDerivs.resize(energyParamDerivExpressions.size());
+    this->energyExpression.setVariableLocations(variableLocations);
+    this->forceExpression.setVariableLocations(variableLocations);
+    expressionSet.registerExpression(this->energyExpression);
+    expressionSet.registerExpression(this->forceExpression);
+    for (int i = 0; i < this->energyParamDerivExpressions.size(); i++) {
+        this->energyParamDerivExpressions[i].setVariableLocations(variableLocations);
+        expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
+    }
 }
 
 CpuCustomNonbondedForce::CpuCustomNonbondedForce(const Lepton::CompiledExpression& energyExpression,
@@ -187,8 +193,8 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
             int atom1 = groupInteractions[i].first;
             int atom2 = groupInteractions[i].second;
             for (int j = 0; j < (int) paramNames.size(); j++) {
-                data.expressionSet.setVariable(data.particleParamIndex[j*2], atomParameters[atom1][j]);
-                data.expressionSet.setVariable(data.particleParamIndex[j*2+1], atomParameters[atom2][j]);
+                data.particleParam[j*2] = atomParameters[atom1][j];
+                data.particleParam[j*2+1] = atomParameters[atom2][j];
             }
             calculateOneIxn(atom1, atom2, data, forces, energy, boxSize, invBoxSize);
         }
@@ -207,12 +213,12 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
                 for (int j = 0; j < (int) paramNames.size(); j++)
-                    data.expressionSet.setVariable(data.particleParamIndex[j*2], atomParameters[first][j]);
+                    data.particleParam[j*2] = atomParameters[first][j];
                 for (int k = 0; k < blockSize; k++) {
                     if ((exclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         for (int j = 0; j < (int) paramNames.size(); j++)
-                            data.expressionSet.setVariable(data.particleParamIndex[j*2+1], atomParameters[second][j]);
+                            data.particleParam[j*2+1] = atomParameters[second][j];
                         calculateOneIxn(first, second, data, forces, energy, boxSize, invBoxSize);
                     }
                 }
@@ -229,8 +235,8 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
             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++) {
-                        data.expressionSet.setVariable(data.particleParamIndex[j*2], atomParameters[ii][j]);
-                        data.expressionSet.setVariable(data.particleParamIndex[j*2+1], atomParameters[jj][j]);
+                        data.particleParam[j*2] = atomParameters[ii][j];
+                        data.particleParam[j*2+1] = atomParameters[jj][j];
                     }
                     calculateOneIxn(ii, jj, data, forces, energy, boxSize, invBoxSize);
                 }
@@ -251,10 +257,10 @@ void CpuCustomNonbondedForce::calculateOneIxn(int ii, int jj, ThreadData& data,
     if (cutoff && r2 >= cutoffDistance*cutoffDistance)
         return;
     float r = sqrtf(r2);
+    data.r = r;
 
     // accumulate forces
 
-    data.expressionSet.setVariable(data.rIndex, r);
     double dEdR = (includeForce ? data.forceExpression.evaluate()/r : 0.0);
     double energy = (includeEnergy ? data.energyExpression.evaluate() : 0.0);
     double switchValue = 1.0;

platforms/reference/include/ReferenceCustomDynamics.h

@@ -51,13 +51,14 @@ private:
     std::vector<CustomIntegratorUtilities::Comparison> comparisons;
     std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
     std::vector<int> forceGroupFlags, blockEnd;
-    RealOpenMM energy;
     std::map<std::string, double> energyParamDerivs;
     Lepton::CompiledExpression kineticEnergyExpression;
     bool kineticEnergyNeedsForce;
     CompiledExpressionSet expressionSet;
-    int xIndex, vIndex, mIndex, fIndex, energyIndex, gaussianIndex, uniformIndex;
-    std::vector<int> forceVariableIndex, energyVariableIndex, perDofVariableIndex, stepVariableIndex;
+    double x, v, m, f, energy, gaussian, uniform;
+    int xIndex, vIndex;
+    std::vector<int> perDofVariableIndex, stepVariableIndex;
+    std::vector<double> perDofVariable;
 
     void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals);
     
@@ -65,7 +66,7 @@ private:
     
     void computePerDof(int numberOfAtoms, std::vector<OpenMM::RealVec>& results, const std::vector<OpenMM::RealVec>& atomCoordinates,
                   const std::vector<OpenMM::RealVec>& velocities, const std::vector<OpenMM::RealVec>& forces, const std::vector<RealOpenMM>& masses,
-                  const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
+                  const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression);
     
     void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals);
 

platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp

@@ -78,11 +78,6 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
         string expression;
         integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
     }
-    kineticEnergyExpression = Parser::parse(integrator.getKineticEnergyExpression()).optimize().createCompiledExpression();
-    expressionSet.registerExpression(kineticEnergyExpression);
-    kineticEnergyNeedsForce = false;
-    if (kineticEnergyExpression.getVariables().find("f") != kineticEnergyExpression.getVariables().end())
-        kineticEnergyNeedsForce = true;
 }
 
 /**---------------------------------------------------------------------------------------
@@ -98,6 +93,28 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM
     // Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
     // Context parameters.  Instead, we do it the first time update() or computeKineticEnergy() is called.
 
+    std::map<std::string, double*> variableLocations;
+    variableLocations["x"] = &x;
+    variableLocations["v"] = &v;
+    variableLocations["m"] = &m;
+    variableLocations["f"] = &f;
+    variableLocations["energy"] = &energy;
+    variableLocations["gaussian"] = &gaussian;
+    variableLocations["uniform"] = &uniform;
+    perDofVariable.resize(integrator.getNumPerDofVariables());
+    for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
+        variableLocations[integrator.getPerDofVariableName(i)] = &perDofVariable[i];
+    for (int i = 0; i < 32; i++) {
+        stringstream fname;
+        fname << "f" << i;
+        variableLocations[fname.str()] = &f;
+        stringstream ename;
+        ename << "energy" << i;
+        variableLocations[ename.str()] = &energy;
+    }
+    
+    // Parse the expressions.
+    
     int numSteps = stepType.size();
     vector<int> forceGroup;
     vector<vector<ParsedExpression> > expressions;
@@ -107,37 +124,25 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM
         stepExpressions[i].resize(expressions[i].size());
         for (int j = 0; j < (int) expressions[i].size(); j++) {
             stepExpressions[i][j] = ParsedExpression(replaceDerivFunctions(expressions[i][j].getRootNode(), context)).createCompiledExpression();
+            stepExpressions[i][j].setVariableLocations(variableLocations);
             expressionSet.registerExpression(stepExpressions[i][j]);
         }
         if (stepType[i] == CustomIntegrator::WhileBlockStart)
             blockEnd[blockEnd[i]] = i; // Record where to branch back to.
     }
+    kineticEnergyExpression = Parser::parse(integrator.getKineticEnergyExpression()).optimize().createCompiledExpression();
+    kineticEnergyExpression.setVariableLocations(variableLocations);
+    expressionSet.registerExpression(kineticEnergyExpression);
+    kineticEnergyNeedsForce = false;
+    if (kineticEnergyExpression.getVariables().find("f") != kineticEnergyExpression.getVariables().end())
+        kineticEnergyNeedsForce = true;
 
-    // Record the variable names and flags for the force and energy in each step.
+    // Record the force group flags for each step.
 
     forceGroupFlags.resize(numSteps, -1);
-    fIndex = expressionSet.getVariableIndex("f");
-    energyIndex = expressionSet.getVariableIndex("energy");
-    forceVariableIndex.resize(numSteps, fIndex);
-    energyVariableIndex.resize(numSteps, energyIndex);
-    vector<string> forceGroupName;
-    vector<string> energyGroupName;
-    for (int i = 0; i < 32; i++) {
-        stringstream fname;
-        fname << "f" << i;
-        forceGroupName.push_back(fname.str());
-        stringstream ename;
-        ename << "energy" << i;
-        energyGroupName.push_back(ename.str());
-    }
-    for (int i = 0; i < numSteps; i++) {
-        if (needsForces[i] && forceGroup[i] > -1)
-            forceVariableIndex[i] = expressionSet.getVariableIndex(forceGroupName[forceGroup[i]]);
-        if (needsEnergy[i] && forceGroup[i] > -1)
-            energyVariableIndex[i] = expressionSet.getVariableIndex(energyGroupName[forceGroup[i]]);
+    for (int i = 0; i < numSteps; i++)
         if (forceGroup[i] > -1)
             forceGroupFlags[i] = 1<<forceGroup[i];
-    }
 
     // Build the list of inverse masses.
 
@@ -150,13 +155,10 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM
             inverseMasses[i] = 1.0/masses[i];
     }
 
-    // Record indices of other variables.
+    // Record indices of variables.
 
     xIndex = expressionSet.getVariableIndex("x");
     vIndex = expressionSet.getVariableIndex("v");
-    mIndex = expressionSet.getVariableIndex("m");
-    gaussianIndex = expressionSet.getVariableIndex("gaussian");
-    uniformIndex = expressionSet.getVariableIndex("uniform");
     for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
         perDofVariableIndex.push_back(expressionSet.getVariableIndex(integrator.getPerDofVariableName(i)));
     for (int i = 0; i < stepVariable.size(); i++)
@@ -222,15 +224,14 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
             }
             forcesAreValid = true;
         }
-        expressionSet.setVariable(energyVariableIndex[step], energy);
         
         // Execute the step.
 
         int nextStep = step+1;
         switch (stepType[step]) {
             case CustomIntegrator::ComputeGlobal: {
-                expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
-                expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+                uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
+                gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
                 RealOpenMM result = stepExpressions[step][0].evaluate();
                 globals[stepVariable[step]] = result;
                 expressionSet.setVariable(stepVariableIndex[step], result);
@@ -249,11 +250,11 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
                 }
                 if (results == NULL)
                     throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
-                computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0], forceVariableIndex[step]);
+                computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
                 break;
             }
             case CustomIntegrator::ComputeSum: {
-                computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0], forceVariableIndex[step]);
+                computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
                 RealOpenMM sum = 0.0;
                 for (int j = 0; j < numberOfAtoms; j++)
                     if (masses[j] != 0.0)
@@ -306,22 +307,22 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
 
 void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>& results, const vector<RealVec>& atomCoordinates,
               const vector<RealVec>& velocities, const vector<RealVec>& forces, const vector<RealOpenMM>& masses,
-              const vector<vector<RealVec> >& perDof, const CompiledExpression& expression, int forceIndex) {
+              const vector<vector<RealVec> >& perDof, const CompiledExpression& expression) {
     // Loop over all degrees of freedom.
 
     for (int i = 0; i < numberOfAtoms; i++) {
         if (masses[i] != 0.0) {
-            expressionSet.setVariable(mIndex, masses[i]);
+            m = masses[i];
             for (int j = 0; j < 3; j++) {
                 // Compute the expression.
 
-                expressionSet.setVariable(xIndex, atomCoordinates[i][j]);
-                expressionSet.setVariable(vIndex, velocities[i][j]);
-                expressionSet.setVariable(forceIndex, forces[i][j]);
-                expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
-                expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+                x = atomCoordinates[i][j];
+                v = velocities[i][j];
+                f = forces[i][j];
+                uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
+                gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
                 for (int k = 0; k < (int) perDof.size(); k++)
-                    expressionSet.setVariable(perDofVariableIndex[k], perDof[k][i][j]);
+                    perDofVariable[k] = perDof[k][i][j];
                 results[i][j] = expression.evaluate();
             }
         }
@@ -329,8 +330,8 @@ void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>&
 }
 
 bool ReferenceCustomDynamics::evaluateCondition(int step) {
-    expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
-    expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+    uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
+    gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
     double lhs = stepExpressions[step][0].evaluate();
     double rhs = stepExpressions[step][1].evaluate();
     switch (comparisons[step]) {
@@ -390,7 +391,7 @@ double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& contex
         energy = context.calcForcesAndEnergy(true, true, -1);
         forcesAreValid = true;
     }
-    computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, kineticEnergyExpression, fIndex);
+    computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, kineticEnergyExpression);
     RealOpenMM sum = 0.0;
     for (int j = 0; j < numberOfAtoms; j++)
         if (masses[j] != 0.0)