AmoebaGeneralizedKirkwoodForceProxy.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  *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
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 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
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#include "openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/AmoebaGeneralizedKirkwoodForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

AmoebaGeneralizedKirkwoodForceProxy::AmoebaGeneralizedKirkwoodForceProxy() : SerializationProxy("AmoebaGeneralizedKirkwoodForce") {
}

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

    node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric() );
    node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric",  force.getSoluteDielectric() );
    //node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset",  force.getDielectricOffset() );
    node.setDoubleProperty("GeneralizedKirkwoodProbeRadius",       force.getProbeRadius() );
    node.setDoubleProperty("GeneralizedKirkwoodSurfaceAreaFactor", force.getSurfaceAreaFactor() );
    node.setIntProperty(   "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm() );

    SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles").setIntProperty( "size", force.getNumParticles() );
    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
        double radius, charge, scalingFactor;
        force.getParticleParameters( ii, charge, radius, scalingFactor );
        particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);
    }

}

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

        force->setSolventDielectric(   node.getDoubleProperty( "GeneralizedKirkwoodSolventDielectric" ) );
        force->setSoluteDielectric(    node.getDoubleProperty( "GeneralizedKirkwoodSoluteDielectric" ) );
        //force->setDielectricOffset(    node.getDoubleProperty( "GeneralizedKirkwoodDielectricOffset" ) );
        force->setProbeRadius(         node.getDoubleProperty( "GeneralizedKirkwoodProbeRadius" ) );
        force->setSurfaceAreaFactor(   node.getDoubleProperty( "GeneralizedKirkwoodSurfaceAreaFactor" ) );
        force->setIncludeCavityTerm(   node.getIntProperty(    "GeneralizedKirkwoodIncludeCavityTerm" ) );

        const SerializationNode& particles = node.getChildNode("GeneralizedKirkwoodParticles");
        for (unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
            const SerializationNode& particle = particles.getChildren()[ii];
            force->addParticle( particle.getDoubleProperty("charge"), particle.getDoubleProperty("radius"), particle.getDoubleProperty("scaleFactor"));
        }
    }
    catch (...) {
        delete force;
        throw;
    }

    return force;
}