CustomIntegratorProxy.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, Yutong Zhao                                        *
 * Contributors:                                                              *
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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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#include "openmm/serialization/CustomIntegratorProxy.h"
#include <OpenMM.h>

using namespace std;
using namespace OpenMM;

CustomIntegratorProxy::CustomIntegratorProxy() : SerializationProxy("CustomIntegrator") {

}

void CustomIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 2);
    const CustomIntegrator& integrator = *reinterpret_cast<const CustomIntegrator*>(object);
    SerializationNode& globalVariablesNode = node.createChildNode("GlobalVariables");
    for (int i = 0; i < integrator.getNumGlobalVariables(); i++) {
        globalVariablesNode.setDoubleProperty(integrator.getGlobalVariableName(i), integrator.getGlobalVariable(i));
    }
    SerializationNode& perDofVariablesNode = node.createChildNode("PerDofVariables");
    for (int i = 0; i < integrator.getNumPerDofVariables(); i++) {
        SerializationNode& perDofValuesNode = perDofVariablesNode.createChildNode(integrator.getPerDofVariableName(i));
        vector<Vec3> perDofValues; integrator.getPerDofVariable(i, perDofValues);
        for (int j = 0; j < perDofValues.size(); j++) {
            perDofValuesNode.createChildNode("Value").setDoubleProperty("x",perDofValues[j][0]).setDoubleProperty("y",perDofValues[j][1]).setDoubleProperty("z",perDofValues[j][2]);
        }
    }
    SerializationNode& computationsNode = node.createChildNode("Computations");
    for (int i = 0; i < integrator.getNumComputations(); i++) {
        CustomIntegrator::ComputationType computationType;
        string computationVariable;
        string computationExpression;
        integrator.getComputationStep(i, computationType, computationVariable, computationExpression);
        computationsNode.createChildNode("Computation").setIntProperty("computationType",static_cast<int>(computationType))
            .setStringProperty("computationVariable",computationVariable).setStringProperty("computationExpression",computationExpression);
    }
    SerializationNode& functions = node.createChildNode("Functions");
    for (int i = 0; i < integrator.getNumTabulatedFunctions(); i++)
        functions.createChildNode("Function", &integrator.getTabulatedFunction(i)).setStringProperty("name", integrator.getTabulatedFunctionName(i));
    node.setStringProperty("kineticEnergyExpression",integrator.getKineticEnergyExpression());
    node.setIntProperty("randomSeed",integrator.getRandomNumberSeed());
    node.setDoubleProperty("stepSize",integrator.getStepSize());
    node.setDoubleProperty("constraintTolerance",integrator.getConstraintTolerance());
}

void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
    int version = node.getIntProperty("version");
    if (version < 1 || version > 2)
        throw OpenMMException("Unsupported version number");
    CustomIntegrator* integrator = new CustomIntegrator(node.getDoubleProperty("stepSize"));
    const SerializationNode& globalVariablesNode = node.getChildNode("GlobalVariables");
    for (auto& prop : globalVariablesNode.getProperties())
        integrator->addGlobalVariable(prop.first, globalVariablesNode.getDoubleProperty(prop.first));
    const SerializationNode& perDofVariablesNode = node.getChildNode("PerDofVariables");
    int count = 0;
    for (auto& var : perDofVariablesNode.getChildren()) {
        integrator->addPerDofVariable(var.getName(), 0);
        vector<Vec3> perDofValues;
        for (auto& child : var.getChildren())
            perDofValues.push_back(Vec3(child.getDoubleProperty("x"), child.getDoubleProperty("y"), child.getDoubleProperty("z")));
        integrator->setPerDofVariable(count, perDofValues);
        count++;
    }
    const SerializationNode& computationsNode = node.getChildNode("Computations");
    for (auto& comp : computationsNode.getChildren()) {
        CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(comp.getIntProperty("computationType"));
        // make sure that the int casts to a valid enum
        if (computationType == CustomIntegrator::ComputeGlobal) {
            integrator->addComputeGlobal(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
        } else if (computationType == CustomIntegrator::ComputePerDof) {
            integrator->addComputePerDof(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
        } else if (computationType == CustomIntegrator::ComputeSum) {
            integrator->addComputeSum(comp.getStringProperty("computationVariable"), comp.getStringProperty("computationExpression"));
        } else if (computationType == CustomIntegrator::ConstrainPositions) {
            integrator->addConstrainPositions();
        } else if (computationType == CustomIntegrator::ConstrainVelocities) {
            integrator->addConstrainVelocities();
        } else if (computationType == CustomIntegrator::UpdateContextState) {
            integrator->addUpdateContextState();
        } else if (computationType == CustomIntegrator::IfBlockStart) {
            integrator->beginIfBlock(comp.getStringProperty("computationExpression"));
        } else if (computationType == CustomIntegrator::WhileBlockStart) {
            integrator->beginWhileBlock(comp.getStringProperty("computationExpression"));
        } else if (computationType == CustomIntegrator::BlockEnd) {
            integrator->endBlock();
        } else {
            throw(OpenMMException("Custom Integrator Deserialization: Unknown computation type"));
        }
    }
    if (version > 1) {
        const SerializationNode& functions = node.getChildNode("Functions");
        for (auto& function : functions.getChildren())
            integrator->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
    }
    integrator->setKineticEnergyExpression(node.getStringProperty("kineticEnergyExpression"));
    integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
    return integrator;
}