Serialization proxies were storing unnecessary information

plugins/amoeba/serialization/src/AmoebaAngleForceProxy.cpp

@@ -51,7 +51,7 @@ void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& nod
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalAnglePentic());
     node.setDoubleProperty("sextic",  force.getAmoebaGlobalAngleSextic());
 
-    SerializationNode& bonds = node.createChildNode("Angles").setIntProperty( "size", force.getNumAngles() );
+    SerializationNode& bonds = node.createChildNode("Angles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
         int particle1, particle2, particle3;
         double distance, k;

plugins/amoeba/serialization/src/AmoebaBondForceProxy.cpp

@@ -48,7 +48,7 @@ void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalBondCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalBondQuartic());
 
-    SerializationNode& bonds = node.createChildNode("Bonds").setIntProperty( "size", force.getNumBonds() );
+    SerializationNode& bonds = node.createChildNode("Bonds");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumBonds()); ii++) {
         int particle1, particle2;
         double distance, k;

plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp

@@ -52,11 +52,11 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
     node.setDoubleProperty("GeneralizedKirkwoodSurfaceAreaFactor", force.getSurfaceAreaFactor() );
     node.setIntProperty(   "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm() );
 
-    SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles").setIntProperty( "size", force.getNumParticles() );
+    SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
         double radius, charge, scalingFactor;
         force.getParticleParameters( ii, charge, radius, scalingFactor );
-        particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);
+        particles.createChildNode("Particle").setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);
     }
 
 }

plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.cpp

@@ -51,7 +51,7 @@ void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNo
     node.setDoubleProperty("pentic",     force.getAmoebaGlobalInPlaneAnglePentic());
     node.setDoubleProperty("sextic",     force.getAmoebaGlobalInPlaneAngleSextic());
 
-    SerializationNode& bonds = node.createChildNode("InPlaneAngles").setIntProperty( "size", force.getNumAngles() );
+    SerializationNode& bonds = node.createChildNode("InPlaneAngles");
     for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
         int particle1, particle2, particle3, particle4;
         double distance, k;

plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp

@@ -56,8 +56,6 @@ static void getCovalentTypes( std::vector<std::string>& covalentTypes ){
 
 static void addCovalentMap( SerializationNode& particleExclusions, int particleIndex, std::string mapName, std::vector< int > covalentMap ){
     SerializationNode& map   = particleExclusions.createChildNode(mapName);
-    map.setIntProperty( "index", particleIndex );
-    map.setIntProperty( "size", covalentMap.size() );
     for (unsigned int ii = 0; ii < covalentMap.size(); ii++) {
         map.createChildNode("Cv").setIntProperty( "v", covalentMap[ii] );
     }
@@ -93,7 +91,7 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
     std::vector<std::string> covalentTypes;
     getCovalentTypes( covalentTypes );
 
-    SerializationNode& particles = node.createChildNode("MultipoleParticles").setIntProperty( "size", force.getNumMultipoles() );
+    SerializationNode& particles = node.createChildNode("MultipoleParticles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
 
         int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
@@ -106,13 +104,13 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
                                       axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity );
 
         SerializationNode& particle    = particles.createChildNode("Particle");
-        particle.setIntProperty("index", ii).setIntProperty("axisType", axisType).setIntProperty("multipoleAtomZ", multipoleAtomZ).setIntProperty("multipoleAtomX", multipoleAtomX).setIntProperty("multipoleAtomY", multipoleAtomY);
+        particle.setIntProperty("axisType", axisType).setIntProperty("multipoleAtomZ", multipoleAtomZ).setIntProperty("multipoleAtomX", multipoleAtomX).setIntProperty("multipoleAtomY", multipoleAtomY);
         particle.setDoubleProperty("charge", charge).setDoubleProperty("thole", thole).setDoubleProperty("damp", dampingFactor).setDoubleProperty("polarity", polarity);
 
-        SerializationNode& dipole      = particle.createChildNode("Dipole").setIntProperty( "size", 3 );
+        SerializationNode& dipole      = particle.createChildNode("Dipole");
         dipole.setDoubleProperty( "d0", molecularDipole[0] ).setDoubleProperty( "d1", molecularDipole[1] ).setDoubleProperty( "d2", molecularDipole[2] );
 
-        SerializationNode& quadrupole  = particle.createChildNode("Quadrupole").setIntProperty( "size", 9 );
+        SerializationNode& quadrupole  = particle.createChildNode("Quadrupole");
         quadrupole.setDoubleProperty( "q0", molecularQuadrupole[0] ).setDoubleProperty( "q1", molecularQuadrupole[1] ).setDoubleProperty( "q2", molecularQuadrupole[2] );
         quadrupole.setDoubleProperty( "q3", molecularQuadrupole[3] ).setDoubleProperty( "q4", molecularQuadrupole[4] ).setDoubleProperty( "q5", molecularQuadrupole[5] );
         quadrupole.setDoubleProperty( "q6", molecularQuadrupole[6] ).setDoubleProperty( "q7", molecularQuadrupole[7] ).setDoubleProperty( "q8", molecularQuadrupole[8] );

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp

@@ -49,7 +49,7 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalOutOfPlaneBendPentic());
     node.setDoubleProperty("sextic",  force.getAmoebaGlobalOutOfPlaneBendSextic());
 
-    SerializationNode& bonds = node.createChildNode("OutOfPlaneBend").setIntProperty( "size", force.getNumOutOfPlaneBends() );
+    SerializationNode& bonds = node.createChildNode("OutOfPlaneBend");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumOutOfPlaneBends()); ii++) {
         int particle1, particle2, particle3, particle4;
         double k;

plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp

@@ -44,7 +44,7 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
 void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
-    SerializationNode& bonds = node.createChildNode("PiTorsion").setIntProperty( "size", force.getNumPiTorsions() );
+    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;
         double k;

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp

@@ -44,7 +44,7 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
 void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
-    SerializationNode& bonds = node.createChildNode("StretchBendAngles").setIntProperty( "size", force.getNumStretchBends() );
+    SerializationNode& bonds = node.createChildNode("StretchBendAngles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
         int particle1, particle2, particle3;
         double distanceAB, distanceCB, angle, k;

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp

@@ -76,7 +76,6 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
     // value5 = F_xy       partial f wrt x,y
 
     SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
-    grids.setIntProperty("size", static_cast<int>(force.getNumTorsionTorsionGrids()));
     for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) {
 
         const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( kk );
@@ -87,11 +86,10 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
             gridCount += grid[ii].size();
         }
 
-        SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid").setIntProperty("size", static_cast<int>(gridCount) );
+        SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid");
         for ( unsigned int ii = 0; ii < grid.size(); ii++) {
             SerializationNode& gridSerializationRow = gridNode.createChildNode("RowNode");
             gridSerializationRow.setIntProperty("dim", ii );
-            gridSerializationRow.setIntProperty("size", static_cast<int>(grid[ii].size() ) );
             for ( unsigned int jj = 0; jj < grid[ii].size(); jj++) {
                 SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode");
                 gridSerializationColumnNode.setIntProperty("dim", jj );

plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp

@@ -51,7 +51,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
 
     node.setIntProperty("method", (int) force.getNonbondedMethod());
 
-    SerializationNode& particles = node.createChildNode("VdwParticles").setIntProperty("size", force.getNumParticles() );
+    SerializationNode& particles = node.createChildNode("VdwParticles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
 
         int ivIndex;
@@ -59,14 +59,12 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
         force.getParticleParameters( ii, ivIndex, sigma, epsilon, reductionFactor );
 
         SerializationNode& particle = particles.createChildNode("Particle");
-        particle.setIntProperty("index", ii).setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor);
+        particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor);
 
         std::vector< int > exclusions;
         force.getParticleExclusions( ii,  exclusions );
 
         SerializationNode& particleExclusions = particle.createChildNode("ParticleExclusions");
-        particleExclusions.setIntProperty("size", exclusions.size() );
-        particleExclusions.setIntProperty("index", ii );
         for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
             particleExclusions.createChildNode( "excl" ).setIntProperty( "index", exclusions[jj] );
         }

plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp

@@ -53,11 +53,11 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
     node.setDoubleProperty("Dispoff", force.getDispoff());
     node.setDoubleProperty("Slevy",   force.getSlevy());
 
-    SerializationNode& particles = node.createChildNode("WcaDispersionParticles").setIntProperty( "size", force.getNumParticles() );
+    SerializationNode& particles = node.createChildNode("WcaDispersionParticles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
         double radius, epsilon;
         force.getParticleParameters( ii,  radius, epsilon );
-        particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
+        particles.createChildNode("Particle").setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
     }
 
 }