Merge pull request #1547 from peastman/paramderivs

Energy derivatives with respect to global parameters

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

 
-/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -44,23 +44,20 @@ using namespace OpenMM;
    --------------------------------------------------------------------------------------- */
 
 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) {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn";
-
-   // ---------------------------------------------------------------------------------------
-
-    energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
-    forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
+        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames,
+        const vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
+            cutoff(false), useSwitch(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression),
+            paramNames(parameterNames), 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");
     for (int i = 0; i < (int) paramNames.size(); i++) {
         for (int j = 1; j < 3; j++) {
             stringstream name;
             name << paramNames[i] << j;
-            energyParticleParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, name.str()));
-            forceParticleParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, name.str()));
+            particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
         }
     }
 }
@@ -167,12 +164,10 @@ 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) {
+                                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
 
-    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);
-    }
+    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
+        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
     if (interactionGroups.size() > 0) {
         // The user has specified interaction groups, so compute only the requested interactions.
         
@@ -186,12 +181,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
                     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++) {
-                        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]);
+                        expressionSet.setVariable(particleParamIndex[j*2], atomParameters[*atom1][j]);
+                        expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[*atom2][j]);
                     }
-                    calculateOneIxn(*atom1, *atom2, atomCoordinates, forces, energyByAtom, totalEnergy);
+                    calculateOneIxn(*atom1, *atom2, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
                 }
             }
         }
@@ -202,12 +195,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
         for (int i = 0; i < (int) neighborList->size(); i++) {
             OpenMM::AtomPair pair = (*neighborList)[i];
             for (int j = 0; j < (int) paramNames.size(); 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]);
+                expressionSet.setVariable(particleParamIndex[j*2], atomParameters[pair.first][j]);
+                expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[pair.second][j]);
             }
-            calculateOneIxn(pair.first, pair.second, atomCoordinates, forces, energyByAtom, totalEnergy);
+            calculateOneIxn(pair.first, pair.second, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
         }
     }
     else {
@@ -217,12 +208,10 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
             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++) {
-                        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]);
+                        expressionSet.setVariable(particleParamIndex[j*2], atomParameters[ii][j]);
+                        expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[jj][j]);
                     }
-                    calculateOneIxn(ii, jj, atomCoordinates, forces, energyByAtom, totalEnergy);
+                    calculateOneIxn(ii, jj, atomCoordinates, forces, energyByAtom, totalEnergy, energyParamDerivs);
                 }
             }
         }
@@ -244,24 +233,7 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
      --------------------------------------------------------------------------------------- */
 
 void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
-                        RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) {
-
-    // ---------------------------------------------------------------------------------------
-
-    static const std::string methodName = "\nReferenceCustomNonbondedIxn::calculateOneIxn";
-
-    // ---------------------------------------------------------------------------------------
-
-    // constants -- reduce Visual Studio warnings regarding conversions between float & double
-
-    static const RealOpenMM zero        =  0.0;
-    static const RealOpenMM one         =  1.0;
-    static const RealOpenMM two         =  2.0;
-    static const RealOpenMM three       =  3.0;
-    static const RealOpenMM six         =  6.0;
-    static const RealOpenMM twelve      = 12.0;
-    static const RealOpenMM oneM        = -1.0;
-
+                        RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
     // get deltaR, R2, and R between 2 atoms
 
     RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
@@ -275,14 +247,14 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec
 
     // accumulate forces
 
-    ReferenceForce::setVariable(energyR, r);
-    ReferenceForce::setVariable(forceR, r);
+    expressionSet.setVariable(rIndex, r);
     RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate()/(deltaR[ReferenceForce::RIndex]));
     RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
+    RealOpenMM switchValue = 1.0;
     if (useSwitch) {
         if (r > switchingDistance) {
             RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
-            RealOpenMM switchValue = 1+t*t*t*(-10+t*(15-t*6));
+            switchValue = 1+t*t*t*(-10+t*(15-t*6));
             RealOpenMM switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
             dEdR = switchValue*dEdR + energy*switchDeriv/r;
             energy *= switchValue;
@@ -293,6 +265,8 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec
        forces[ii][kk]   += force;
        forces[jj][kk]   -= force;
     }
+    for (int i = 0; i < energyParamDerivExpressions.size(); i++)
+        energyParamDerivs[i] += switchValue*energyParamDerivExpressions[i].evaluate();
 
     // accumulate energies
 

platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp

@@ -38,20 +38,19 @@ using namespace OpenMM;
    --------------------------------------------------------------------------------------- */
 
 ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression,
-        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
-        energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
-
-    energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
-    forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
+        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters,
+        const vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
+        energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false), energyParamDerivExpressions(energyParamDerivExpressions) {
+    expressionSet.registerExpression(this->energyExpression);
+    expressionSet.registerExpression(this->forceExpression);
+    for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
+        expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
+    thetaIndex = expressionSet.getVariableIndex("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);
-    }
+    for (int i = 0; i < (int) numParameters; i++)
+        torsionParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
+    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
+        expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
 }
 
 /**---------------------------------------------------------------------------------------
@@ -86,18 +85,10 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
                                                 vector<RealVec>& atomCoordinates,
                                                 RealOpenMM* parameters,
                                                 vector<RealVec>& forces,
-                                                RealOpenMM* totalEnergy) const {
-
-   static const std::string methodName = "\nReferenceCustomTorsionIxn::calculateTorsionIxn";
-
-   static const RealOpenMM zero        = 0.0;
-   static const RealOpenMM one         = 1.0;
-
+                                                RealOpenMM* totalEnergy, double* energyParamDerivs) {
    RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
-   for (int i = 0; i < numParameters; i++) {
-       ReferenceForce::setVariable(energyParams[i], parameters[i]);
-       ReferenceForce::setVariable(forceParams[i], parameters[i]);
-   }
+   for (int i = 0; i < numParameters; i++)
+       expressionSet.setVariable(torsionParamIndex[i], parameters[i]);
 
    // ---------------------------------------------------------------------------------------
 
@@ -130,8 +121,7 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
    RealOpenMM dotDihedral;
    RealOpenMM signOfAngle;
    RealOpenMM angle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2], crossProduct, &dotDihedral, deltaR[0], &signOfAngle, 1);
-   ReferenceForce::setVariable(energyTheta, angle);
-   ReferenceForce::setVariable(forceTheta, angle);
+   expressionSet.setVariable(thetaIndex, angle);
 
    // evaluate delta angle, dE/d(angle)
 
@@ -174,6 +164,11 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
       forces[atomDIndex][ii] += internalF[3][ii];
    }
 
+   // Record parameter derivatives.
+
+   for (int i = 0; i < energyParamDerivExpressions.size(); i++)
+       energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
+
    // accumulate energies
 
    if (totalEnergy != NULL)

platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp

@@ -74,7 +74,7 @@ void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
                                                 vector<RealVec>& atomCoordinates,
                                                 RealOpenMM* parameters,
                                                 vector<RealVec>& forces,
-                                                RealOpenMM* totalEnergy) const {
+                                                RealOpenMM* totalEnergy, double* energyParamDerivs) {
 
    static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
 

platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -81,7 +81,7 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14() {
 
 void ReferenceLJCoulomb14::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
                                      RealOpenMM* parameters, vector<RealVec>& forces,
-                                     RealOpenMM* totalEnergy) const {
+                                     RealOpenMM* totalEnergy, double* energyParamDerivs) {
 
    static const std::string methodName = "\nReferenceLJCoulomb14::calculateBondIxn";
 

platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp

@@ -75,7 +75,7 @@ void ReferenceProperDihedralBond::calculateBondIxn(int* atomIndices,
                                                    vector<RealVec>& atomCoordinates,
                                                    RealOpenMM* parameters,
                                                    vector<RealVec>& forces,
-                                                   RealOpenMM* totalEnergy) const {
+                                                   RealOpenMM* totalEnergy, double* energyParamDerivs) {
 
    static const std::string methodName = "\nReferenceProperDihedralBond::calculateBondIxn";
 

platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp

@@ -73,7 +73,7 @@ void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
                                                vector<RealVec>& atomCoordinates,
                                                RealOpenMM* parameters,
                                                vector<RealVec>& forces,
-                                               RealOpenMM* totalEnergy) const {
+                                               RealOpenMM* totalEnergy, double* energyParamDerivs) {
 
    static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";
 

serialization/src/CustomAngleForceProxy.cpp

@@ -42,7 +42,7 @@ CustomAngleForceProxy::CustomAngleForceProxy() : SerializationProxy("CustomAngle
 }
 
 void CustomAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const CustomAngleForce& force = *reinterpret_cast<const CustomAngleForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
@@ -55,6 +55,10 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& angles = node.createChildNode("Angles");
     for (int i = 0; i < force.getNumAngles(); i++) {
         int p1, p2, p3;
@@ -72,7 +76,7 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
 
 void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     CustomAngleForce* force = NULL;
     try {
@@ -90,6 +94,13 @@ void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 2) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& angles = node.getChildNode("Angles");
         vector<double> params(force->getNumPerAngleParameters());
         for (int i = 0; i < (int) angles.getChildren().size(); i++) {

serialization/src/CustomBondForceProxy.cpp

@@ -42,7 +42,7 @@ CustomBondForceProxy::CustomBondForceProxy() : SerializationProxy("CustomBondFor
 }
 
 void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
@@ -55,6 +55,10 @@ void CustomBondForceProxy::serialize(const void* object, SerializationNode& node
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& bonds = node.createChildNode("Bonds");
     for (int i = 0; i < force.getNumBonds(); i++) {
         int p1, p2;
@@ -72,7 +76,7 @@ void CustomBondForceProxy::serialize(const void* object, SerializationNode& node
 
 void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     CustomBondForce* force = NULL;
     try {
@@ -90,6 +94,13 @@ void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 2) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& bonds = node.getChildNode("Bonds");
         vector<double> params(force->getNumPerBondParameters());
         for (int i = 0; i < (int) bonds.getChildren().size(); i++) {

serialization/src/CustomCentroidBondForceProxy.cpp

@@ -42,7 +42,7 @@ CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProx
 }
 
 void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
@@ -56,6 +56,10 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& groups = node.createChildNode("Groups");
     for (int i = 0; i < force.getNumGroups(); i++) {
         vector<int> particles;
@@ -95,7 +99,7 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
 
 void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     CustomCentroidBondForce* force = NULL;
     try {
@@ -113,6 +117,13 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 2) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& groups = node.getChildNode("Groups");
         for (int i = 0; i < (int) groups.getChildren().size(); i++) {
             const SerializationNode& group = groups.getChildren()[i];

serialization/src/CustomCompoundBondForceProxy.cpp

@@ -42,7 +42,7 @@ CustomCompoundBondForceProxy::CustomCompoundBondForceProxy() : SerializationProx
 }
 
 void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const CustomCompoundBondForce& force = *reinterpret_cast<const CustomCompoundBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
@@ -56,6 +56,10 @@ void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNo
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& bonds = node.createChildNode("Bonds");
     for (int i = 0; i < force.getNumBonds(); i++) {
         vector<int> particles;
@@ -82,7 +86,7 @@ void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNo
 
 void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     CustomCompoundBondForce* force = NULL;
     try {
@@ -100,6 +104,13 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 2) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& bonds = node.getChildNode("Bonds");
         vector<int> particles(force->getNumParticlesPerBond());
         vector<double> params(force->getNumPerBondParameters());

serialization/src/CustomGBForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,7 +42,7 @@ CustomGBForceProxy::CustomGBForceProxy() : SerializationProxy("CustomGBForce") {
 }
 
 void CustomGBForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomGBForce& force = *reinterpret_cast<const CustomGBForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
@@ -55,6 +55,10 @@ void CustomGBForceProxy::serialize(const void* object, SerializationNode& node)
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& computedValues = node.createChildNode("ComputedValues");
     for (int i = 0; i < force.getNumComputedValues(); i++) {
         string name, expression;
@@ -93,7 +97,8 @@ void CustomGBForceProxy::serialize(const void* object, SerializationNode& node)
 }
 
 void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomGBForce* force = NULL;
     try {
@@ -111,6 +116,13 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 1) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& computedValues = node.getChildNode("ComputedValues");
         for (int i = 0; i < (int) computedValues.getChildren().size(); i++) {
             const SerializationNode& value = computedValues.getChildren()[i];

serialization/src/CustomNonbondedForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,7 +42,7 @@ CustomNonbondedForceProxy::CustomNonbondedForceProxy() : SerializationProxy("Cus
 }
 
 void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomNonbondedForce& force = *reinterpret_cast<const CustomNonbondedForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
@@ -59,6 +59,10 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
         vector<double> params;
@@ -97,7 +101,8 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomNonbondedForce* force = NULL;
     try {
@@ -118,6 +123,13 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 1) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& particles = node.getChildNode("Particles");
         vector<double> params(force->getNumPerParticleParameters());
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {

serialization/src/CustomTorsionForceProxy.cpp

@@ -42,7 +42,7 @@ CustomTorsionForceProxy::CustomTorsionForceProxy() : SerializationProxy("CustomT
 }
 
 void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const CustomTorsionForce& force = *reinterpret_cast<const CustomTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
@@ -55,6 +55,10 @@ void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& n
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
     }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int p1, p2, p3, p4;
@@ -72,7 +76,7 @@ void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& n
 
 void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     CustomTorsionForce* force = NULL;
     try {
@@ -90,6 +94,13 @@ void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const
             const SerializationNode& parameter = globalParams.getChildren()[i];
             force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
         }
+        if (version > 2) {
+            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+            for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
+                const SerializationNode& parameter = energyDerivs.getChildren()[i];
+                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+            }
+        }
         const SerializationNode& torsions = node.getChildNode("Torsions");
         vector<double> params(force->getNumPerTorsionParameters());
         for (int i = 0; i < (int) torsions.getChildren().size(); i++) {

serialization/tests/TestSerializeCustomAngleForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerAngleParameter("z");
+    force.addEnergyParameterDerivative("y");
     vector<double> params(1);
     params[0] = 1.0;
     force.addAngle(1, 2, 3, params);
@@ -74,6 +75,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
     for (int i = 0; i < force.getNumAngles(); i++) {

serialization/tests/TestSerializeCustomBondForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerBondParameter("z");
+    force.addEnergyParameterDerivative("y");
     vector<double> params(1);
     params[0] = 1.0;
     force.addBond(1, 2, params);
@@ -74,6 +75,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {

serialization/tests/TestSerializeCustomCentroidBondForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerBondParameter("z");
+    force.addEnergyParameterDerivative("y");
     for (int i = 0; i < 3; i++) {
         vector<int> particles;
         vector<double> weights;
@@ -99,6 +100,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumGroups(), force2.getNumGroups());
     for (int i = 0; i < force.getNumGroups(); i++) {

serialization/tests/TestSerializeCustomCompoundBondForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerBondParameter("z");
+    force.addEnergyParameterDerivative("y");
     vector<int> particles(3);
     vector<double> params(1);
     particles[0] = 0;
@@ -89,6 +90,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {

serialization/tests/TestSerializeCustomGBForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,6 +48,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerParticleParameter("z");
+    force.addEnergyParameterDerivative("y");
     force.addComputedValue("a", "x+1", CustomGBForce::ParticlePairNoExclusions);
     force.addComputedValue("b", "y-1", CustomGBForce::SingleParticle);
     force.addEnergyTerm("a*b", CustomGBForce::SingleParticle);
@@ -86,6 +87,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.getNumComputedValues(), force2.getNumComputedValues());
     for (int i = 0; i < force.getNumComputedValues(); i++) {
         string name1, name2, expression1, expression2;

serialization/tests/TestSerializeCustomNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,6 +51,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerParticleParameter("z");
+    force.addEnergyParameterDerivative("y");
     vector<double> params(1);
     params[0] = 1.0;
     force.addParticle(params);
@@ -94,6 +95,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
     for (int i = 0; i < force.getNumParticles(); i++) {
         vector<double> params1, params2;

serialization/tests/TestSerializeCustomTorsionForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerTorsionParameter("z");
+    force.addEnergyParameterDerivative("y");
     vector<double> params(1);
     params[0] = 1.0;
     force.addTorsion(1, 2, 3, 4, params);
@@ -74,6 +75,9 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
     ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {