Merge pull request #413 from peastman/master

Include force groups when serializing forces

serialization/src/AndersenThermostatProxy.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:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void AndersenThermostatProxy::serialize(const void* object, SerializationNode& n
     node.setDoubleProperty("temperature", force.getDefaultTemperature());
     node.setDoubleProperty("frequency", force.getDefaultCollisionFrequency());
     node.setIntProperty("randomSeed", force.getRandomNumberSeed());
+    node.setIntProperty("forceGroup", force.getForceGroup());
 }
 
 void* AndersenThermostatProxy::deserialize(const SerializationNode& node) const {
@@ -55,6 +56,7 @@ void* AndersenThermostatProxy::deserialize(const SerializationNode& node) const
     AndersenThermostat* force = NULL;
     try {
         AndersenThermostat* force = new AndersenThermostat(node.getDoubleProperty("temperature"), node.getDoubleProperty("frequency"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
         return force;
     }

serialization/src/CMAPTorsionForceProxy.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 @@ CMAPTorsionForceProxy::CMAPTorsionForceProxy() : SerializationProxy("CMAPTorsion
 void CMAPTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const CMAPTorsionForce& force = *reinterpret_cast<const CMAPTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& maps = node.createChildNode("Maps");
     for (int i = 0; i < force.getNumMaps(); i++) {
         int size;
@@ -66,6 +67,7 @@ void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     CMAPTorsionForce* force = new CMAPTorsionForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& maps = node.getChildNode("Maps");
         for (int i = 0; i < (int) maps.getChildren().size(); i++) {
             const SerializationNode& map = maps.getChildren()[i];

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

@@ -44,6 +44,7 @@ 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());
@@ -101,6 +102,7 @@ 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));

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

@@ -44,6 +44,7 @@ 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());
@@ -79,6 +80,7 @@ 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));

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/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());