TestDrudeSCFIntegrator.h

/* -------------------------------------------------------------------------- *
 *                                   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) 2013 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
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/**
 * This tests the Reference implementation of DrudeSCFIntegrator.
 */

#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/VirtualSite.h"
#include "openmm/DrudeForce.h"
#include "openmm/DrudeSCFIntegrator.h"
#include "SimTKOpenMMUtilities.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

void testWater() {
    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
    // and Drude particles.
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const double spacing = 0.6;
    const double boxSize = spacing*(gridSize+1);
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    DrudeForce* drude = new DrudeForce();
    system.addForce(nonbonded);
    system.addForce(drude);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(1.0);
    for (int i = 0; i < numMolecules; i++) {
        int startIndex = system.getNumParticles();
        system.addParticle(15.6); // O
        system.addParticle(0.4);  // D
        system.addParticle(1.0);  // H1
        system.addParticle(1.0);  // H2
        system.addParticle(0.0);  // M
        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
        nonbonded->addParticle(-1.71636, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(-1.11466, 1, 0);
        for (int j = 0; j < 5; j++)
            for (int k = 0; k < j; k++)
                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
        system.addConstraint(startIndex, startIndex+2, 0.09572);
        system.addConstraint(startIndex, startIndex+3, 0.09572);
        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
    }
    vector<Vec3> positions;
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                Vec3 pos(i*spacing, j*spacing, k*spacing);
                positions.push_back(pos);
                positions.push_back(pos);
                positions.push_back(pos+Vec3(0.09572, 0, 0));
                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
                positions.push_back(pos);
            }

    // Simulate it and check energy conservation and the total force on the Drude particles.

    DrudeSCFIntegrator integ(0.0005);
    Context context(system, integ, platform);
    context.setPositions(positions);
    context.applyConstraints(1e-5);
    context.setVelocitiesToTemperature(300.0);
    State state = context.getState(State::Energy);
    double initialEnergy;
    int numSteps = 1000;
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        state = context.getState(State::Energy | State::Forces);
        if (i == 0)
            initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
        else
            ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
        const vector<Vec3>& force = state.getForces();
        double norm = 0.0;
        for (int j = 1; j < (int) force.size(); j += 5)
            norm += sqrt(force[j].dot(force[j]));
        norm = (norm/numMolecules);
        ASSERT(norm < 1.0);
    }
}

void testInitialTemperature() {
    // Check temperature initialization for a collection of randomly placed particles
    const int numRealParticles = 500000;
    const int numParticles = 2 * numRealParticles;
    const int nDoF = 3 * numRealParticles;
    const double targetTemperature = 300;
    const double drudeTemperature = 0;
    const double realMass = 10;
    const double drudeMass = 1;
    System system;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    std::vector<Vec3> positions(numParticles);
    DrudeForce* drude = new DrudeForce();

    for (int i = 0; i < numRealParticles; i++) {
        system.addParticle(realMass);
        system.addParticle(drudeMass);
        positions[2*i][0] = genrand_real2(sfmt);
        positions[2*i][1] = genrand_real2(sfmt);
        positions[2*i][2] = genrand_real2(sfmt);
        positions[2*i+1][0] = positions[2*i][0] + 0.01*genrand_real2(sfmt);
        positions[2*i+1][1] = positions[2*i][1] + 0.01*genrand_real2(sfmt);
        positions[2*i+1][2] = positions[2*i][2] + 0.01*genrand_real2(sfmt);
        drude->addParticle(2*i+1, 2*i, -1, -1, -1, -1.0, 0.001, 1, 1);
    }
    system.addForce(drude);

    DrudeSCFIntegrator integrator(0.001);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(targetTemperature);
    auto velocities = context.getState(State::Velocities).getVelocities();
    double comKineticEnergy = 0;
    double relKineticEnergy = 0;
    for (int i = 0; i < numRealParticles; i++) {
        int m1 = realMass;
        int m2 = drudeMass;
        Vec3 v1 = velocities[2*i];
        Vec3 v2 = velocities[2*i + 1];
        double invMass = 1.0 / (m1 + m2);
        double redMass = m1 * m2 * invMass;
        double fracM1 = m1 * invMass;
        double fracM2 = m2 * invMass;
        Vec3 comVelocity = fracM1 * v1 + fracM2 * v2;
        Vec3 relVelocity = v2 - v1;

        comKineticEnergy += 0.5 * (m1 + m2) * comVelocity.dot(comVelocity);
        relKineticEnergy += 0.5 * redMass * relVelocity.dot(relVelocity);
    }
    double comTemperature = (2*comKineticEnergy / (nDoF*BOLTZ));
    double relTemperature = (2*relKineticEnergy / (nDoF*BOLTZ));
    ASSERT_USUALLY_EQUAL_TOL(targetTemperature, comTemperature, 0.01);
    ASSERT_USUALLY_EQUAL_TOL(drudeTemperature, relTemperature, 0.01);
}

void setupKernels(int argc, char* argv[]);
void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        setupKernels(argc, argv);
        testWater();
        runPlatformTests();
        testInitialTemperature();
    }
    catch(const std::exception& e) {
        std::cout << "exception: " << e.what() << std::endl;
        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
        return 1;
    }
    std::cout << "Done" << std::endl;
    return 0;
}