Serialization of periodic boundary conditions for AMOEBA bonded forces

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++) {