Merge branch 'master' into qc

serialization/src/CMMotionRemoverProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CMMotionRemoverProxy::CMMotionRemoverProxy() : SerializationProxy("CMMotionRemov
 void CMMotionRemoverProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CMMotionRemover& force = *reinterpret_cast<const CMMotionRemover*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("frequency", force.getFrequency());
 }
 
@@ -53,6 +54,7 @@ void* CMMotionRemoverProxy::deserialize(const SerializationNode& node) const {
     CMMotionRemover* force = NULL;
     try {
         CMMotionRemover* force = new CMMotionRemover(node.getIntProperty("frequency"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         return force;
     }
     catch (...) {

serialization/src/CustomAngleForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomAngleForceProxy::CustomAngleForceProxy() : SerializationProxy("CustomAngle
 void CustomAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomAngleForce& force = *reinterpret_cast<const CustomAngleForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perAngleParams = node.createChildNode("PerAngleParameters");
     for (int i = 0; i < force.getNumPerAngleParameters(); i++) {
@@ -74,6 +75,7 @@ void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
     CustomAngleForce* force = NULL;
     try {
         CustomAngleForce* force = new CustomAngleForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perAngleParams = node.getChildNode("PerAngleParameters");
         for (int i = 0; i < (int) perAngleParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perAngleParams.getChildren()[i];

serialization/src/CustomBondForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomBondForceProxy::CustomBondForceProxy() : SerializationProxy("CustomBondFor
 void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
     for (int i = 0; i < force.getNumPerBondParameters(); i++) {
@@ -74,6 +75,7 @@ void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
     CustomBondForce* force = NULL;
     try {
         CustomBondForce* force = new CustomBondForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
         for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perBondParams.getChildren()[i];

serialization/src/CustomCompoundBondForceProxy.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) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomCompoundBondForceProxy::CustomCompoundBondForceProxy() : SerializationProx
 void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomCompoundBondForce& force = *reinterpret_cast<const CustomCompoundBondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("particles", force.getNumParticlesPerBond());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
@@ -84,6 +85,7 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
     CustomCompoundBondForce* force = NULL;
     try {
         CustomCompoundBondForce* force = new CustomCompoundBondForce(node.getIntProperty("particles"), node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
         for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perBondParams.getChildren()[i];

serialization/src/CustomExternalForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomExternalForceProxy::CustomExternalForceProxy() : SerializationProxy("Custo
 void CustomExternalForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomExternalForce& force = *reinterpret_cast<const CustomExternalForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
     for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
@@ -74,6 +75,7 @@ void* CustomExternalForceProxy::deserialize(const SerializationNode& node) const
     CustomExternalForce* force = NULL;
     try {
         CustomExternalForce* force = new CustomExternalForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
         for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perParticleParams.getChildren()[i];

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomGBForceProxy::CustomGBForceProxy() : SerializationProxy("CustomGBForce") {
 void CustomGBForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomGBForce& force = *reinterpret_cast<const CustomGBForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
     SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
@@ -97,6 +98,7 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
     CustomGBForce* force = NULL;
     try {
         CustomGBForce* force = new CustomGBForce();
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((CustomGBForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");

serialization/src/CustomHbondForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomHbondForceProxy::CustomHbondForceProxy() : SerializationProxy("CustomHbond
 void CustomHbondForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomHbondForce& force = *reinterpret_cast<const CustomHbondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
@@ -102,6 +103,7 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
     CustomHbondForce* force = NULL;
     try {
         CustomHbondForce* force = new CustomHbondForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((CustomHbondForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         const SerializationNode& perDonorParams = node.getChildNode("PerDonorParameters");

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:                                                              *
  *                                                                            *
@@ -44,9 +44,13 @@ CustomNonbondedForceProxy::CustomNonbondedForceProxy() : SerializationProxy("Cus
 void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomNonbondedForce& force = *reinterpret_cast<const CustomNonbondedForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
+    node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
+    node.setBoolProperty("useLongRangeCorrection", force.getUseLongRangeCorrection());
     SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
     for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
         perParticleParams.createChildNode("Parameter").setStringProperty("name", force.getPerParticleParameterName(i));
@@ -76,6 +80,20 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
     SerializationNode& functions = node.createChildNode("Functions");
     for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
         functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
+
+    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);
+    }
 }
 
 void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) const {
@@ -84,8 +102,12 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
     CustomNonbondedForce* force = NULL;
     try {
         CustomNonbondedForce* force = new CustomNonbondedForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((CustomNonbondedForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        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];
@@ -121,7 +143,7 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
             }
             else {
                 // This is an old file created before TabulatedFunction existed.
-                
+
                 const SerializationNode& valuesNode = function.getChildNode("Values");
                 vector<double> values;
                 for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
@@ -129,6 +151,28 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
+        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;
     }
     catch (...) {

serialization/src/CustomTorsionForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ CustomTorsionForceProxy::CustomTorsionForceProxy() : SerializationProxy("CustomT
 void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CustomTorsionForce& force = *reinterpret_cast<const CustomTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perTorsionParams = node.createChildNode("PerTorsionParameters");
     for (int i = 0; i < force.getNumPerTorsionParameters(); i++) {
@@ -74,6 +75,7 @@ void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const
     CustomTorsionForce* force = NULL;
     try {
         CustomTorsionForce* force = new CustomTorsionForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& perTorsionParams = node.getChildNode("PerTorsionParameters");
         for (int i = 0; i < (int) perTorsionParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perTorsionParams.getChildren()[i];

serialization/src/GBSAOBCForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ GBSAOBCForceProxy::GBSAOBCForceProxy() : SerializationProxy("GBSAOBCForce") {
 void GBSAOBCForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const GBSAOBCForce& force = *reinterpret_cast<const GBSAOBCForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
     node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
@@ -61,6 +62,7 @@ void* GBSAOBCForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     GBSAOBCForce* force = new GBSAOBCForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((GBSAOBCForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));

serialization/src/GBVIForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ GBVIForceProxy::GBVIForceProxy() : SerializationProxy("GBVIForce") {
 void GBVIForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 2);
     const GBVIForce& force = *reinterpret_cast<const GBVIForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setIntProperty("scalingMethod", (int) force.getBornRadiusScalingMethod());
     node.setDoubleProperty("quinticLowerLimitFactor", force.getQuinticLowerLimitFactor());
@@ -71,6 +72,7 @@ void* GBVIForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     GBVIForce* force = new GBVIForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((GBVIForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
         force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));

serialization/src/HarmonicAngleForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ HarmonicAngleForceProxy::HarmonicAngleForceProxy() : SerializationProxy("Harmoni
 void HarmonicAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const HarmonicAngleForce& force = *reinterpret_cast<const HarmonicAngleForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& bonds = node.createChildNode("Angles");
     for (int i = 0; i < force.getNumAngles(); i++) {
         int particle1, particle2, particle3;
@@ -58,6 +59,7 @@ void* HarmonicAngleForceProxy::deserialize(const SerializationNode& node) const
         throw OpenMMException("Unsupported version number");
     HarmonicAngleForce* force = new HarmonicAngleForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& angles = node.getChildNode("Angles");
         for (int i = 0; i < (int) angles.getChildren().size(); i++) {
             const SerializationNode& angle = angles.getChildren()[i];

serialization/src/HarmonicBondForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ HarmonicBondForceProxy::HarmonicBondForceProxy() : SerializationProxy("HarmonicB
 void HarmonicBondForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const HarmonicBondForce& force = *reinterpret_cast<const HarmonicBondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& bonds = node.createChildNode("Bonds");
     for (int i = 0; i < force.getNumBonds(); i++) {
         int particle1, particle2;
@@ -58,6 +59,7 @@ void* HarmonicBondForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     HarmonicBondForce* force = new HarmonicBondForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& bonds = node.getChildNode("Bonds");
         for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
             const SerializationNode& bond = bonds.getChildren()[i];

serialization/src/MonteCarloBarostatProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ MonteCarloBarostatProxy::MonteCarloBarostatProxy() : SerializationProxy("MonteCa
 void MonteCarloBarostatProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const MonteCarloBarostat& force = *reinterpret_cast<const MonteCarloBarostat*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("pressure", force.getDefaultPressure());
     node.setDoubleProperty("temperature", force.getTemperature());
     node.setIntProperty("frequency", force.getFrequency());
@@ -56,6 +57,7 @@ void* MonteCarloBarostatProxy::deserialize(const SerializationNode& node) const
     MonteCarloBarostat* force = NULL;
     try {
         MonteCarloBarostat* force = new MonteCarloBarostat(node.getDoubleProperty("pressure"), node.getDoubleProperty("temperature"), node.getIntProperty("frequency"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
         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:                                                              *
  *                                                                            *
@@ -44,11 +44,22 @@ NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce"
 void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
+    node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
     node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
     node.setDoubleProperty("rfDielectric", force.getReactionFieldDielectric());
     node.setIntProperty("dispersionCorrection", force.getUseDispersionCorrection());
+    double alpha;
+    int nx, ny, nz;
+    force.getPMEParameters(alpha, nx, ny, nz);
+    node.setDoubleProperty("alpha", alpha);
+    node.setIntProperty("nx", nx);
+    node.setIntProperty("ny", ny);
+    node.setIntProperty("nz", nz);
+    node.setIntProperty("recipForceGroup", force.getReciprocalSpaceForceGroup());
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge, sigma, epsilon;
@@ -69,11 +80,20 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     NonbondedForce* force = new NonbondedForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
         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));
         const SerializationNode& particles = node.getChildNode("Particles");
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {
             const SerializationNode& particle = particles.getChildren()[i];

serialization/src/PeriodicTorsionForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ PeriodicTorsionForceProxy::PeriodicTorsionForceProxy() : SerializationProxy("Per
 void PeriodicTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const PeriodicTorsionForce& force = *reinterpret_cast<const PeriodicTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int particle1, particle2, particle3, particle4, periodicity;
@@ -58,6 +59,7 @@ void* PeriodicTorsionForceProxy::deserialize(const SerializationNode& node) cons
         throw OpenMMException("Unsupported version number");
     PeriodicTorsionForce* force = new PeriodicTorsionForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& torsions = node.getChildNode("Torsions");
         for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
             const SerializationNode& torsion = torsions.getChildren()[i];

serialization/src/RBTorsionForceProxy.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:                                                              *
  *                                                                            *
@@ -44,6 +44,7 @@ RBTorsionForceProxy::RBTorsionForceProxy() : SerializationProxy("RBTorsionForce"
 void RBTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const RBTorsionForce& force = *reinterpret_cast<const RBTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int particle1, particle2, particle3, particle4;
@@ -58,6 +59,7 @@ void* RBTorsionForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     RBTorsionForce* force = new RBTorsionForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& torsions = node.getChildNode("Torsions");
         for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
             const SerializationNode& torsion = torsions.getChildren()[i];

serialization/src/SerializationNode.cpp

@@ -121,6 +121,32 @@ SerializationNode& SerializationNode::setIntProperty(const string& name, int val
     return *this;
 }
 
+
+bool SerializationNode::getBoolProperty(const string& name) const {
+    map<string, string>::const_iterator iter = properties.find(name);
+    if (iter == properties.end())
+        throw OpenMMException("Unknown property '"+name+"' in node '"+getName()+"'");
+    bool value;
+    stringstream(iter->second) >> value;
+    return value;
+}
+
+bool SerializationNode::getBoolProperty(const string& name, bool defaultValue) const {
+    map<string, string>::const_iterator iter = properties.find(name);
+    if (iter == properties.end())
+        return defaultValue;
+    bool value;
+    stringstream(iter->second) >> value;
+    return value;
+}
+
+SerializationNode& SerializationNode::setBoolProperty(const string& name, bool value) {
+    stringstream s;
+    s << value;
+    properties[name] = s.str();
+    return *this;
+}
+
 double SerializationNode::getDoubleProperty(const string& name) const {
     map<string, string>::const_iterator iter = properties.find(name);
     if (iter == properties.end())

serialization/src/SystemProxy.cpp

@@ -67,6 +67,18 @@ void SystemProxy::serialize(const void* object, SerializationNode& node) const {
                 const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
                 particle.createChildNode("OutOfPlaneSite").setIntProperty("p1", site.getParticle(0)).setIntProperty("p2", site.getParticle(1)).setIntProperty("p3", site.getParticle(2)).setDoubleProperty("w12", site.getWeight12()).setDoubleProperty("w13", site.getWeight13()).setDoubleProperty("wc", site.getWeightCross());
             }
+            else if (typeid(system.getVirtualSite(i)) == typeid(LocalCoordinatesSite)) {
+                const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
+                Vec3 wo = site.getOriginWeights();
+                Vec3 wx = site.getXWeights();
+                Vec3 wy = site.getYWeights();
+                Vec3 p = site.getLocalPosition();
+                particle.createChildNode("LocalCoordinatesSite").setIntProperty("p1", site.getParticle(0)).setIntProperty("p2", site.getParticle(1)).setIntProperty("p3", site.getParticle(2)).
+                        setDoubleProperty("wo1", wo[0]).setDoubleProperty("wo2", wo[1]).setDoubleProperty("wo3", wo[2]).
+                        setDoubleProperty("wx1", wx[0]).setDoubleProperty("wx2", wx[1]).setDoubleProperty("wx3", wx[2]).
+                        setDoubleProperty("wy1", wy[0]).setDoubleProperty("wy2", wy[1]).setDoubleProperty("wy3", wy[2]).
+                        setDoubleProperty("pos1", p[0]).setDoubleProperty("pos2", p[1]).setDoubleProperty("pos3", p[2]);
+            }
         }
     }
     SerializationNode& constraints = node.createChildNode("Constraints");
@@ -105,6 +117,13 @@ void* SystemProxy::deserialize(const SerializationNode& node) const {
                     system->setVirtualSite(i, new ThreeParticleAverageSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), vsite.getDoubleProperty("w1"), vsite.getDoubleProperty("w2"), vsite.getDoubleProperty("w3")));
                 else if (vsite.getName() == "OutOfPlaneSite")
                     system->setVirtualSite(i, new OutOfPlaneSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), vsite.getDoubleProperty("w12"), vsite.getDoubleProperty("w13"), vsite.getDoubleProperty("wc")));
+                else if (vsite.getName() == "LocalCoordinatesSite") {
+                    Vec3 wo(vsite.getDoubleProperty("wo1"), vsite.getDoubleProperty("wo2"), vsite.getDoubleProperty("wo3"));
+                    Vec3 wx(vsite.getDoubleProperty("wx1"), vsite.getDoubleProperty("wx2"), vsite.getDoubleProperty("wx3"));
+                    Vec3 wy(vsite.getDoubleProperty("wy1"), vsite.getDoubleProperty("wy2"), vsite.getDoubleProperty("wy3"));
+                    Vec3 p(vsite.getDoubleProperty("pos1"), vsite.getDoubleProperty("pos2"), vsite.getDoubleProperty("pos3"));
+                    system->setVirtualSite(i, new LocalCoordinatesSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), wo, wx, wy, p));
+                }
             }
         }
         const SerializationNode& constraints = node.getChildNode("Constraints");

serialization/tests/TestSerializeAndersenThermostat.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:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     AndersenThermostat force(250.0, 0.2);
+    force.setForceGroup(3);
     force.setRandomNumberSeed(3);
 
     // Serialize and then deserialize it.
@@ -53,6 +54,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     AndersenThermostat& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getDefaultCollisionFrequency(), force2.getDefaultCollisionFrequency());
     ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());