AndersenThermostatImpl.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 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
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#include "internal/AndersenThermostatImpl.h"
#include "internal/OpenMMContextImpl.h"
#include "Integrator.h"
#include "System.h"
#include "kernels.h"
#include <vector>

using namespace OpenMM;
using std::vector;

AndersenThermostatImpl::AndersenThermostatImpl(AndersenThermostat& owner) : owner(owner) {
}

void AndersenThermostatImpl::initialize(OpenMMContextImpl& context) {
    kernel = context.getPlatform().createKernel(ApplyAndersenThermostatKernel::Name(), context);
    const System& system = context.getSystem();
    vector<double> masses(system.getNumAtoms());
    for (int i = 0; i < system.getNumAtoms(); ++i)
        masses[i] = system.getAtomMass(i);
    dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).initialize(masses);
}

void AndersenThermostatImpl::updateContextState(OpenMMContextImpl& context) {
    dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).execute(context.getVelocities(), context.getParameter(AndersenThermostat::Temperature),
            context.getParameter(AndersenThermostat::CollisionFrequency), context.getIntegrator().getStepSize());
}

std::map<std::string, double> AndersenThermostatImpl::getDefaultParameters() {
    std::map<std::string, double> parameters;
    parameters[AndersenThermostat::Temperature] = getOwner().getDefaultTemperature();
    parameters[AndersenThermostat::CollisionFrequency] = getOwner().getDefaultCollisionFrequency();
    return parameters;
}

std::vector<std::string> AndersenThermostatImpl::getKernelNames() {
    std::vector<std::string> names;
    names.push_back(ApplyAndersenThermostatKernel::Name());
    return names;
}