Merge pull request #412 from peastman/master

Cleanup to the recent serialization code changes

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -82,16 +82,16 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
 
     SerializationNode& interactionGroups = node.createChildNode("InteractionGroups");
     for (int i = 0; i < force.getNumInteractionGroups(); i++) {
-      SerializationNode& interactionGroup = interactionGroups.createChildNode("InteractionGroup");
-      std::set<int> set1;
-      std::set<int> set2;
-      force.getInteractionGroupParameters(i, set1, set2);
-      SerializationNode& set1node = interactionGroup.createChildNode("Set1");
-      for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
-          set1node.createChildNode("Particle").setIntProperty("index", *it);
-      SerializationNode& set2node = interactionGroup.createChildNode("Set2");
-      for (std::set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
-          set2node.createChildNode("Particle").setIntProperty("index", *it);
+        SerializationNode& interactionGroup = interactionGroups.createChildNode("InteractionGroup");
+        std::set<int> set1;
+        std::set<int> set2;
+        force.getInteractionGroupParameters(i, set1, set2);
+        SerializationNode& set1node = interactionGroup.createChildNode("Set1");
+        for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
+            set1node.createChildNode("Particle").setIntProperty("index", *it);
+        SerializationNode& set2node = interactionGroup.createChildNode("Set2");
+        for (std::set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
+            set2node.createChildNode("Particle").setIntProperty("index", *it);
     }
 }
 
@@ -102,7 +102,7 @@ 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", 1.0));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
         force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
         force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
@@ -149,25 +149,27 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
-        // 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");
-            std::set<int> set1;
-            for (int j = 0; j < (int) set1node.getChildren().size(); j++)
-              set1.insert(set1node.getChildren()[j].getIntProperty("index"));
-            // Get set 2.
-            const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
-            std::set<int> set2;
-            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
+        bool hasInteractionGroups = false; // Older files will be missing this block.
+        for (int i = 0; i < (int) node.getChildren().size(); i++) {
+            if (node.getChildren()[i].getName() == "InteractionGroups")
+                hasInteractionGroups = true;
+        }
+        if (hasInteractionGroups) {
+            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");
+                std::set<int> set1;
+                for (int j = 0; j < (int) set1node.getChildren().size(); j++)
+                    set1.insert(set1node.getChildren()[j].getIntProperty("index"));
+                // Get set 2.
+                const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
+                std::set<int> set2;
+                for (int j = 0; j < (int) set2node.getChildren().size(); j++)
+                    set2.insert(set2node.getChildren()[j].getIntProperty("index"));
+                force->addInteractionGroup(set1, set2);
+            }
         }
         return force;
     }

serialization/src/NonbondedForceProxy.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -80,20 +80,18 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
     NonbondedForce* force = new NonbondedForce();
     try {
         force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff",1.0));
-        force->setUseSwitchingFunction(node.getBoolProperty("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",0.0);
-        nx = node.getIntProperty("nx",0);
-        ny = node.getIntProperty("ny",0);
-        nz = node.getIntProperty("nz",0);
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
+        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
+        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
+        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
+        double alpha = node.getDoubleProperty("alpha", 0.0);
+        int nx = node.getIntProperty("nx", 0);
+        int ny = node.getIntProperty("ny", 0);
+        int nz = node.getIntProperty("nz", 0);
         force->setPMEParameters(alpha, nx, ny, nz);
-        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup",-1));
+        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];

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -66,6 +66,7 @@ void testSerialization() {
     std::set<int> set1, set2;
     set1.insert(0);
     set2.insert(1);
+    set2.insert(2);
     force.addInteractionGroup(set1, set2);
 
     // Serialize and then deserialize it.