Merge pull request #1340 from peastman/amoebagroups

Record force group for AMOEBA forces

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 +42,11 @@ AmoebaAngleForceProxy::AmoebaAngleForceProxy() : SerializationProxy("AmoebaAngle
 }
 
 void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
 
     const AmoebaAngleForce& force = *reinterpret_cast<const AmoebaAngleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalAngleCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalAngleQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalAnglePentic());
@@ -61,11 +62,13 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaAngleForce* force = new AmoebaAngleForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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 +42,10 @@ AmoebaBondForceProxy::AmoebaBondForceProxy() : SerializationProxy("AmoebaBondFor
 }
 
 void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaBondForce& force = *reinterpret_cast<const AmoebaBondForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalBondCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalBondQuartic());
 
@@ -58,10 +59,13 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaBondForce* force = new AmoebaBondForce();
     try {
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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 +43,10 @@ AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProx
 
 void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
 
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaInPlaneAngleForce& force = *reinterpret_cast<const AmoebaInPlaneAngleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",      force.getAmoebaGlobalInPlaneAngleCubic());
     node.setDoubleProperty("quartic",    force.getAmoebaGlobalInPlaneAngleQuartic());
     node.setDoubleProperty("pentic",     force.getAmoebaGlobalInPlaneAnglePentic());
@@ -61,11 +62,13 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaInPlaneAngleForce* force = new AmoebaInPlaneAngleForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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:                                                              *
  *                                                                            *
@@ -68,9 +68,10 @@ void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentM
 }
 
 void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 3);
+    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());
@@ -133,12 +134,13 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
 
 void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 0 || version > 3)
+    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 (version >= 2)
             force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));

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 +42,9 @@ AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : Serialization
 }
 
 void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaOutOfPlaneBendForce& force = *reinterpret_cast<const AmoebaOutOfPlaneBendForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalOutOfPlaneBendCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalOutOfPlaneBendQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalOutOfPlaneBendPentic());
@@ -59,11 +60,13 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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 +42,9 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
 }
 
 void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     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 +55,13 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaPiTorsionForce* force = new AmoebaPiTorsionForce();
     try {
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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 +42,9 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
 }
 
 void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& bonds = node.createChildNode("StretchBendAngles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
         int particle1, particle2, particle3;
@@ -56,10 +57,12 @@ 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 > 3)
         throw OpenMMException("Unsupported version number");
     AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
     try {
+        if (version > 2)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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 +63,9 @@ 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", 2);
     const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
 
     // grid[xIdx][yIdx][6 values]
 
@@ -116,12 +117,14 @@ 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 > 2)
         throw OpenMMException("Unsupported version number");
 
     AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         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:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ 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());
@@ -72,11 +73,13 @@ 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"));

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);
@@ -62,6 +63,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.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:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ 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);
@@ -60,6 +61,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaBondForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.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);
@@ -65,6 +66,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaInPlaneAngleForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleCubic(),    force2.getAmoebaGlobalInPlaneAngleCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleQuartic(),  force2.getAmoebaGlobalInPlaneAngleQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAnglePentic(),   force2.getAmoebaGlobalInPlaneAnglePentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.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:                                                              *
  *                                                                            *
@@ -59,6 +59,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaMultipoleForce force1;
+    force1.setForceGroup(3);
     force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
     force1.setCutoffDistance(0.9);
     force1.setAEwald(0.544);
@@ -111,6 +112,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaMultipoleForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getCutoffDistance(),                force2.getCutoffDistance());
     ASSERT_EQUAL(force1.getNonbondedMethod(),               force2.getNonbondedMethod());
     ASSERT_EQUAL(force1.getAEwald(),                        force2.getAEwald());

plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.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() {
 
     AmoebaOutOfPlaneBendForce force1;
 
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalOutOfPlaneBendCubic(12.3);
     force1.setAmoebaGlobalOutOfPlaneBendQuartic(98.7);
     force1.setAmoebaGlobalOutOfPlaneBendPentic(91.7);
@@ -65,6 +66,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaOutOfPlaneBendForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendCubic(), force2.getAmoebaGlobalOutOfPlaneBendCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendQuartic(), force2.getAmoebaGlobalOutOfPlaneBendQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendPentic(), force2.getAmoebaGlobalOutOfPlaneBendPentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.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.
 
     AmoebaPiTorsionForce force1;
+    force1.setForceGroup(3);
     force1.addPiTorsion(0, 1, 3, 4, 5, 6, 2.0);
     force1.addPiTorsion(0, 2, 3, 5, 12, 13, 2.1);
     force1.addPiTorsion(2, 3, 5, 6, 81, 91, 2.2);
@@ -58,6 +59,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaPiTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.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

@@ -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.
 
     AmoebaStretchBendForce force1;
+    force1.setForceGroup(3);
     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.);
@@ -57,6 +58,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaStretchBendForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.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

@@ -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:                                                              *
  *                                                                            *
@@ -81,6 +81,7 @@ void testSerialization() {
 
     AmoebaTorsionTorsionForce force1;
 
+    force1.setForceGroup(3);
     for (unsigned int ii = 0; ii < 5; ii++) {
         std::vector< std::vector< std::vector<double> > > gridVector;
         loadTorsionTorsionGrid(gridVector);
@@ -99,6 +100,7 @@ void testSerialization() {
     // Compare the two force1s to see if they are identical.  
 
     AmoebaTorsionTorsionForce & force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsions()); ii++) {