void GayBerneForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const GayBerneForce& force = *reinterpret_cast<const GayBerneForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("method", (int) force.getNonbondedMethod());
node.setDoubleProperty("cutoff", force.getCutoffDistance());
node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
double sigma, epsilon, sx, sy, sz, ex, ey, ez;
int xparticle, yparticle;
force.getParticleParameters(i, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
particles.createChildNode("Particle").setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon).setDoubleProperty("sx", sx)
.setDoubleProperty("sy", sy).setDoubleProperty("sz", sz).setDoubleProperty("ex", ex).setDoubleProperty("ey", ey).setDoubleProperty("ez", ez)
.setIntProperty("xparticle", xparticle).setIntProperty("yparticle", yparticle);
}
SerializationNode& exceptions = node.createChildNode("Exceptions");
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, sigma, epsilon);
exceptions.createChildNode("Exception").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
}
}
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 MonteCarloBarostatProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const MonteCarloBarostat& force = *reinterpret_cast<const MonteCarloBarostat*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setDoubleProperty("pressure", force.getDefaultPressure());
node.setDoubleProperty("temperature", force.getTemperature());
node.setIntProperty("frequency", force.getFrequency());
node.setIntProperty("randomSeed", force.getRandomNumberSeed());
}
void BrownianIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const BrownianIntegrator& integrator = *reinterpret_cast<const BrownianIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("friction", integrator.getFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
}
void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
node.setIntProperty("polarizationType", force.getPolarizationType());
//node.setIntProperty("pmeBSplineOrder", force.getPmeBSplineOrder());
//node.setIntProperty("mutualInducedIterationMethod", force.getMutualInducedIterationMethod());
node.setIntProperty("mutualInducedMaxIterations", force.getMutualInducedMaxIterations());
node.setDoubleProperty("cutoffDistance", force.getCutoffDistance());
node.setDoubleProperty("aEwald", force.getAEwald());
node.setDoubleProperty("mutualInducedTargetEpsilon", force.getMutualInducedTargetEpsilon());
//node.setDoubleProperty("electricConstant", force.getElectricConstant());
node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance());
std::vector<int> gridDimensions;
force.getPmeGridDimensions(gridDimensions);
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension");
gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]);
std::vector<std::string> covalentTypes;
getCovalentTypes(covalentTypes);
SerializationNode& particles = node.createChildNode("MultipoleParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity;
std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole;
force.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole,
axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity);
SerializationNode& particle = particles.createChildNode("Particle");
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");
dipole.setDoubleProperty("d0", molecularDipole[0]).setDoubleProperty("d1", molecularDipole[1]).setDoubleProperty("d2", molecularDipole[2]);
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]);
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap;
force.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
addCovalentMap(particle, ii, covalentTypes[jj], covalentMap);
}
}
}
void CustomGBForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
const CustomGBForce& force = *reinterpret_cast<const CustomGBForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
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& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& computedValues = node.createChildNode("ComputedValues");
for (int i = 0; i < force.getNumComputedValues(); i++) {
string name, expression;
CustomGBForce::ComputationType type;
force.getComputedValueParameters(i, name, expression, type);
computedValues.createChildNode("Value").setStringProperty("name", name).setStringProperty("expression", expression).setIntProperty("type", (int) type);
}
SerializationNode& energyTerms = node.createChildNode("EnergyTerms");
for (int i = 0; i < force.getNumEnergyTerms(); i++) {
string expression;
CustomGBForce::ComputationType type;
force.getEnergyTermParameters(i, expression, type);
energyTerms.createChildNode("Term").setStringProperty("expression", expression).setIntProperty("type", (int) type);
}
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));
}
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 StateProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const State& s = *reinterpret_cast<const State*>(object);
node.setDoubleProperty("time", s.getTime());
Vec3 a,b,c;
s.getPeriodicBoxVectors(a,b,c);
SerializationNode& boxVectorsNode = node.createChildNode("PeriodicBoxVectors");
boxVectorsNode.createChildNode("A").setDoubleProperty("x", a[0]).setDoubleProperty("y", a[1]).setDoubleProperty("z", a[2]);
boxVectorsNode.createChildNode("B").setDoubleProperty("x", b[0]).setDoubleProperty("y", b[1]).setDoubleProperty("z", b[2]);
boxVectorsNode.createChildNode("C").setDoubleProperty("x", c[0]).setDoubleProperty("y", c[1]).setDoubleProperty("z", c[2]);
try {
s.getParameters();
SerializationNode& parametersNode = node.createChildNode("Parameters");
map<string, double> stateParams = s.getParameters();
map<string, double>::const_iterator it;
for (it = stateParams.begin(); it!=stateParams.end();it++) {
parametersNode.setDoubleProperty(it->first, it->second);
}
} catch (const OpenMMException &) {
// do nothing
}
try {
s.getPotentialEnergy();
SerializationNode& energiesNode = node.createChildNode("Energies");
energiesNode.setDoubleProperty("PotentialEnergy", s.getPotentialEnergy());
energiesNode.setDoubleProperty("KineticEnergy", s.getKineticEnergy());
} catch (const OpenMMException &) {
// do nothing
}
try {
s.getPositions();
SerializationNode& positionsNode = node.createChildNode("Positions");
vector<Vec3> statePositions = s.getPositions();
for (int i=0; i<statePositions.size();i++) {
positionsNode.createChildNode("Position").setDoubleProperty("x", statePositions[i][0]).setDoubleProperty("y", statePositions[i][1]).setDoubleProperty("z", statePositions[i][2]);
}
} catch (const OpenMMException &) {
// do nothing
}
try {
s.getVelocities();
SerializationNode& velocitiesNode = node.createChildNode("Velocities");
vector<Vec3> stateVelocities = s.getVelocities();
for (int i=0; i<stateVelocities.size();i++) {
velocitiesNode.createChildNode("Velocity").setDoubleProperty("x", stateVelocities[i][0]).setDoubleProperty("y", stateVelocities[i][1]).setDoubleProperty("z", stateVelocities[i][2]);
}
} catch (const OpenMMException &) {
// do nothing
}
try {
s.getForces();
SerializationNode& forcesNode = node.createChildNode("Forces");
vector<Vec3> stateForces = s.getForces();
for (int i=0; i<stateForces.size();i++) {
forcesNode.createChildNode("Force").setDoubleProperty("x", stateForces[i][0]).setDoubleProperty("y", stateForces[i][1]).setDoubleProperty("z", stateForces[i][2]);
}
} catch (const OpenMMException &) {
// do nothing
}
}
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));
}
void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const AmoebaWcaDispersionForce& force = *reinterpret_cast<const AmoebaWcaDispersionForce*>(object);
node.setDoubleProperty("Epso", force.getEpso());
node.setDoubleProperty("Epsh", force.getEpsh());
node.setDoubleProperty("Rmino", force.getRmino());
node.setDoubleProperty("Rminh", force.getRminh());
node.setDoubleProperty("Awater", force.getAwater());
node.setDoubleProperty("Shctd", force.getShctd());
node.setDoubleProperty("Dispoff", force.getDispoff());
node.setDoubleProperty("Slevy", force.getSlevy());
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").setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
}
}