Merge branch 'master' into gayberne

plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp

@@ -183,7 +183,7 @@ int main(int argc, char* argv[]) {
     try {
         registerDrudeCudaKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", string(argv[1]));
+            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
         testSinglePair();
         testWater();
     }

plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp

@@ -110,7 +110,7 @@ void testWater() {
     State state = context.getState(State::Energy);
     double initialEnergy;
     int numSteps = 1000;
-    double maxNorm = (platform.getPropertyValue(context, "CudaPrecision") == "double" ? 1.0 : 5.0);
+    double maxNorm = (platform.getPropertyValue(context, "Precision") == "double" ? 1.0 : 5.0);
     for (int i = 0; i < numSteps; i++) {
         integ.step(1);
         state = context.getState(State::Energy | State::Forces);
@@ -131,7 +131,7 @@ int main(int argc, char* argv[]) {
     try {
         registerDrudeCudaKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", string(argv[1]));
+            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
         testWater();
     }
     catch(const std::exception& e) {

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp

@@ -197,7 +197,7 @@ int main(int argc, char* argv[]) {
     try {
         registerDrudeOpenCLKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
+            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", std::string(argv[1]));
         testSingleParticle();
         testAnisotropicParticle();
         testThole();

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp

@@ -183,7 +183,7 @@ int main(int argc, char* argv[]) {
     try {
         registerDrudeOpenCLKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
+            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
         testSinglePair();
         testWater();
     }

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp

@@ -110,7 +110,7 @@ void testWater() {
     State state = context.getState(State::Energy);
     double initialEnergy;
     int numSteps = 1000;
-    double maxNorm = (platform.getPropertyValue(context, "OpenCLPrecision") == "double" ? 1.0 : 5.0);
+    double maxNorm = (platform.getPropertyValue(context, "Precision") == "double" ? 1.0 : 5.0);
     for (int i = 0; i < numSteps; i++) {
         integ.step(1);
         state = context.getState(State::Energy | State::Forces);
@@ -131,7 +131,7 @@ int main(int argc, char* argv[]) {
     try {
         registerDrudeOpenCLKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
+            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
         testWater();
     }
     catch(const std::exception& e) {

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -554,7 +554,7 @@ int main(int argc, char* argv[]) {
     try {
         registerRPMDCudaKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", string(argv[1]));
+            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
         testFreeParticles();
         testParaHydrogen();
         testCMMotionRemoval();

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -555,7 +555,7 @@ int main(int argc, char* argv[]) {
     try {
         registerRPMDOpenCLKernelFactories();
         if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
+            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
         testFreeParticles();
         testParaHydrogen();
         testCMMotionRemoval();

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CMAPTorsionForceProxy::CMAPTorsionForceProxy() : SerializationProxy("CMAPTorsion
 }
 
 void CMAPTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CMAPTorsionForce& force = *reinterpret_cast<const CMAPTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& maps = node.createChildNode("Maps");
     for (int i = 0; i < force.getNumMaps(); i++) {
         int size;
@@ -63,11 +64,14 @@ void CMAPTorsionForceProxy::serialize(const void* object, SerializationNode& nod
 }
 
 void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CMAPTorsionForce* force = new CMAPTorsionForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& maps = node.getChildNode("Maps");
         for (int i = 0; i < (int) maps.getChildren().size(); i++) {
             const SerializationNode& map = maps.getChildren()[i];

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CustomAngleForceProxy::CustomAngleForceProxy() : SerializationProxy("CustomAngle
 }
 
 void CustomAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomAngleForce& force = *reinterpret_cast<const CustomAngleForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perAngleParams = node.createChildNode("PerAngleParameters");
     for (int i = 0; i < force.getNumPerAngleParameters(); i++) {
@@ -70,12 +71,15 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
 }
 
 void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomAngleForce* force = NULL;
     try {
         CustomAngleForce* force = new CustomAngleForce(node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CustomBondForceProxy::CustomBondForceProxy() : SerializationProxy("CustomBondFor
 }
 
 void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
     for (int i = 0; i < force.getNumPerBondParameters(); i++) {
@@ -70,12 +71,15 @@ void CustomBondForceProxy::serialize(const void* object, SerializationNode& node
 }
 
 void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomBondForce* force = NULL;
     try {
         CustomBondForce* force = new CustomBondForce(node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
         for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perBondParams.getChildren()[i];

serialization/src/CustomCentroidBondForceProxy.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) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProx
 }
 
 void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setIntProperty("groups", force.getNumGroupsPerBond());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
@@ -93,12 +94,15 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
 }
 
 void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomCentroidBondForce* force = NULL;
     try {
         CustomCentroidBondForce* force = new CustomCentroidBondForce(node.getIntProperty("groups"), node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CustomCompoundBondForceProxy::CustomCompoundBondForceProxy() : SerializationProx
 }
 
 void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomCompoundBondForce& force = *reinterpret_cast<const CustomCompoundBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setIntProperty("particles", force.getNumParticlesPerBond());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
@@ -80,12 +81,15 @@ void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNo
 }
 
 void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomCompoundBondForce* force = NULL;
     try {
         CustomCompoundBondForce* force = new CustomCompoundBondForce(node.getIntProperty("particles"), node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
         for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perBondParams.getChildren()[i];

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ CustomTorsionForceProxy::CustomTorsionForceProxy() : SerializationProxy("CustomT
 }
 
 void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const CustomTorsionForce& force = *reinterpret_cast<const CustomTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perTorsionParams = node.createChildNode("PerTorsionParameters");
     for (int i = 0; i < force.getNumPerTorsionParameters(); i++) {
@@ -70,12 +71,15 @@ void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& n
 }
 
 void* CustomTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     CustomTorsionForce* force = NULL;
     try {
         CustomTorsionForce* force = new CustomTorsionForce(node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perTorsionParams = node.getChildNode("PerTorsionParameters");
         for (int i = 0; i < (int) perTorsionParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perTorsionParams.getChildren()[i];

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ HarmonicAngleForceProxy::HarmonicAngleForceProxy() : SerializationProxy("Harmoni
 }
 
 void HarmonicAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const HarmonicAngleForce& force = *reinterpret_cast<const HarmonicAngleForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& bonds = node.createChildNode("Angles");
     for (int i = 0; i < force.getNumAngles(); i++) {
         int particle1, particle2, particle3;
@@ -55,11 +56,14 @@ void HarmonicAngleForceProxy::serialize(const void* object, SerializationNode& n
 }
 
 void* HarmonicAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     HarmonicAngleForce* force = new HarmonicAngleForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ HarmonicBondForceProxy::HarmonicBondForceProxy() : SerializationProxy("HarmonicB
 }
 
 void HarmonicBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const HarmonicBondForce& force = *reinterpret_cast<const HarmonicBondForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& bonds = node.createChildNode("Bonds");
     for (int i = 0; i < force.getNumBonds(); i++) {
         int particle1, particle2;
@@ -55,11 +56,14 @@ void HarmonicBondForceProxy::serialize(const void* object, SerializationNode& no
 }
 
 void* HarmonicBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     HarmonicBondForce* force = new HarmonicBondForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& bonds = node.getChildNode("Bonds");
         for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
             const SerializationNode& bond = bonds.getChildren()[i];

serialization/src/MonteCarloAnisotropicBarostatProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -52,7 +52,7 @@ void MonteCarloAnisotropicBarostatProxy::serialize(const void* object, Serializa
     node.setBoolProperty("scalex", force.getScaleX());
     node.setBoolProperty("scaley", force.getScaleY());
     node.setBoolProperty("scalez", force.getScaleZ());
-    node.setDoubleProperty("temperature", force.getTemperature());
+    node.setDoubleProperty("temperature", force.getDefaultTemperature());
     node.setIntProperty("frequency", force.getFrequency());
     node.setIntProperty("randomSeed", force.getRandomNumberSeed());
 }

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,7 +46,7 @@ void MonteCarloBarostatProxy::serialize(const void* object, SerializationNode& n
     const MonteCarloBarostat& force = *reinterpret_cast<const MonteCarloBarostat*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("pressure", force.getDefaultPressure());
-    node.setDoubleProperty("temperature", force.getTemperature());
+    node.setDoubleProperty("temperature", force.getDefaultTemperature());
     node.setIntProperty("frequency", force.getFrequency());
     node.setIntProperty("randomSeed", force.getRandomNumberSeed());
 }

serialization/src/MonteCarloMembraneBarostatProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -47,7 +47,7 @@ void MonteCarloMembraneBarostatProxy::serialize(const void* object, Serializatio
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("pressure", force.getDefaultPressure());
     node.setDoubleProperty("surfaceTension", force.getDefaultSurfaceTension());
-    node.setDoubleProperty("temperature", force.getTemperature());
+    node.setDoubleProperty("temperature", force.getDefaultTemperature());
     node.setIntProperty("xymode", force.getXYMode());
     node.setIntProperty("zmode", force.getZMode());
     node.setIntProperty("frequency", force.getFrequency());

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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ PeriodicTorsionForceProxy::PeriodicTorsionForceProxy() : SerializationProxy("Per
 }
 
 void PeriodicTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const PeriodicTorsionForce& force = *reinterpret_cast<const PeriodicTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int particle1, particle2, particle3, particle4, periodicity;
@@ -55,11 +56,14 @@ void PeriodicTorsionForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* PeriodicTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     PeriodicTorsionForce* force = new PeriodicTorsionForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ RBTorsionForceProxy::RBTorsionForceProxy() : SerializationProxy("RBTorsionForce"
 }
 
 void RBTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const RBTorsionForce& force = *reinterpret_cast<const RBTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& torsions = node.createChildNode("Torsions");
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int particle1, particle2, particle3, particle4;
@@ -55,11 +56,14 @@ void RBTorsionForceProxy::serialize(const void* object, SerializationNode& node)
 }
 
 void* RBTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     RBTorsionForce* force = new RBTorsionForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 1)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& torsions = node.getChildNode("Torsions");
         for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
             const SerializationNode& torsion = torsions.getChildren()[i];