CustomCentroidBondForceProxy.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
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 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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 * Authors: Peter Eastman                                                     *
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#include "openmm/serialization/CustomCentroidBondForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/CustomCentroidBondForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProxy("CustomCentroidBondForce") {
}

void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 3);
    const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
    node.setIntProperty("forceGroup", force.getForceGroup());
    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
    node.setIntProperty("groups", force.getNumGroupsPerBond());
    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& groups = node.createChildNode("Groups");
    for (int i = 0; i < force.getNumGroups(); i++) {
        vector<int> particles;
        vector<double> weights;
        force.getGroupParameters(i, particles, weights);
        SerializationNode& group = groups.createChildNode("Group");
        for (int j = 0; j < (int) particles.size(); j++) {
            SerializationNode& node = group.createChildNode("Particle");
            node.setIntProperty("p", particles[j]);
            if (j < weights.size())
                node.setDoubleProperty("weight", weights[j]);
        }
    }
    SerializationNode& bonds = node.createChildNode("Bonds");
    for (int i = 0; i < force.getNumBonds(); i++) {
        vector<int> groups;
        vector<double> params;
        force.getBondParameters(i, groups, params);
        SerializationNode& bond = bonds.createChildNode("Bond");
        for (int j = 0; j < (int) groups.size(); j++) {
            stringstream key;
            key << "g";
            key << j+1;
            bond.setIntProperty(key.str(), groups[j]);
        }
        for (int j = 0; j < (int) params.size(); j++) {
            stringstream key;
            key << "param";
            key << j+1;
            bond.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* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
    int version = node.getIntProperty("version");
    if (version < 1 || version > 3)
        throw OpenMMException("Unsupported version number");
    CustomCentroidBondForce* force = NULL;
    try {
        CustomCentroidBondForce* force = new CustomCentroidBondForce(node.getIntProperty("groups"), node.getStringProperty("energy"));
        force->setForceGroup(node.getIntProperty("forceGroup", 0));
        if (version > 1)
            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
        const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
        for (auto& parameter : perBondParams.getChildren())
            force->addPerBondParameter(parameter.getStringProperty("name"));
        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
        for (auto& parameter : globalParams.getChildren())
            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
        if (version > 2) {
            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
            for (auto& parameter : energyDerivs.getChildren())
                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
        }
        const SerializationNode& groups = node.getChildNode("Groups");
        for (auto& group : groups.getChildren()) {
            vector<int> particles;
            vector<double> weights;
            for (auto& child : group.getChildren()) {
                particles.push_back(child.getIntProperty("p"));
                if (child.hasProperty("weight"))
                    weights.push_back(child.getDoubleProperty("weight"));
            }
            force->addGroup(particles, weights);
        }
        const SerializationNode& bonds = node.getChildNode("Bonds");
        vector<int> bondGroups(force->getNumGroupsPerBond());
        vector<double> params(force->getNumPerBondParameters());
        for (auto& bond : bonds.getChildren()) {
            for (int j = 0; j < (int) bondGroups.size(); j++) {
                stringstream key;
                key << "g";
                key << j+1;
                bondGroups[j] = bond.getIntProperty(key.str());
            }
            for (int j = 0; j < (int) params.size(); j++) {
                stringstream key;
                key << "param";
                key << j+1;
                params[j] = bond.getDoubleProperty(key.str());
            }
            force->addBond(bondGroups, params);
        }
        const SerializationNode& functions = node.getChildNode("Functions");
        for (auto& function : functions.getChildren()) {
            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 (auto& child : valuesNode.getChildren())
                    values.push_back(child.getDoubleProperty("v"));
                force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
            }
        }
        return force;
    }
    catch (...) {
        if (force != NULL)
            delete force;
        throw;
    }
}