Context.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) 2008-2009 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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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 *
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#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"

using namespace OpenMM;
using namespace std;

Context::Context(System& system, Integrator& integrator) : properties(map<string, string>()) {
    impl = new ContextImpl(*this, system, integrator, 0, properties);
    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
}

Context::Context(System& system, Integrator& integrator, Platform& platform) : properties(map<string, string>()) {
    impl = new ContextImpl(*this, system, integrator, &platform, properties);
    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
}

Context::Context(System& system, Integrator& integrator, Platform& platform, const map<string, string>& properties) : properties(properties) {
    impl = new ContextImpl(*this, system, integrator, &platform, properties);
    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
}

Context::~Context() {
	delete impl;
}

const System& Context::getSystem() const {
    return impl->getSystem();

}

System& Context::getSystem() {
    return impl->getSystem();
}

const Integrator& Context::getIntegrator() const {
    return impl->getIntegrator();
}

Integrator& Context::getIntegrator() {
    return impl->getIntegrator();
}

const Platform& Context::getPlatform() const {
    return impl->getPlatform();
}

Platform& Context::getPlatform() {
    return impl->getPlatform();
}

State Context::getState(int types) const {
    State state(impl->getTime(), impl->getSystem().getNumParticles(), State::DataType(types));
    if (types&State::Energy)
        state.setEnergy(impl->calcKineticEnergy(), impl->calcPotentialEnergy());
    if (types&State::Forces) {
        impl->calcForces();
        impl->getForces(state.updForces());
    }
    if (types&State::Parameters) {
        for (map<string, double>::const_iterator iter = impl->parameters.begin(); iter != impl->parameters.end(); iter++)
            state.updParameters()[iter->first] = iter->second;
    }
    if (types&State::Positions)
        impl->getPositions(state.updPositions());
    if (types&State::Velocities)
        impl->getVelocities(state.updVelocities());
    return state;
}

void Context::setTime(double time) {
    impl->setTime(time);
}

void Context::setPositions(const vector<Vec3>& positions) {
    if ((int) positions.size() != impl->getSystem().getNumParticles())
        throw OpenMMException("Called setPositions() on a Context with the wrong number of positions");
    impl->setPositions(positions);
}

void Context::setVelocities(const vector<Vec3>& velocities) {
    if ((int) velocities.size() != impl->getSystem().getNumParticles())
        throw OpenMMException("Called setVelocities() on a Context with the wrong number of velocities");
    impl->setVelocities(velocities);
}

double Context::getParameter(const string& name) {
    return impl->getParameter(name);
}

void Context::setParameter(const string& name, double value) {
    impl->setParameter(name, value);
}

void Context::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
    a = periodicBoxVectors[0];
    b = periodicBoxVectors[1];
    c = periodicBoxVectors[2];
}

void Context::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
    if (a[1] != 0.0 || a[2] != 0.0)
        throw OpenMMException("First periodic box vector must be parallel to x.");
    if (b[0] != 0.0 || b[2] != 0.0)
        throw OpenMMException("Second periodic box vector must be parallel to y.");
    if (c[0] != 0.0 || c[1] != 0.0)
        throw OpenMMException("Third periodic box vector must be parallel to z.");
    periodicBoxVectors[0] = a;
    periodicBoxVectors[1] = b;
    periodicBoxVectors[2] = c;
}

void Context::reinitialize() {
    System& system = impl->getSystem();
    Integrator& integrator = impl->getIntegrator();
    Platform& platform = impl->getPlatform();
    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
    delete impl;
    impl = new ContextImpl(*this, system, integrator, &platform, properties);
}