TestCpuEwald.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
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 * 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        *
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 * Authors: Peter Eastman                                                     *
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/**
 * This tests the Ewald summation method CPU implementation of NonbondedForce.
 */

#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

CpuPlatform platform;

const double TOL = 1e-5;

void testEwaldPME(bool includeExceptions) {

//      Use amorphous NaCl system for the tests

    const int numParticles = 894;
    const double cutoff = 1.2;
    const double boxSize = 3.00646;
    double tol = 1e-5;

    ReferencePlatform reference;
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setEwaldErrorTolerance(tol);

    for (int i = 0; i < numParticles/2; i++)
        system.addParticle(22.99);
    for (int i = 0; i < numParticles/2; i++)
        system.addParticle(35.45);
    for (int i = 0; i < numParticles/2; i++)
        nonbonded->addParticle(1.0, 1.0,0.0);
    for (int i = 0; i < numParticles/2; i++)
        nonbonded->addParticle(-1.0, 1.0,0.0);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(nonbonded);

    vector<Vec3> positions(numParticles);
    #include "nacl_amorph.dat"
    if (includeExceptions) {
        // Add some exclusions.

        for (int i = 0; i < numParticles-1; i++) {
            Vec3 delta = positions[i]-positions[i+1];
            if (sqrt(delta.dot(delta)) < 0.5*cutoff)
                nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
        }
    }

//    (1)  Check whether the Reference and CPU platforms agree when using Ewald Method

    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context cpuContext(system, integrator1, platform);
    Context referenceContext(system, integrator2, reference);
    cpuContext.setPositions(positions);
    referenceContext.setPositions(positions);
    State cpuState = cpuContext.getState(State::Forces | State::Energy);
    State referenceState = referenceContext.getState(State::Forces | State::Energy);
    tol = 1e-2;
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
    }
    tol = 1e-5;
    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);

//    (2) Check whether Ewald method in CPU is self-consistent

    double norm = 0.0;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 f = cpuState.getForces()[i];
        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
    }

    norm = std::sqrt(norm);
    const double delta = 5e-3;
    double step = delta/norm;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 p = positions[i];
        Vec3 f = cpuState.getForces()[i];
        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
    }
    VerletIntegrator integrator3(0.01);
    Context cpuContext2(system, integrator3, platform);
    cpuContext2.setPositions(positions);

    tol = 1e-2;
    State cpuState2 = cpuContext2.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (cpuState2.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)

//    (3)  Check whether the Reference and CPU platforms agree when using PME

    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    cpuContext.reinitialize();
    referenceContext.reinitialize();
    cpuContext.setPositions(positions);
    referenceContext.setPositions(positions);
    cpuState = cpuContext.getState(State::Forces | State::Energy);
    referenceState = referenceContext.getState(State::Forces | State::Energy);
    tol = 1e-2;
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
    }
    tol = 1e-5;
    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);

//    (4) Check whether PME method in CPU is self-consistent

    norm = 0.0;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 f = cpuState.getForces()[i];
        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
    }

    norm = std::sqrt(norm);
    step = delta/norm;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 p = positions[i];
        Vec3 f = cpuState.getForces()[i];
        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
    }
    VerletIntegrator integrator4(0.01);
    Context cpuContext3(system, integrator4, platform);
    cpuContext3.setPositions(positions);

    tol = 1e-2;
    State cpuState3 = cpuContext3.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (cpuState3.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
}

void testEwald2Ions() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->addParticle(1.0, 1, 0);
    nonbonded->addParticle(-1.0, 1, 0);
    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
    const double cutoff = 2.0;
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setEwaldErrorTolerance(TOL);
    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
    system.addForce(nonbonded);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(3.048000,2.764000,3.156000);
    positions[1] = Vec3(2.809000,2.888000,2.571000);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state.getForces();

    ASSERT_EQUAL_VEC(Vec3(-123.711,  64.1877, -302.716), forces[0], 10*TOL);
    ASSERT_EQUAL_VEC(Vec3( 123.711, -64.1877,  302.716), forces[1], 10*TOL);
    ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
}

void testTriclinic() {
    // Create a triclinic box containing eight particles.

    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
    for (int i = 0; i < 8; i++)
        system.addParticle(1.0);
    NonbondedForce* force = new NonbondedForce();
    system.addForce(force);
    force->setNonbondedMethod(NonbondedForce::PME);
    force->setCutoffDistance(1.0);
    force->setPMEParameters(3.45891, 32, 40, 48);
    for (int i = 0; i < 4; i++)
        force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
    for (int i = 0; i < 4; i++)
        force->addParticle(1, 0.332840, 0.0115897); // Na parameters
    vector<Vec3> positions(8);
    positions[0] = Vec3(1.744, 2.788, 3.162);
    positions[1] = Vec3(1.048, 0.762, 2.340);
    positions[2] = Vec3(2.489, 1.570, 2.817);
    positions[3] = Vec3(1.027, 1.893, 3.271);
    positions[4] = Vec3(0.937, 0.825, 0.009);
    positions[5] = Vec3(2.290, 1.887, 3.352);
    positions[6] = Vec3(1.266, 1.111, 2.894);
    positions[7] = Vec3(0.933, 1.862, 3.490);

    // Compute the forces and energy.

    VerletIntegrator integ(0.001);
    Context context(system, integ, platform);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);

    // Compare them to values computed by Gromacs.

    double expectedEnergy = -963.370;
    vector<Vec3> expectedForce(8);
    expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
    expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
    expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
    expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
    expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
    expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
    expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
    expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
    for (int i = 0; i < 8; i++) {
        ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
    }
    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}

void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
    // Create a cloud of random point charges.

    const int numParticles = 51;
    const double boxWidth = 5.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
    NonbondedForce* force = new NonbondedForce();
    system.addForce(force);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i < numParticles; i++) {
        system.addParticle(1.0);
        force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
        positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
    }
    force->setNonbondedMethod(method);

    // For various values of the cutoff and error tolerance, see if the actual error is reasonable.

    for (double cutoff = 1.0; cutoff < boxWidth/2; cutoff *= 1.2) {
        force->setCutoffDistance(cutoff);
        vector<Vec3> refForces;
        double norm = 0.0;
        for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
            force->setEwaldErrorTolerance(tol);
            VerletIntegrator integrator(0.01);
            Context context(system, integrator, platform);
            context.setPositions(positions);
            State state = context.getState(State::Forces);
            if (refForces.size() == 0) {
                refForces = state.getForces();
                for (int i = 0; i < numParticles; i++)
                    norm += refForces[i].dot(refForces[i]);
                norm = sqrt(norm);
            }
            else {
                double diff = 0.0;
                for (int i = 0; i < numParticles; i++) {
                    Vec3 delta = refForces[i]-state.getForces()[i];
                    diff += delta.dot(delta);
                }
                diff = sqrt(diff)/norm;
                ASSERT(diff < 2*tol);
            }
            if (method == NonbondedForce::PME) {
                // See if the PME parameters were calculated correctly.

                double expectedAlpha, actualAlpha;
                int expectedSize[3], actualSize[3];
                NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2]);
                force->getPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]);
                ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
                for (int i = 0; i < 3; i++) {
                    ASSERT(actualSize[i] >= expectedSize[i]);
                    ASSERT(actualSize[i] < expectedSize[i]+10);
                }
            }
        }
    }
}

int main(int argc, char* argv[]) {
    try {
        if (!CpuPlatform::isProcessorSupported()) {
            cout << "CPU is not supported.  Exiting." << endl;
            return 0;
        }
        testEwaldPME(false);
        testEwaldPME(true);
//        testEwald2Ions();
        testTriclinic();
        testErrorTolerance(NonbondedForce::Ewald);
        testErrorTolerance(NonbondedForce::PME);
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}