Merged fork with latest original master

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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,10 +42,12 @@ AmoebaAngleForceProxy::AmoebaAngleForceProxy() : SerializationProxy("AmoebaAngle
 }
 
 void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    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());
@@ -61,11 +63,15 @@ void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& nod
 }
 
 void* AmoebaAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,11 @@ AmoebaBondForceProxy::AmoebaBondForceProxy() : SerializationProxy("AmoebaBondFor
 }
 
 void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    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());
 
@@ -58,10 +60,15 @@ void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node
 }
 
 void* AmoebaBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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/AmoebaGeneralizedKirkwoodForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ AmoebaGeneralizedKirkwoodForceProxy::AmoebaGeneralizedKirkwoodForceProxy() : Ser
 }
 
 void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaGeneralizedKirkwoodForce& force = *reinterpret_cast<const AmoebaGeneralizedKirkwoodForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric());
     node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric",  force.getSoluteDielectric());
     //node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset",  force.getDielectricOffset());
@@ -62,11 +63,13 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
 }
 
 void* AmoebaGeneralizedKirkwoodForceProxy::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");
     AmoebaGeneralizedKirkwoodForce* force = new AmoebaGeneralizedKirkwoodForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setSolventDielectric(  node.getDoubleProperty("GeneralizedKirkwoodSolventDielectric"));
         force->setSoluteDielectric(   node.getDoubleProperty("GeneralizedKirkwoodSoluteDielectric"));
         //force->setDielectricOffset(   node.getDoubleProperty("GeneralizedKirkwoodDielectricOffset"));

plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -43,9 +43,11 @@ AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProx
 
 void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
 
-    node.setIntProperty("version", 1);
+    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());
@@ -61,11 +63,15 @@ void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNo
 }
 
 void* AmoebaInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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/AmoebaMultipoleForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -68,25 +68,32 @@ void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentM
 }
 
 void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 4);
     const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("nonbondedMethod",                  force.getNonbondedMethod());
     node.setIntProperty("polarizationType",                 force.getPolarizationType());
-    //node.setIntProperty("pmeBSplineOrder",                  force.getPmeBSplineOrder());
-    //node.setIntProperty("mutualInducedIterationMethod",     force.getMutualInducedIterationMethod());
     node.setIntProperty("mutualInducedMaxIterations",       force.getMutualInducedMaxIterations());
 
     node.setDoubleProperty("cutoffDistance",                force.getCutoffDistance());
-    node.setDoubleProperty("aEwald",                        force.getAEwald());
+    double alpha;
+    int nx, ny, nz;
+    force.getPMEParameters(alpha, nx, ny, nz);
+    node.setDoubleProperty("aEwald",                        alpha);
     node.setDoubleProperty("mutualInducedTargetEpsilon",    force.getMutualInducedTargetEpsilon());
-    //node.setDoubleProperty("electricConstant",              force.getElectricConstant());
     node.setDoubleProperty("ewaldErrorTolerance",           force.getEwaldErrorTolerance());
 
-    std::vector<int> gridDimensions;
-    force.getPmeGridDimensions(gridDimensions);
     SerializationNode& gridDimensionsNode  = node.createChildNode("MultipoleParticleGridDimension");
-    gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]); 
+    gridDimensionsNode.setIntProperty("d0", nx).setIntProperty("d1", ny).setIntProperty("d2", nz); 
+    
+    SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
+    vector<double> coeff = force.getExtrapolationCoefficients();
+    for (int i = 0; i < coeff.size(); i++) {
+        stringstream key;
+        key << "c" << i;
+        coefficients.setDoubleProperty(key.str(), coeff[i]);
+    }
 
     std::vector<std::string> covalentTypes;
     getCovalentTypes(covalentTypes);
@@ -124,33 +131,38 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") > 2)
+    int version = node.getIntProperty("version");
+    if (version < 0 || version > 4)
         throw OpenMMException("Unsupported version number");
     AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
 
     try {
-
+        if (version > 3)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
-        if (node.getIntProperty("version") == 2) {
+        if (version >= 2)
             force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
-        }
-        //force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
-        //force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
         force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
 
         force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
-        force->setAEwald(node.getDoubleProperty("aEwald"));
         force->setMutualInducedTargetEpsilon(node.getDoubleProperty("mutualInducedTargetEpsilon"));
-        //force->setElectricConstant(node.getDoubleProperty("electricConstant"));
         force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldErrorTolerance"));
 
-        std::vector<int> gridDimensions;
         const SerializationNode& gridDimensionsNode  = node.getChildNode("MultipoleParticleGridDimension");
-        gridDimensions.push_back(gridDimensionsNode.getIntProperty("d0"));
-        gridDimensions.push_back(gridDimensionsNode.getIntProperty("d1"));
-        gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
-        force->setPmeGridDimensions(gridDimensions);
+        force->setPMEParameters(node.getDoubleProperty("aEwald"), gridDimensionsNode.getIntProperty("d0"), gridDimensionsNode.getIntProperty("d1"), gridDimensionsNode.getIntProperty("d2"));
     
+        if (version >= 3) {
+            const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
+            vector<double> coeff;
+            for (int i = 0; ; i++) {
+                stringstream key;
+                key << "c" << i;
+                if (coefficients.getProperties().find(key.str()) == coefficients.getProperties().end())
+                    break;
+                coeff.push_back(coefficients.getDoubleProperty(key.str()));
+            }
+            force->setExtrapolationCoefficients(coeff);
+        }
         std::vector<std::string> covalentTypes;
         getCovalentTypes(covalentTypes);
 

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,10 @@ AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : Serialization
 }
 
 void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    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());
@@ -59,11 +61,15 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
 }
 
 void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,10 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
 }
 
 void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    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;
@@ -54,10 +56,15 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* AmoebaPiTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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

@@ -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:                                                              *
  *                                                                            *
@@ -42,8 +42,10 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
 }
 
 void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    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;
@@ -56,10 +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 != 2)
+    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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -63,8 +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", 1);
+    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]
 
@@ -116,12 +118,16 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
 
 void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {
 
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    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/src/AmoebaVdwForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,12 +42,13 @@ AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce"
 }
 
 void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
     node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
-    node.setDoubleProperty("VdwCutoff", force.getCutoff());
+    node.setDoubleProperty("VdwCutoff", force.getCutoffDistance());
 
     node.setIntProperty("method", (int) force.getNonbondedMethod());
 
@@ -72,14 +73,16 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
 }
 
 void* AmoebaVdwForceProxy::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");
     AmoebaVdwForce* force = new AmoebaVdwForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
         force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
-        force->setCutoff(node.getDoubleProperty("VdwCutoff"));
+        force->setCutoffDistance(node.getDoubleProperty("VdwCutoff"));
         force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));
 
         const SerializationNode& particles = node.getChildNode("VdwParticles");

plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,9 @@ AmoebaWcaDispersionForceProxy::AmoebaWcaDispersionForceProxy() : SerializationPr
 }
 
 void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaWcaDispersionForce& force = *reinterpret_cast<const AmoebaWcaDispersionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("Epso",    force.getEpso());
     node.setDoubleProperty("Epsh",    force.getEpsh());
     node.setDoubleProperty("Rmino",   force.getRmino());
@@ -63,12 +64,14 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
 }
 
 void* AmoebaWcaDispersionForceProxy::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");
     AmoebaWcaDispersionForce* force = new AmoebaWcaDispersionForce();
 
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setEpso(   node.getDoubleProperty("Epso"));
         force->setEpsh(   node.getDoubleProperty("Epsh"));
         force->setRmino(  node.getDoubleProperty("Rmino"));

plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaAngleForce force1;
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalAngleCubic(12.3);
     force1.setAmoebaGlobalAngleQuartic(98.7);
     force1.setAmoebaGlobalAnglePentic(91.7);
@@ -53,6 +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.
 
@@ -62,6 +64,8 @@ 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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,12 +45,14 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaBondForce force1;
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalBondCubic(12.3);
     force1.setAmoebaGlobalBondQuartic(98.7);
     force1.addBond(0, 1, 1.0, 2.0);
     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.
 
@@ -60,6 +62,8 @@ 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/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaGeneralizedKirkwoodForce force1;
+    force1.setForceGroup(3);
     force1.setSolventDielectric(  80.0);
     force1.setSoluteDielectric(   1.0);
     //force1.setDielectricOffset(   0.09);
@@ -64,6 +65,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaGeneralizedKirkwoodForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getSolventDielectric(),    force2.getSolventDielectric());
     ASSERT_EQUAL(force1.getSoluteDielectric(),     force2.getSoluteDielectric());
     //ASSERT_EQUAL(force1.getDielectricOffset(),     force2.getDielectricOffset());

plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaInPlaneAngleForce force1;
 
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalInPlaneAngleCubic(12.3);
     force1.setAmoebaGlobalInPlaneAngleQuartic(98.7);
     force1.setAmoebaGlobalInPlaneAnglePentic(91.7);
@@ -55,6 +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.
 
@@ -65,6 +67,8 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     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());