ATMForceProxy.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.               *
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 * Authors: Peter Eastman                                                     *
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#include "openmm/serialization/ATMForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/ATMForce.h"
#include "openmm/OpenMMException.h"
#include <vector>
#include <sstream>

using namespace OpenMM;
using namespace std;

ATMForceProxy::ATMForceProxy() : SerializationProxy("ATMForce") {
}

void ATMForceProxy::storeParams(int numParticles, ATMForce& force, const SerializationNode& particles) const {
    for (auto& p : particles.getChildren()){

        //support older serialized ATMForce instances that did not store the transformation type
        //or the particle offset displacement indexes
        if (p.hasProperty("type")) {
            //normal behavior
            string type = p.getStringProperty("type");
            if (type == "fixed") {
                force.addParticle(new ATMForce::FixedDisplacement(Vec3(p.getDoubleProperty("d1x"), p.getDoubleProperty("d1y"), p.getDoubleProperty("d1z")), Vec3(p.getDoubleProperty("d0x"), p.getDoubleProperty("d0y"), p.getDoubleProperty("d0z"))));
            }
            else if (type == "offset") {
                force.addParticle(new ATMForce::ParticleOffsetDisplacement(p.getIntProperty("pj1"), p.getIntProperty("pi1"), p.getIntProperty("pj0"), p.getIntProperty("pi0")));
            }
            else {
                throw OpenMMException("storeParams(): invalid particle transformation type");
            }
        }
        else if (p.hasProperty("pj1") &&  p.getIntProperty("pj1") >= 0) {
            //missing type, but particle offset indexes are present
            force.addParticle(new ATMForce::ParticleOffsetDisplacement(p.getIntProperty("pj1"), p.getIntProperty("pi1"), p.getIntProperty("pj0"), p.getIntProperty("pi0")));
        }
        else {
            //only displacements are present
            force.addParticle(new ATMForce::FixedDisplacement(Vec3(p.getDoubleProperty("d1x"), p.getDoubleProperty("d1y"), p.getDoubleProperty("d1z")), Vec3(p.getDoubleProperty("d0x"), p.getDoubleProperty("d0y"), p.getDoubleProperty("d0z"))));
        }

    }
}

void ATMForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 0);
    const ATMForce& force = *reinterpret_cast<const ATMForce*> (object);
    node.setIntProperty("forceGroup", force.getForceGroup());
    node.setStringProperty("name", force.getName());
    node.setStringProperty("energy", force.getEnergyFunction());
    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& forces = node.createChildNode("Forces");
    for (int i = 0; i < force.getNumForces(); i++) {
        SerializationNode& f = forces.createChildNode("Force");
        f.createChildNode("Force", &force.getForce(i));
    }
    SerializationNode& particles = node.createChildNode("Particles");

    int numParticles = force.getNumParticles();
    string type;
    int j1, i1, j0, i0;
    Vec3 d1, d0;
    for (int i = 0; i < force.getNumParticles(); i++) {
        const ATMForce::CoordinateTransformation& transformation = force.getParticleTransformation(i);
        if (dynamic_cast<const ATMForce::FixedDisplacement*>(&transformation) != nullptr) {
            const ATMForce::FixedDisplacement* fd = dynamic_cast<const ATMForce::FixedDisplacement*>(&transformation);
            d1 = fd->getFixedDisplacement1();
            d0 = fd->getFixedDisplacement0();
            j1 = i1 = j0 = i0 = -1;
            type = "fixed";
        }
        else if (dynamic_cast<const ATMForce::ParticleOffsetDisplacement*>(&transformation) != nullptr) {
            const ATMForce::ParticleOffsetDisplacement* vd = dynamic_cast<const ATMForce::ParticleOffsetDisplacement*>(&transformation);
            d1 = Vec3(0, 0, 0);
            d0 = Vec3(0, 0, 0);
            j1 = vd->getDestinationParticle1();
            i1 = vd->getOriginParticle1();
            j0 = vd->getDestinationParticle0();
            i0 = vd->getOriginParticle0();
            type = "offset";
        }
        else {
            throw OpenMMException("serialize(): invalid particle CoordinateTransformation");
        }
        particles.createChildNode("Particle").setStringProperty("type", type)
            .setDoubleProperty("d1x", d1[0]).setDoubleProperty("d1y", d1[1]).setDoubleProperty("d1z", d1[2])
            .setDoubleProperty("d0x", d0[0]).setDoubleProperty("d0y", d0[1]).setDoubleProperty("d0z", d0[2])
            .setIntProperty("pj1", j1).setIntProperty("pi1", i1).setIntProperty("pj0", j0).setIntProperty("pi0", i0);
    }
}

void* ATMForceProxy::deserialize(const SerializationNode& node) const {
    int version = node.getIntProperty("version");
    if (version != 0)
        throw OpenMMException("Unsupported version number");
    ATMForce* force = nullptr;
    try {
        ATMForce* force = new ATMForce(node.getStringProperty("energy"));
        force->setForceGroup(node.getIntProperty("forceGroup", 0));
        force->setName(node.getStringProperty("name", force->getName()));
        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
        for (auto& parameter : globalParams.getChildren())
            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
        const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
        for (auto& parameter : energyDerivs.getChildren())
            force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
        const SerializationNode& forces = node.getChildNode("Forces");
        for (auto& f : forces.getChildren())
            force->addForce(f.getChildren()[0].decodeObject<Force>());
        const SerializationNode& particles = node.getChildNode("Particles");

        storeParams(force->getNumParticles(), *force, particles);

        return force;
    }
    catch (...) {
        if (force != NULL)
            delete force;
        throw;
    }
}