resolved conflict

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp

@@ -42,9 +42,10 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
 }
 
 void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 3);
+    node.setIntProperty("version", 4);
     const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& bonds = node.createChildNode("StretchBendAngles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
         int particle1, particle2, particle3;
@@ -57,12 +58,14 @@ void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNod
 
 void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 3)
+    if (version < 1 || version > 4)
         throw OpenMMException("Unsupported version number");
     AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
     try {
         if (version > 2)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 3)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& bonds = node.getChildNode("StretchBendAngles");
         for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
             const SerializationNode& bond = bonds.getChildren()[ii];

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp

@@ -63,9 +63,10 @@ static void loadGrid(const SerializationNode& grid, std::vector< std::vector< st
 }
 
 void AmoebaTorsionTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
 
     // grid[xIdx][yIdx][6 values]
 
@@ -118,13 +119,15 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
 void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {
 
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
 
     AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& grids                    = node.getChildNode("TorsionTorsionGrids");
         const std::vector<SerializationNode>& gridList    = grids.getChildren();
         for (unsigned int ii = 0; ii < gridList.size(); ii++) {

plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp

@@ -54,6 +54,7 @@ void testSerialization() {
     force1.addAngle(0, 2, 3, 2.0, 2.1);
     force1.addAngle(2, 3, 5, 3.0, 2.2);
     force1.addAngle(5, 1, 8, 4.0, 2.3);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -64,6 +65,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaAngleForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getAmoebaGlobalAngleCubic(),   force2.getAmoebaGlobalAngleCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalAngleQuartic(), force2.getAmoebaGlobalAngleQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalAnglePentic(),  force2.getAmoebaGlobalAnglePentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp

@@ -52,6 +52,7 @@ void testSerialization() {
     force1.addBond(0, 2, 2.0, 2.1);
     force1.addBond(2, 3, 3.0, 2.2);
     force1.addBond(5, 1, 4.0, 2.3);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -62,6 +63,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaBondForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getAmoebaGlobalBondCubic(), force2.getAmoebaGlobalBondCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalBondQuartic(), force2.getAmoebaGlobalBondQuartic());
     ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds());

plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp

@@ -56,6 +56,7 @@ void testSerialization() {
     force1.addAngle(0, 2, 3, 5, 2.0, 2.1);
     force1.addAngle(2, 3, 5, 6, 3.0, 2.2);
     force1.addAngle(5, 1, 8, 8, 4.0, 2.3);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -67,6 +68,7 @@ void testSerialization() {
     AmoebaInPlaneAngleForce& force2 = *copy;
 
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleCubic(),    force2.getAmoebaGlobalInPlaneAngleCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleQuartic(),  force2.getAmoebaGlobalInPlaneAngleQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAnglePentic(),   force2.getAmoebaGlobalInPlaneAnglePentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp

@@ -56,6 +56,7 @@ void testSerialization() {
     force1.addOutOfPlaneBend(0, 2, 3, 5, 2.1);
     force1.addOutOfPlaneBend(2, 3, 5, 6, 2.2);
     force1.addOutOfPlaneBend(5, 1, 8, 8, 2.3);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -67,6 +68,7 @@ void testSerialization() {
     AmoebaOutOfPlaneBendForce& force2 = *copy;
 
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendCubic(), force2.getAmoebaGlobalOutOfPlaneBendCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendQuartic(), force2.getAmoebaGlobalOutOfPlaneBendQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendPentic(), force2.getAmoebaGlobalOutOfPlaneBendPentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.cpp

@@ -50,6 +50,7 @@ void testSerialization() {
     force1.addPiTorsion(0, 2, 3, 5, 12, 13, 2.1);
     force1.addPiTorsion(2, 3, 5, 6, 81, 91, 2.2);
     force1.addPiTorsion(5, 1, 8, 8, 101, 102, 2.3);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -60,6 +61,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaPiTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getNumPiTorsions(), force2.getNumPiTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumPiTorsions()); ii++) {
         int a1, a2, a3, a4, a5, a6, b1, b2, b3, b4, b5, b6;

plugins/amoeba/serialization/tests/TestSerializeAmoebaStretchBendForce.cpp

@@ -49,6 +49,7 @@ void testSerialization() {
     force1.addStretchBend(0, 1, 3, 1.0, 1.2, 150.1, 83.2, 100.);
     force1.addStretchBend(2, 4, 4, 1.1, 2.2, 180.1, 89.2, 100.);
     force1.addStretchBend(5, 0, 1, 3.1, 8.2, 140.1, 98.2, 100.);
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -59,6 +60,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaStretchBendForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getNumStretchBends(), force2.getNumStretchBends());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumStretchBends()); ii++) {
         int p11, p12, p13;

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -90,6 +90,7 @@ void testSerialization() {
     for (unsigned int ii = 0; ii < 5; ii++) {
         force1.addTorsionTorsion(ii, ii+1,ii+3, ii+4, ii+5, ((ii % 2) ? 1 : 0), (ii % 4));
     }
+    force1.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -101,6 +102,7 @@ void testSerialization() {
 
     AmoebaTorsionTorsionForce & force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsions()); ii++) {
 

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

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

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];