void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
CustomNonbondedForce* force = NULL;
try {
CustomNonbondedForce* force = new CustomNonbondedForce(node.getStringProperty("energy"));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setNonbondedMethod((CustomNonbondedForce::NonbondedMethod) node.getIntProperty("method"));
force->setCutoffDistance(node.getDoubleProperty("cutoff"));
force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
const SerializationNode& parameter = perParticleParams.getChildren()[i];
force->addPerParticleParameter(parameter.getStringProperty("name"));
}
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
const SerializationNode& parameter = globalParams.getChildren()[i];
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 1) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& particles = node.getChildNode("Particles");
vector<double> params(force->getNumPerParticleParameters());
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
params[j] = particle.getDoubleProperty(key.str());
}
force->addParticle(params);
}
const SerializationNode& exclusions = node.getChildNode("Exclusions");
for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
const SerializationNode& exclusion = exclusions.getChildren()[i];
force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
}
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
if (function.hasProperty("type")) {
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
else {
// This is an old file created before TabulatedFunction existed.
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
bool hasInteractionGroups = false; // Older files will be missing this block.
for (int i = 0; i < (int) node.getChildren().size(); i++) {
if (node.getChildren()[i].getName() == "InteractionGroups")
hasInteractionGroups = true;
}
if (hasInteractionGroups) {
const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
// Get set 1.
const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
std::set<int> set1;
for (int j = 0; j < (int) set1node.getChildren().size(); j++)
set1.insert(set1node.getChildren()[j].getIntProperty("index"));
// Get set 2.
const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
std::set<int> set2;
for (int j = 0; j < (int) set2node.getChildren().size(); j++)
set2.insert(set2node.getChildren()[j].getIntProperty("index"));
force->addInteractionGroup(set1, set2);
}
}
return force;
}
catch (...) {
if (force != NULL)
delete force;
throw;
}
}
