resolved conflict

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];

serialization/tests/TestSerializeCMAPTorsion.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:                                                              *
  *                                                                            *
@@ -55,6 +55,7 @@ void testSerialization() {
     force.addTorsion(0, 0, 2, 3, 4, 5, 6, 7, 8);
     force.addTorsion(1, 2, 3, 4, 7, 1, 2, 3, 4);
     force.addTorsion(1, 5, 1, 2, 3, 2, 3, 4, 8);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -66,6 +67,7 @@ void testSerialization() {
 
     CMAPTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumMaps(), force2.getNumMaps());
     for (int i = 0; i < force.getNumMaps(); i++) {
         int size1, size2;

serialization/tests/TestSerializeCustomAngleForce.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:                                                              *
  *                                                                            *
@@ -53,6 +53,7 @@ void testSerialization() {
     force.addAngle(4, 0, 1, params);
     params[0] = 2.1;
     force.addAngle(3, 7, 6, params);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -73,6 +74,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
     for (int i = 0; i < force.getNumAngles(); i++) {
         int a1, a2, b1, b2, c1, c2;

serialization/tests/TestSerializeCustomBondForce.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:                                                              *
  *                                                                            *
@@ -53,6 +53,7 @@ void testSerialization() {
     force.addBond(4, 0, params);
     params[0] = 2.1;
     force.addBond(3, 7, params);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -73,6 +74,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         int a1, a2, b1, b2;

serialization/tests/TestSerializeCustomCentroidBondForce.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:                                                              *
  *                                                                            *
@@ -77,6 +77,7 @@ void testSerialization() {
     for (int i = 0; i < 10; i++)
         values[i] = sin((double) i);
     force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -98,6 +99,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumGroups(), force2.getNumGroups());
     for (int i = 0; i < force.getNumGroups(); i++) {
         vector<int> particles1, particles2;

serialization/tests/TestSerializeCustomCompoundBondForce.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:                                                              *
  *                                                                            *
@@ -67,6 +67,7 @@ void testSerialization() {
     for (int i = 0; i < 10; i++)
         values[i] = sin((double) i);
     force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -88,6 +89,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         vector<int> particles1, particles2;

serialization/tests/TestSerializeCustomTorsionForce.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:                                                              *
  *                                                                            *
@@ -53,6 +53,7 @@ void testSerialization() {
     force.addTorsion(4, 0, 1, 5, params);
     params[0] = 2.1;
     force.addTorsion(3, 7, 6, 8, params);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -73,6 +74,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, b1, b2, c1, c2, d1, d2;

serialization/tests/TestSerializeHarmonicAngleForce.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:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void testSerialization() {
     force.addAngle(0, 2, 3, 2.0, 2.1);
     force.addAngle(2, 3, 4, 3.0, 2.2);
     force.addAngle(5, 1, 2, 4.0, 2.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -58,6 +59,7 @@ void testSerialization() {
 
     HarmonicAngleForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
     for (int i = 0; i < force.getNumAngles(); i++) {
         int a1, a2, a3, b1, b2, b3;

serialization/tests/TestSerializeHarmonicBondForce.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:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void testSerialization() {
     force.addBond(0, 2, 2.0, 2.1);
     force.addBond(2, 3, 3.0, 2.2);
     force.addBond(5, 1, 4.0, 2.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -58,6 +59,7 @@ void testSerialization() {
 
     HarmonicBondForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         int a1, a2, b1, b2;

serialization/tests/TestSerializeMonteCarloAnisotropicBarostat.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:                                                              *
  *                                                                            *
@@ -56,7 +56,7 @@ void testSerialization() {
     MonteCarloAnisotropicBarostat& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL_VEC(force.getDefaultPressure(), force2.getDefaultPressure(), 0.0);
-    ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getScaleX(), force2.getScaleX());
     ASSERT_EQUAL(force.getScaleY(), force2.getScaleY());
     ASSERT_EQUAL(force.getScaleZ(), force2.getScaleZ());

serialization/tests/TestSerializeMonteCarloBarostat.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:                                                              *
  *                                                                            *
@@ -56,7 +56,7 @@ void testSerialization() {
     MonteCarloBarostat& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
-    ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
     ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
 }