TestRMSDForce.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) 2018 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
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#include "openmm/internal/AssertionUtilities.h"
#include "openmm/RMSDForce.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <cmath>
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

double estimateRMSD(vector<Vec3>& positions, vector<Vec3>& referencePos, vector<int>& particles) {
    // Estimate the RMSD.  For simplicity we omit the orientation alignment, but they should
    // already be almost perfectly aligned.
    
    Vec3 center1, center2;
    for (int i : particles) {
        center1 += referencePos[i];
        center2 += positions[i];
    }
    center1 /= particles.size();
    center2 /= particles.size();
    double estimate = 0.0;
    for (int i : particles) {
        Vec3 delta = (referencePos[i]-center1) - (positions[i]-center2);
        estimate += delta.dot(delta);
    }
    return sqrt(estimate/particles.size());
}

void testRMSD() {
    const int numParticles = 20;
    System system;
    vector<Vec3> referencePos(numParticles);
    vector<Vec3> positions(numParticles);
    vector<int> particles;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(1.0);
        referencePos[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*10;
        positions[i] = referencePos[i] + Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*0.2;
        if (i%5 != 0)
            particles.push_back(i);
    }
    RMSDForce* force = new RMSDForce(referencePos, particles);
    system.addForce(force);
    VerletIntegrator integrator(0.001);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    double estimate = estimateRMSD(positions, referencePos, particles);
    
    // Have the force compute the RMSD.  It should be very slightly less than
    // what we calculated above (since that omitted the rotation).
    
    State state1 = context.getState(State::Energy);
    double rmsd = state1.getPotentialEnergy();
    ASSERT(rmsd <= estimate);
    ASSERT(rmsd > 0.9*estimate);

    // Translate and rotate all the particles.  This should have no effect on the RMSD.

    vector<Vec3> transformedPos(numParticles);
    double cs = cos(1.1), sn = sin(1.1);
    for (int i = 0; i < numParticles; i++) {
        Vec3 p = positions[i];
        transformedPos[i] = Vec3( cs*p[0] + sn*p[1] + 0.1,
                                 -sn*p[0] + cs*p[1] - 11.3,
                                  p[2] + 1.5);
    }
    context.setPositions(transformedPos);
    state1 = context.getState(State::Energy | State::Forces);
    ASSERT_EQUAL_TOL(rmsd, state1.getPotentialEnergy(), 1e-4);

    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.

    const vector<Vec3>& forces = state1.getForces();
    double norm = 0.0;
    for (int i = 0; i < (int) forces.size(); ++i)
        norm += forces[i].dot(forces[i]);
    norm = std::sqrt(norm);
    const double stepSize = 0.1;
    double step = 0.5*stepSize/norm;
    vector<Vec3> positions2(numParticles), positions3(numParticles);
    for (int i = 0; i < (int) positions.size(); ++i) {
        Vec3 p = transformedPos[i];
        Vec3 f = forces[i];
        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
    }
    context.setPositions(positions2);
    State state2 = context.getState(State::Energy);
    context.setPositions(positions3);
    State state3 = context.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
    
    // Check that updateParametersInContext() works correctly.
    
    context.setPositions(transformedPos);
    force->setReferencePositions(transformedPos);
    force->updateParametersInContext(context);
    ASSERT_EQUAL_TOL(0.0, context.getState(State::Energy).getPotentialEnergy(), 1e-2);
    context.setPositions(referencePos);
    ASSERT_EQUAL_TOL(rmsd, context.getState(State::Energy).getPotentialEnergy(), 1e-4);

    // Verify that giving an empty list of particles is interpreted to mean all particles.

    vector<int> allParticles;
    for (int i = 0; i < numParticles; i++)
        allParticles.push_back(i);
    estimate = estimateRMSD(positions, referencePos, allParticles);
    force->setParticles(allParticles);
    force->setReferencePositions(referencePos);
    force->updateParametersInContext(context);
    context.setPositions(positions);
    double rmsd1 = context.getState(State::Energy).getPotentialEnergy();
    force->setParticles(vector<int>());
    force->updateParametersInContext(context);
    double rmsd2 = context.getState(State::Energy).getPotentialEnergy();
    ASSERT_EQUAL_TOL(rmsd1, rmsd2, 1e-4);
    ASSERT(rmsd1 <= estimate);
    ASSERT(rmsd1 > 0.9*estimate);
}

void testEnergyConservation() {
    const int numParticles = 50;
    System system;
    vector<Vec3> referencePos(numParticles);
    vector<Vec3> positions(numParticles);
    vector<int> particles;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    NonbondedForce* nb = new NonbondedForce(); // Add a nonbonded force to activate reordering on the GPU
    nb->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    system.addForce(nb);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        nb->addParticle(0.0, 0.1, 0.01);
        positions[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*5;
        referencePos[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*5;
        if (genrand_real2(sfmt) < 0.5)
            particles.push_back(i);
    }
    RMSDForce* force = new RMSDForce(referencePos, particles);
    system.addForce(force);
    VerletIntegrator integrator(0.001);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(300.0, 0);
    integrator.step(5);
    State initialState = context.getState(State::Energy);
    double energy = initialState.getPotentialEnergy()+initialState.getKineticEnergy();
    for (int i = 0; i < 100; i++) {
        integrator.step(5);
        State state = context.getState(State::Energy);
        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy()+state.getKineticEnergy(), 1e-4);
    }

    // If we modify the reference positions, the energy should change.

    for (int i = 0; i < numParticles; ++i)
        referencePos[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*5;
    force->setReferencePositions(referencePos);
    force->updateParametersInContext(context);
    State state2 = context.getState(State::Energy);
    double energy2 = state2.getPotentialEnergy()+state2.getKineticEnergy();
    ASSERT(fabs(energy-energy2) > 1e-3);

    // Make sure it's still conserved.

    for (int i = 0; i < 100; i++) {
        integrator.step(5);
        State state = context.getState(State::Energy);
        ASSERT_EQUAL_TOL(energy2, state.getPotentialEnergy()+state.getKineticEnergy(), 1e-4);
    }
}

void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        initializeTests(argc, argv);
        testRMSD();
        testEnergyConservation();
        runPlatformTests();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}