State.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) 2008-2016 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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 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
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#include "openmm/OpenMMException.h"
#include "openmm/State.h"

using namespace OpenMM;
using namespace std;

double State::getTime() const {
    return time;
}
long long State::getStepCount() const {
    return stepCount;
}
const vector<Vec3>& State::getPositions() const {
    if ((types&Positions) == 0)
        throw OpenMMException("Invoked getPositions() on a State which does not contain positions.");
    return positions;
}
const vector<Vec3>& State::getVelocities() const {
    if ((types&Velocities) == 0)
        throw OpenMMException("Invoked getVelocities() on a State which does not contain velocities.");
    return velocities;
}
const vector<Vec3>& State::getForces() const {
    if ((types&Forces) == 0)
        throw OpenMMException("Invoked getForces() on a State which does not contain forces.");
    return forces;
}
double State::getKineticEnergy() const {
    if ((types&Energy) == 0)
        throw OpenMMException("Invoked getKineticEnergy() on a State which does not contain energies.");
    return ke;
}
double State::getPotentialEnergy() const {
    if ((types&Energy) == 0)
        throw OpenMMException("Invoked getPotentialEnergy() on a State which does not contain energies.");
    return pe;
}
void State::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
    a = periodicBoxVectors[0];
    b = periodicBoxVectors[1];
    c = periodicBoxVectors[2];
}
double State::getPeriodicBoxVolume() const {
    return periodicBoxVectors[0].dot(periodicBoxVectors[1].cross(periodicBoxVectors[2]));
}
const map<string, double>& State::getParameters() const {
    if ((types&Parameters) == 0)
        throw OpenMMException("Invoked getParameters() on a State which does not contain parameters.");
    return parameters;
}
const map<string, double>& State::getEnergyParameterDerivatives() const {
    if ((types&ParameterDerivatives) == 0)
        throw OpenMMException("Invoked getEnergyParameterDerivatives() on a State which does not contain parameter derivatives.");
    return energyParameterDerivatives;
}
const SerializationNode& State::getIntegratorParameters() const {
    if ((types&IntegratorParameters) == 0)
        throw OpenMMException("Invoked getPIntegratorarameters() on a State which does not contain integrator parameters.");
    return integratorParameters;
}
SerializationNode& State::updateIntegratorParameters() {
    types |= IntegratorParameters;
    integratorParameters.setName("IntegratorParameters");
    return integratorParameters;
}
int State::getDataTypes() const {
    return types;
}
State::State(double time, long long stepCount) : types(0), time(time), stepCount(stepCount), ke(0), pe(0) {
}
State::State() : types(0), time(0.0), ke(0), pe(0) {
}
void State::setPositions(const std::vector<Vec3>& pos) {
    positions = pos;
    types |= Positions;
}

void State::setVelocities(const std::vector<Vec3>& vel) {
    velocities = vel;
    types |= Velocities;
}

void State::setForces(const std::vector<Vec3>& force) {
    forces = force;
    types |= Forces;
}

void State::setParameters(const std::map<std::string, double>& params) {
    parameters = params;
    types |= Parameters;
}

void State::setEnergyParameterDerivatives(const std::map<std::string, double>& derivs) {
    energyParameterDerivatives = derivs;
    types |= ParameterDerivatives;
}

void State::setEnergy(double kinetic, double potential) {
    ke = kinetic;
    pe = potential;
    types |= Energy;
}

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

State::StateBuilder::StateBuilder(double time, long long stepCount) : state(time, stepCount) {
}

State State::StateBuilder::getState() {
    return state;
}

void State::StateBuilder::setPositions(const std::vector<Vec3>& pos) {
    state.setPositions(pos);
}

void State::StateBuilder::setVelocities(const std::vector<Vec3>& vel) {
    state.setVelocities(vel);
}

void State::StateBuilder::setForces(const std::vector<Vec3>& force) {
    state.setForces(force);
}

void State::StateBuilder::setParameters(const std::map<std::string, double>& params) {
    state.setParameters(params);
}

void State::StateBuilder::setEnergyParameterDerivatives(const std::map<std::string, double>& derivs) {
    state.setEnergyParameterDerivatives(derivs);
}

void State::StateBuilder::setEnergy(double ke, double pe) {
    state.setEnergy(ke, pe);
}

void State::StateBuilder::setPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c) {
    state.setPeriodicBoxVectors(a, b, c);
}

SerializationNode& State::StateBuilder::updateIntegratorParameters() {
    return state.updateIntegratorParameters();
}