NonbondedForceProxy.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * 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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#include "openmm/serialization/NonbondedForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/NonbondedForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce") {
}

void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 1);
    const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
    node.setIntProperty("method", (int) force.getNonbondedMethod());
    node.setDoubleProperty("cutoff", force.getCutoffDistance());
    node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
    node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
    node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
    node.setDoubleProperty("rfDielectric", force.getReactionFieldDielectric());
    node.setIntProperty("dispersionCorrection", force.getUseDispersionCorrection());
    double alpha;
    int nx, ny, nz;
    force.getPMEParameters(alpha, nx, ny, nz);
    node.setDoubleProperty("alpha", alpha);
    node.setIntProperty("nx", nx);
    node.setIntProperty("ny", ny);
    node.setIntProperty("nz", nz);
    node.setIntProperty("recipForceGroup", force.getReciprocalSpaceForceGroup());
    SerializationNode& particles = node.createChildNode("Particles");
    for (int i = 0; i < force.getNumParticles(); i++) {
        double charge, sigma, epsilon;
        force.getParticleParameters(i, charge, sigma, epsilon);
        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
    }
    SerializationNode& exceptions = node.createChildNode("Exceptions");
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
        exceptions.createChildNode("Exception").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("q", chargeProd).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
    }
}

void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
    if (node.getIntProperty("version") != 1)
        throw OpenMMException("Unsupported version number");
    NonbondedForce* force = new NonbondedForce();
    try {
        force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
        force->setCutoffDistance(node.getDoubleProperty("cutoff",1.0));
        force->setUseSwitchingFunction(node.getDoubleProperty("useSwitchingFunction",false));
        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance",-1.0));
        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance",5e-4));
        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric",78.3));
        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection",true));
        double alpha;
        int nx, ny, nz;
        alpha = node.getDoubleProperty("alpha",0.0);
        nx = node.getIntProperty("nx",0);
        ny = node.getIntProperty("ny",0);
        nz = node.getIntProperty("nz",0);
        force->setPMEParameters(alpha, nx, ny, nz);
        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup",-1));
        const SerializationNode& particles = node.getChildNode("Particles");
        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
            const SerializationNode& particle = particles.getChildren()[i];
            force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"));
        }
        const SerializationNode& exceptions = node.getChildNode("Exceptions");
        for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
            const SerializationNode& exception = exceptions.getChildren()[i];
            force->addException(exception.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("q"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
        }
    }
    catch (...) {
        delete force;
        throw;
    }
    return force;
}