Added defaults for backward compatibility.

serialization/src/CustomNonbondedForceProxy.cpp

@@ -102,10 +102,10 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
     try {
         CustomNonbondedForce* force = new CustomNonbondedForce(node.getStringProperty("energy"));
         force->setNonbondedMethod((CustomNonbondedForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction"));
-        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));
-        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff", 1.0));
+        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
+        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
         for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perParticleParams.getChildren()[i];
@@ -149,8 +149,10 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
-        const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
-        for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
+        // Catch exceptions if InteractionGroups node is missing, in order to give backwards compatibility.
+        try{
+          const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
+          for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
             const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
             // Get set 1.
             const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
@@ -163,6 +165,9 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
             for (int j = 0; j < (int) set2node.getChildren().size(); j++)
               set2.insert(set2node.getChildren()[j].getIntProperty("index"));
             force->addInteractionGroup(set1, set2);
+          }
+        } catch (...) {
+          // do nothing to allow backwards-compatibility
         }
         return force;
     }

serialization/src/NonbondedForceProxy.cpp

@@ -80,20 +80,20 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
     NonbondedForce* force = new NonbondedForce();
     try {
         force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setUseSwitchingFunction(node.getDoubleProperty("useSwitchingFunction"));
-        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));
-        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
-        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
-        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff",1.0));
+        force->setUseSwitchingFunction(node.getDoubleProperty("useSwitchingFunction",false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance",-1.0));
+        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance",5e-4));
+        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric",78.3));
+        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection",true));
         double alpha;
         int nx, ny, nz;
-        alpha = node.getDoubleProperty("alpha");
-        nx = node.getIntProperty("nx");
-        ny = node.getIntProperty("ny");
-        nz = node.getIntProperty("nz");
+        alpha = node.getDoubleProperty("alpha",0.0);
+        nx = node.getIntProperty("nx",0);
+        ny = node.getIntProperty("ny",0);
+        nz = node.getIntProperty("nz",0);
         force->setPMEParameters(alpha, nx, ny, nz);
-        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup"));
+        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup",-1));
         const SerializationNode& particles = node.getChildNode("Particles");
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {
             const SerializationNode& particle = particles.getChildren()[i];