AmoebaVdwForceProxy.cpp

/* -------------------------------------------------------------------------- *
 *                                OpenMMAmoeba                                *
 * -------------------------------------------------------------------------- *
 * 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.               *
 *                                                                            *
 * Portions copyright (c) 2010 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
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#include "openmm/serialization/AmoebaVdwForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/AmoebaVdwForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce") {
}

void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 1);
    const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);

    node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
    node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
    node.setDoubleProperty("VdwCutoff", force.getCutoff());

    node.setIntProperty("method", (int) force.getNonbondedMethod());

    SerializationNode& particles = node.createChildNode("VdwParticles").setIntProperty("size", force.getNumParticles() );
    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {

        int ivIndex;
        double sigma, epsilon, reductionFactor;
        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);

        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] );
        }
    }
}

void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
    if (node.getIntProperty("version") != 1)
        throw OpenMMException("Unsupported version number");
    AmoebaVdwForce* force = new AmoebaVdwForce();
    try {

        force->setSigmaCombiningRule(node.getStringProperty( "SigmaCombiningRule" ) );
        force->setEpsilonCombiningRule(node.getStringProperty( "EpsilonCombiningRule" ) );
        force->setCutoff(node.getDoubleProperty( "VdwCutoff" ) );
        force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));

        const SerializationNode& particles = node.getChildNode("VdwParticles");
        for (unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
            const SerializationNode& particle = particles.getChildren()[ii];
            force->addParticle(particle.getIntProperty("ivIndex"), particle.getDoubleProperty("sigma"), particle.getDoubleProperty("epsilon"), particle.getDoubleProperty("reductionFactor"));

            // exclusions

            const SerializationNode& particleExclusions = particle.getChildNode("ParticleExclusions");
            std::vector< int > exclusions;
            for (unsigned int jj = 0; jj < particleExclusions.getChildren().size(); jj++) {
                exclusions.push_back( particleExclusions.getChildren()[jj].getIntProperty("index") );
            }
            force->setParticleExclusions( ii, exclusions );
        }

    }
    catch (...) {
        delete force;
        throw;
    }
    return force;
}