TestReferenceRpmd.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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 * Portions copyright (c) 2011-2013 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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/**
 * This tests the Reference implementation of RPMDIntegrator.
 */

#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/RPMDIntegrator.h"
#include "openmm/VirtualSite.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

void testFreeParticles() {
    const int numParticles = 100;
    const int numCopies = 30;
    const double temperature = 300.0;
    const double mass = 1.0;
    System system;
    for (int i = 0; i < numParticles; i++)
        system.addParticle(mass);
    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numCopies; i++)
    {
        for (int j = 0; j < numParticles; j++)
            positions[j] = Vec3(0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt));
        integ.setPositions(i, positions);
    }
    const int numSteps = 1000;
    integ.step(1000);
    vector<double> ke(numCopies, 0.0);
    vector<double> rg(numParticles, 0.0);
    const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        vector<State> state(numCopies);
        for (int j = 0; j < numCopies; j++)
            state[j] = integ.getState(j, State::Positions | State::Velocities, true);
        for (int j = 0; j < numParticles; j++) {
            double rg2 = 0.0;
            for (int k = 0; k < numCopies; k++) {
                Vec3 v = state[k].getVelocities()[j];
                ke[k] += 0.5*mass*v.dot(v);
                for (int m = 0; m < numCopies; m++) {
                    Vec3 delta = state[k].getPositions()[j]-state[m].getPositions()[j];
                    rg2 += delta.dot(delta);
                }
            }
            rg[j] += rg2/(2*numCopies*numCopies);
        }
    }
    double meanKE = 0.0;
    for (int i = 0; i < numCopies; i++)
        meanKE += ke[i];
    meanKE /= numSteps*numCopies;
    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
    double meanRg2 = 0.0;
    for (int i = 0; i < numParticles; i++)
        meanRg2 += rg[i];
    meanRg2 /= numSteps*numParticles;
    double expectedRg = hbar/(2*sqrt(mass*BOLTZ*temperature));
    ASSERT_USUALLY_EQUAL_TOL(expectedRg, sqrt(meanRg2), 1e-3);
}

Vec3 calcCM(const vector<Vec3>& values, System& system) {
    Vec3 cm;
    for (int j = 0; j < system.getNumParticles(); ++j) {
        cm[0] += values[j][0]*system.getParticleMass(j);
        cm[1] += values[j][1]*system.getParticleMass(j);
        cm[2] += values[j][2]*system.getParticleMass(j);
    }
    return cm;
}

void testCMMotionRemoval() {
    const int numParticles = 100;
    const int numCopies = 30;
    const double temperature = 300.0;
    const double mass = 1.0;
    System system;
    for (int i = 0; i < numParticles; i++)
        system.addParticle(mass);
    system.addForce(new CMMotionRemover());
    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numCopies; i++)
    {
        for (int j = 0; j < numParticles; j++)
            positions[j] = Vec3(0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt));
        Vec3 cmPos = calcCM(positions, system);
        for (int j = 0; j < numParticles; j++)
            positions[j] -= cmPos*(1/(mass*numParticles));
        integ.setPositions(i, positions);
    }
    
    // Make sure the CMMotionRemover is getting applied.
    
    for (int i = 0; i < 200; ++i) {
        integ.step(1);
        Vec3 pos;
        for (int j = 0; j < numCopies; j++) {
            State state = integ.getState(0, State::Positions | State::Velocities);
            pos += calcCM(state.getPositions(), system);
        }
        pos *= 1.0/numCopies;
        ASSERT_EQUAL_VEC(Vec3(), pos, 0.5);
    }
}

void testVirtualSites() {
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const int numParticles = numMolecules*3;
    const int numCopies = 10;
    const double spacing = 2.0;
    const double cutoff = 3.0;
    const double boxSize = spacing*(gridSize+1);
    const double temperature = 300.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    HarmonicBondForce* bonds = new HarmonicBondForce();
    system.addForce(bonds);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    system.addForce(nonbonded);

    // Create a cloud of molecules.

    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numMolecules; i++) {
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(0.0);
        nonbonded->addParticle(-0.2, 0.2, 0.2);
        nonbonded->addParticle(0.1, 0.2, 0.2);
        nonbonded->addParticle(0.1, 0.2, 0.2);
        nonbonded->addException(3*i, 3*i+1, 0, 1, 0);
        nonbonded->addException(3*i, 3*i+2, 0, 1, 0);
        nonbonded->addException(3*i+1, 3*i+2, 0, 1, 0);
        bonds->addBond(3*i, 3*i+1, 1.0, 10000.0);
        system.setVirtualSite(3*i+2, new TwoParticleAverageSite(3*i, 3*i+1, 0.5, 0.5));
    }
    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    for (int copy = 0; copy < numCopies; copy++) {
        for (int i = 0; i < gridSize; i++)
            for (int j = 0; j < gridSize; j++)
                for (int k = 0; k < gridSize; k++) {
                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
                    int index = k+gridSize*(j+gridSize*i);
                    positions[3*index] = pos;
                    positions[3*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
                    positions[3*index+2] = Vec3();
                }
        integ.setPositions(copy, positions);
    }

    // Check the temperature and virtual site locations.
    
    const int numSteps = 1000;
    integ.step(1000);
    vector<double> ke(numCopies, 0.0);
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        vector<State> state(numCopies);
        for (int j = 0; j < numCopies; j++) {
            state[j] = integ.getState(j, State::Positions | State::Velocities | State::Forces, true);
            const vector<Vec3>& pos = state[j].getPositions();
            for (int k = 0; k < numMolecules; k++)
                ASSERT_EQUAL_VEC((pos[3*k]+pos[3*k+1])*0.5, pos[3*k+2], 1e-5);
        }
        for (int j = 0; j < numParticles; j++) {
            for (int k = 0; k < numCopies; k++) {
                Vec3 v = state[k].getVelocities()[j];
                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
            }
        }
    }
    double meanKE = 0.0;
    for (int i = 0; i < numCopies; i++)
        meanKE += ke[i];
    meanKE /= numSteps*numCopies;
    double expectedKE = 0.5*numCopies*(2*numMolecules)*3*BOLTZ*temperature;
    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}

void testContractions() {
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const int numParticles = numMolecules*2;
    const int numCopies = 10;
    const double spacing = 2.0;
    const double cutoff = 3.0;
    const double boxSize = spacing*(gridSize+1);
    const double temperature = 300.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    HarmonicBondForce* bonds = new HarmonicBondForce();
    system.addForce(bonds);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    nonbonded->setForceGroup(1);
    nonbonded->setReciprocalSpaceForceGroup(2);
    system.addForce(nonbonded);

    // Create a cloud of molecules.

    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numMolecules; i++) {
        system.addParticle(1.0);
        system.addParticle(1.0);
        nonbonded->addParticle(-0.2, 0.2, 0.2);
        nonbonded->addParticle(0.2, 0.2, 0.2);
        nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
        bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
    }
    map<int, int> contractions;
    contractions[1] = 3;
    contractions[2] = 1;
    RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001, contractions);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    for (int copy = 0; copy < numCopies; copy++) {
        for (int i = 0; i < gridSize; i++)
            for (int j = 0; j < gridSize; j++)
                for (int k = 0; k < gridSize; k++) {
                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
                    int index = k+gridSize*(j+gridSize*i);
                    positions[2*index] = pos;
                    positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
                }
        integ.setPositions(copy, positions);
    }

    // Check the temperature.
    
    const int numSteps = 1000;
    integ.step(1000);
    vector<double> ke(numCopies, 0.0);
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        vector<State> state(numCopies);
        for (int j = 0; j < numCopies; j++)
            state[j] = integ.getState(j, State::Velocities, true);
        for (int j = 0; j < numParticles; j++) {
            for (int k = 0; k < numCopies; k++) {
                Vec3 v = state[k].getVelocities()[j];
                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
            }
        }
    }
    double meanKE = 0.0;
    for (int i = 0; i < numCopies; i++)
        meanKE += ke[i];
    meanKE /= numSteps*numCopies;
    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}

int main() {
    try {
        testFreeParticles();
        testCMMotionRemoval();
        testVirtualSites();
        testContractions();
    }
    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;
}