void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
node.setStringProperty("energy", force.getEnergyFunction());
SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
for (int i = 0; i < force.getNumPerBondParameters(); i++) {
perBondParams.createChildNode("Parameter").setStringProperty("name", force.getPerBondParameterName(i));
}
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& bonds = node.createChildNode("Bonds");
for (int i = 0; i < force.getNumBonds(); i++) {
int p1, p2;
vector<double> params;
force.getBondParameters(i, p1, p2, params);
SerializationNode& node = bonds.createChildNode("Bond").setIntProperty("p1", p1).setIntProperty("p2", p2);
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
node.setDoubleProperty(key.str(), params[j]);
}
}
}
void CustomTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
const CustomTorsionForce& force = *reinterpret_cast<const CustomTorsionForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
node.setStringProperty("energy", force.getEnergyFunction());
SerializationNode& perTorsionParams = node.createChildNode("PerTorsionParameters");
for (int i = 0; i < force.getNumPerTorsionParameters(); i++) {
perTorsionParams.createChildNode("Parameter").setStringProperty("name", force.getPerTorsionParameterName(i));
}
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& torsions = node.createChildNode("Torsions");
for (int i = 0; i < force.getNumTorsions(); i++) {
int p1, p2, p3, p4;
vector<double> params;
force.getTorsionParameters(i, p1, p2, p3, p4, params);
SerializationNode& node = torsions.createChildNode("Torsion").setIntProperty("p1", p1).setIntProperty("p2", p2).setIntProperty("p3", p3).setIntProperty("p4", p4);
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
node.setDoubleProperty(key.str(), params[j]);
}
}
}
void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
const CustomNonbondedForce& force = *reinterpret_cast<const CustomNonbondedForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("energy", force.getEnergyFunction());
node.setIntProperty("method", (int) force.getNonbondedMethod());
node.setDoubleProperty("cutoff", force.getCutoffDistance());
node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
node.setBoolProperty("useLongRangeCorrection", force.getUseLongRangeCorrection());
SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
perParticleParams.createChildNode("Parameter").setStringProperty("name", force.getPerParticleParameterName(i));
}
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
vector<double> params;
force.getParticleParameters(i, params);
SerializationNode& node = particles.createChildNode("Particle");
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
node.setDoubleProperty(key.str(), params[j]);
}
}
SerializationNode& exclusions = node.createChildNode("Exclusions");
for (int i = 0; i < force.getNumExclusions(); i++) {
int particle1, particle2;
force.getExclusionParticles(i, particle1, particle2);
exclusions.createChildNode("Exclusion").setIntProperty("p1", particle1).setIntProperty("p2", particle2);
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
SerializationNode& interactionGroups = node.createChildNode("InteractionGroups");
for (int i = 0; i < force.getNumInteractionGroups(); i++) {
SerializationNode& interactionGroup = interactionGroups.createChildNode("InteractionGroup");
std::set<int> set1;
std::set<int> set2;
force.getInteractionGroupParameters(i, set1, set2);
SerializationNode& set1node = interactionGroup.createChildNode("Set1");
for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
set1node.createChildNode("Particle").setIntProperty("index", *it);
SerializationNode& set2node = interactionGroup.createChildNode("Set2");
for (std::set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
set2node.createChildNode("Particle").setIntProperty("index", *it);
}
}
void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const CustomNonbondedForce& force = *reinterpret_cast<const CustomNonbondedForce*>(object);
node.setStringProperty("energy", force.getEnergyFunction());
node.setIntProperty("method", (int) force.getNonbondedMethod());
node.setDoubleProperty("cutoff", force.getCutoffDistance());
SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
perParticleParams.createChildNode("Parameter").setStringProperty("name", force.getPerParticleParameterName(i));
}
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
vector<double> params;
force.getParticleParameters(i, params);
SerializationNode& node = particles.createChildNode("Particle");
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
node.setDoubleProperty(key.str(), params[j]);
}
}
SerializationNode& exclusions = node.createChildNode("Exclusions");
for (int i = 0; i < force.getNumExclusions(); i++) {
int particle1, particle2;
force.getExclusionParticles(i, particle1, particle2);
exclusions.createChildNode("Exclusion").setIntProperty("p1", particle1).setIntProperty("p2", particle2);
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumFunctions(); i++) {
string name;
vector<double> values;
double min, max;
force.getFunctionParameters(i, name, values, min, max);
SerializationNode& node = functions.createChildNode("Function").setStringProperty("name", name).setDoubleProperty("min", min).setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
}
void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 3);
const CustomCompoundBondForce& force = *reinterpret_cast<const CustomCompoundBondForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
node.setIntProperty("particles", force.getNumParticlesPerBond());
node.setStringProperty("energy", force.getEnergyFunction());
SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
for (int i = 0; i < force.getNumPerBondParameters(); i++) {
perBondParams.createChildNode("Parameter").setStringProperty("name", force.getPerBondParameterName(i));
}
SerializationNode& globalParams = node.createChildNode("GlobalParameters");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& bonds = node.createChildNode("Bonds");
for (int i = 0; i < force.getNumBonds(); i++) {
vector<int> particles;
vector<double> params;
force.getBondParameters(i, particles, params);
SerializationNode& node = bonds.createChildNode("Bond");
for (int j = 0; j < (int) particles.size(); j++) {
stringstream key;
key << "p";
key << j+1;
node.setIntProperty(key.str(), particles[j]);
}
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
node.setDoubleProperty(key.str(), params[j]);
}
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
}