Merge branch 'master' into gayberne

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -354,12 +354,57 @@ void testOneAngle() {
     compareWithExpectedForceAndEnergy(context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 4;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaInPlaneAngleForce* amoebaInPlaneAngleForce = new AmoebaInPlaneAngleForce();
+    double angle      = 65.0;
+    double quadraticK = 1.0;
+    double cubicK     = 0.0e-01;
+    double quarticK   = 0.0e-02;
+    double penticK    = 0.0e-03;
+    double sexticK    = 0.0e-04;
+    amoebaInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleCubic(cubicK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleQuartic(quarticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAnglePentic(penticK);
+    amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
+    amoebaInPlaneAngleForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaInPlaneAngleForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 1);
+    positions[3] = Vec3(1, 1, 1);
+
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[2] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneAngle();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -461,12 +461,50 @@ void testOneOutOfPlaneBend2(int setId) {
     }
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 4;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic(0.5600000E-04);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic(-0.7000000E-06);
+    amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07);
+    double kOutOfPlaneBend = 0.328682196E-01;
+    amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend);
+    amoebaOutOfPlaneBendForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaOutOfPlaneBendForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    positions[2] = Vec3(0, 1, 0);
+    positions[3] = Vec3(0, 0, 1);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[3] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneOutOfPlaneBend();
+        testPeriodic();
         //testOneOutOfPlaneBend2(atoi(argv[1]));
         //for (int ii = 1; ii <= 6; ii++) {
         //     testOneOutOfPlaneBend2(ii);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -290,12 +290,48 @@ void testOnePiTorsion() {
     compareWithExpectedForceAndEnergy(context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 6;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaPiTorsionForce* amoebaPiTorsionForce = new AmoebaPiTorsionForce();
+    double kTorsion = 6.85;
+    amoebaPiTorsionForce->addPiTorsion(0, 1, 2, 3, 4, 5, kTorsion);
+    amoebaPiTorsionForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaPiTorsionForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 0.5);
+    positions[3] = Vec3(0.4, 0.4, 0.4);
+    positions[4] = Vec3(1, 0, 1);
+    positions[5] = Vec3(1, 1, 0);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[0] = Vec3(0, -2, 0);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaPiTorsionForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOnePiTorsion();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -270,12 +270,48 @@ void testOneStretchBend() {
     compareWithExpectedForceAndEnergy(context, *amoebaStretchBendForce, TOL, "testOneStretchBend");
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 3;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaStretchBendForce* amoebaStretchBendForce = new AmoebaStretchBendForce();
+    double abLength         = 0.144800000E+01;
+    double cbLength         = 0.101500000E+01;
+    double angleStretchBend = 0.108500000E+03*DegreesToRadians;
+    double kStretchBend     = 1.0;
+    amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend, kStretchBend);
+    amoebaStretchBendForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaStretchBendForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 1);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[2] = Vec3(0, 0, -2);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int numberOfArguments, char* argv[]) {
 
     try {
         std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
         testOneStretchBend();
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -2669,6 +2669,44 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
     ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    int numberOfParticles = 6;
+    for (int ii = 0; ii < numberOfParticles; ii++)
+        system.addParticle(1.0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    AmoebaTorsionTorsionForce* amoebaTorsionTorsionForce = new AmoebaTorsionTorsionForce();
+    int chiralCheckAtomIndex;
+    int gridIndex;
+    chiralCheckAtomIndex  = 5;
+    gridIndex             = 2;
+    amoebaTorsionTorsionForce->addTorsionTorsion(0, 1, 2, 3, 4, chiralCheckAtomIndex, 0);
+    amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, false));
+    amoebaTorsionTorsionForce->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(amoebaTorsionTorsionForce);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    std::vector<Vec3> positions(numberOfParticles);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(0, 0, 0.5);
+    positions[3] = Vec3(0.4, 0.4, 0.4);
+    positions[4] = Vec3(1, 0, 1);
+    positions[5] = Vec3(1, 1, 0);
+    context.setPositions(positions);
+    State s1 = context.getState(State::Forces | State::Energy);
+    
+    // Move one atom to a position that should give identical results.
+
+    positions[0] = Vec3(0, -2, 0);
+    context.setPositions(positions);
+    State s2 = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numberOfParticles; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
 
 int main(int numberOfArguments, char* argv[]) {
 
@@ -2677,6 +2715,7 @@ int main(int numberOfArguments, char* argv[]) {
         registerAmoebaReferenceKernelFactories();
         testTorsionTorsion(1, true);
         testTorsionTorsion(1, false);
+        testPeriodic();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/serialization/src/AmoebaAngleForceProxy.cpp

@@ -42,11 +42,12 @@ AmoebaAngleForceProxy::AmoebaAngleForceProxy() : SerializationProxy("AmoebaAngle
 }
 
 void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
 
     const AmoebaAngleForce& force = *reinterpret_cast<const AmoebaAngleForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalAngleCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalAngleQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalAnglePentic());
@@ -63,12 +64,14 @@ void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& nod
 
 void* AmoebaAngleForceProxy::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");
     AmoebaAngleForce* force = new AmoebaAngleForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         force->setAmoebaGlobalAngleCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalAngleQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalAnglePentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaBondForceProxy.cpp

@@ -42,10 +42,11 @@ AmoebaBondForceProxy::AmoebaBondForceProxy() : SerializationProxy("AmoebaBondFor
 }
 
 void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaBondForce& force = *reinterpret_cast<const AmoebaBondForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalBondCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalBondQuartic());
 
@@ -60,12 +61,14 @@ void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node
 
 void* AmoebaBondForceProxy::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");
     AmoebaBondForce* force = new AmoebaBondForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         force->setAmoebaGlobalBondCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalBondQuartic(node.getDoubleProperty("quartic"));
         const SerializationNode& bonds = node.getChildNode("Bonds");

plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.cpp

@@ -43,10 +43,11 @@ AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProx
 
 void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
 
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaInPlaneAngleForce& force = *reinterpret_cast<const AmoebaInPlaneAngleForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setDoubleProperty("cubic",      force.getAmoebaGlobalInPlaneAngleCubic());
     node.setDoubleProperty("quartic",    force.getAmoebaGlobalInPlaneAngleQuartic());
     node.setDoubleProperty("pentic",     force.getAmoebaGlobalInPlaneAnglePentic());
@@ -63,12 +64,14 @@ void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNo
 
 void* AmoebaInPlaneAngleForceProxy::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");
     AmoebaInPlaneAngleForce* force = new AmoebaInPlaneAngleForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         force->setAmoebaGlobalInPlaneAngleCubic( node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalInPlaneAngleQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalInPlaneAnglePentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp

@@ -42,9 +42,10 @@ AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : Serialization
 }
 
 void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaOutOfPlaneBendForce& force = *reinterpret_cast<const AmoebaOutOfPlaneBendForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalOutOfPlaneBendCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalOutOfPlaneBendQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalOutOfPlaneBendPentic());
@@ -61,12 +62,14 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
 
 void* AmoebaOutOfPlaneBendForceProxy::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");
     AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp

@@ -42,9 +42,10 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
 }
 
 void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& bonds = node.createChildNode("PiTorsion");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
         int particle1, particle2, particle3, particle4, particle5, particle6;
@@ -56,12 +57,14 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
 
 void* AmoebaPiTorsionForceProxy::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");
     AmoebaPiTorsionForce* force = new AmoebaPiTorsionForce();
     try {
         if (version > 1)
             force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        if (version > 2)
+            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& bonds = node.getChildNode("PiTorsion");
         for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
             const SerializationNode& bond = bonds.getChildren()[ii];

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();