TestReferenceAndersenThermostat.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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/**
 * This tests the reference implementation of AndersenThermostat.
 */

#include "../../../tests/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

void testTemperature() {
    const int numParticles = 8;
    const double temp = 100.0;
    const double collisionFreq = 10.0;
    const int numSteps = 10000;
    ReferencePlatform platform;
    System system;
    VerletIntegrator integrator(0.005);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermstat);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numParticles; ++i)
        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
    context.setPositions(positions);
    
    // Let it equilibrate.
    
    integrator.step(10000);
    
    // Now run it for a while and see if the temperature is correct.
    
    double ke = 0.0;
    for (int i = 0; i < numSteps; ++i) {
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
        integrator.step(1);
    }
    ke /= numSteps;
    double expected = 0.5*numParticles*3*BOLTZ*temp;
    ASSERT_EQUAL_TOL(expected, ke, 6/std::sqrt((double) numSteps));
}

void testConstraints() {
    const int numParticles = 8;
    const double temp = 100.0;
    const double collisionFreq = 10.0;
    const int numSteps = 10000;
    ReferencePlatform platform;
    System system;
    VerletIntegrator integrator(0.005);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    system.addConstraint(0, 1, 1);
    system.addConstraint(1, 2, 1);
    system.addConstraint(2, 3, 1);
    system.addConstraint(3, 0, 1);
    system.addConstraint(4, 5, 1);
    system.addConstraint(5, 6, 1);
    system.addConstraint(6, 7, 1);
    system.addConstraint(7, 4, 1);
    AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermstat);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(1, 0, 0);
    positions[2] = Vec3(1, 1, 0);
    positions[3] = Vec3(0, 1, 0);
    positions[4] = Vec3(1, 0, 1);
    positions[5] = Vec3(1, 1, 1);
    positions[6] = Vec3(0, 1, 1);
    positions[7] = Vec3(0, 0, 1);
    context.setPositions(positions);

    // Let it equilibrate.

    integrator.step(10000);

    // Now run it for a while and see if the temperature is correct.

    double ke = 0.0;
    for (int i = 0; i < numSteps; ++i) {
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
        integrator.step(1);
    }
    ke /= numSteps;
    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
    ASSERT_EQUAL_TOL(expected, ke, 6/std::sqrt((double) numSteps));
}

void testRandomSeed() {
    const int numParticles = 8;
    const double temp = 100.0;
    const double collisionFreq = 10.0;
    ReferencePlatform platform;
    System system;
    VerletIntegrator integrator(0.01);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermostat);
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    for (int i = 0; i < numParticles; ++i) {
        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
        velocities[i] = Vec3(0, 0, 0);
    }

    // Try twice with the same random seed.

    thermostat->setRandomNumberSeed(5);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state1 = context.getState(State::Positions);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state2 = context.getState(State::Positions);

    // Try twice with a different random seed.

    thermostat->setRandomNumberSeed(10);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state3 = context.getState(State::Positions);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state4 = context.getState(State::Positions);

    // Compare the results.

    for (int i = 0; i < numParticles; i++) {
        for (int j = 0; j < 3; j++) {
            ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
            ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
        }
    }
}

int main() {
    try {
        testTemperature();
        testConstraints();
        testRandomSeed();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}