TestMonteCarloBarostat.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.               *
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 * Authors: Peter Eastman                                                     *
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#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

void testChangingBoxSize() {
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 5, 0), Vec3(0, 0, 6));
    system.addParticle(1.0);
    NonbondedForce* nb = new NonbondedForce();
    nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nb->setCutoffDistance(2.0);
    nb->addParticle(1, 0.5, 0.5);
    system.addForce(nb);
    LangevinIntegrator integrator(300.0, 1.0, 0.01);
    Context context(system, integrator, platform);
    vector<Vec3> positions;
    positions.push_back(Vec3());
    context.setPositions(positions);
    Vec3 x, y, z;
    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
    ASSERT_EQUAL_VEC(Vec3(4, 0, 0), x, 0);
    ASSERT_EQUAL_VEC(Vec3(0, 5, 0), y, 0);
    ASSERT_EQUAL_VEC(Vec3(0, 0, 6), z, 0);
    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 9));
    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
    ASSERT_EQUAL_VEC(Vec3(7, 0, 0), x, 0);
    ASSERT_EQUAL_VEC(Vec3(0, 8, 0), y, 0);
    ASSERT_EQUAL_VEC(Vec3(0, 0, 9), z, 0);
    
    // Shrinking the box too small should produce an exception.
    
    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 3.9, 0), Vec3(0, 0, 9));
    bool ok = true;
    try {
        context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
        ok = false;
    }
    catch (exception& ex) {
    }
    ASSERT(ok);
}

void testIdealGas() {
    const int numParticles = 64;
    const int frequency = 10;
    const int steps = 1000;
    const double pressure = 1.5;
    const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
    const double temp[] = {300.0, 600.0, 1000.0};
    const double initialVolume = numParticles*BOLTZ*temp[1]/pressureInMD;
    const double initialLength = std::pow(initialVolume, 1.0/3.0);

    // Create a gas of noninteracting particles.

    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(1.0);
        positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
    }
    MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
    system.addForce(barostat);
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->setUsesPeriodicBoundaryConditions(true);
    system.addForce(bonds); // So it won't complain the system is non-periodic.

    // Test it for three different temperatures.

    for (int i = 0; i < 3; i++) {
        barostat->setDefaultTemperature(temp[i]);
        LangevinIntegrator integrator(temp[i], 0.1, 0.01);
        Context context(system, integrator, platform);
        context.setPositions(positions);

        // Let it equilibrate.

        integrator.step(10000);

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

        double volume = 0.0;
        double avgPressure = 0.0;
        for (int j = 0; j < steps; ++j) {
            Vec3 box[3];
            context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
            volume += box[0][0]*box[1][1]*box[2][2];
            ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
            ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
            integrator.step(frequency);
            avgPressure += barostat->computeCurrentPressure(context);
        }
        volume /= steps;
        avgPressure /= steps;
        double expected = (numParticles+1)*BOLTZ*temp[i]/pressureInMD;
        ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
        ASSERT_USUALLY_EQUAL_TOL(pressure, avgPressure, 0.1);
    }
}

void testMolecularGas() {
    const int numMolecules = 64;
    const int frequency = 10;
    const int steps = 1000;
    const double pressure = 1.5;
    const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
    const double temp = 300.0;
    const double initialVolume = numMolecules*BOLTZ*temp/pressureInMD;
    const double initialLength = std::pow(initialVolume, 1.0/3.0);

    // Create a gas of noninteracting molecules.

    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
    MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
    system.addForce(barostat);
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->setUsesPeriodicBoundaryConditions(true);
    system.addForce(bonds);
    vector<Vec3> positions;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numMolecules; ++i) {
        system.addParticle(1.0);
        system.addParticle(2.0);
        system.addParticle(3.0);
        Vec3 pos(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
        bonds->addBond(positions.size(), positions.size()+1, 0.1, 10.0);
        system.addConstraint(positions.size(), positions.size()+2, 0.1);
        positions.push_back(pos);
        positions.push_back(pos+Vec3(0.1, 0.0, 0.0));
        positions.push_back(pos+Vec3(0.0, 0.1, 0.0));
    }

    // Simulate it and see if the pressure is correct..

    LangevinIntegrator integrator(temp, 0.1, 0.01);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    integrator.step(10000);
    double avgPressure = 0.0;
    for (int j = 0; j < steps; ++j) {
        integrator.step(frequency);
        avgPressure += barostat->computeCurrentPressure(context);
    }
    avgPressure /= steps;
    ASSERT_USUALLY_EQUAL_TOL(pressure, avgPressure, 0.1);
}

void testRandomSeed() {
    const int numParticles = 8;
    const double temp = 100.0;
    const double pressure = 1.5;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(8, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 8));
    VerletIntegrator integrator(0.01);
    NonbondedForce* forceField = new NonbondedForce();
    forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    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);
    MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
    system.addForce(barostat);
    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.

    barostat->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.

    barostat->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]);
        }
    }
}

void testWater() {
    const int gridSize = 8;
    const int numMolecules = gridSize*gridSize*gridSize;
    const int frequency = 10;
    const int steps = 400;
    const double temp = 273.15;
    const double pressure = 3;
    const double spacing = 0.32;
    const double angle = 109.47*M_PI/180;
    const double dOH = 0.1;
    const double dHH = dOH*2*std::sin(0.5*angle);

    // Create a box of SPC water molecules.

    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(gridSize*spacing, 0, 0), Vec3(0, gridSize*spacing, 0), Vec3(0, 0, gridSize*spacing));
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setUseDispersionCorrection(true);
    vector<Vec3> positions;
    Vec3 offset1(dOH, 0, 0);
    Vec3 offset2(dOH*std::cos(angle), dOH*std::sin(angle), 0);
    for (int i = 0; i < gridSize; ++i) {
        for (int j = 0; j < gridSize; ++j) {
            for (int k = 0; k < gridSize; ++k) {
                int firstParticle = system.getNumParticles();
                system.addParticle(16.0);
                system.addParticle(1.0);
                system.addParticle(1.0);
                nonbonded->addParticle(-0.82, 0.316557, 0.650194);
                nonbonded->addParticle(0.41, 1, 0);
                nonbonded->addParticle(0.41, 1, 0);
                Vec3 pos = Vec3(spacing*i, spacing*j, spacing*k);
                positions.push_back(pos);
                positions.push_back(pos+offset1);
                positions.push_back(pos+offset2);
                system.addConstraint(firstParticle, firstParticle+1, dOH);
                system.addConstraint(firstParticle, firstParticle+2, dOH);
                system.addConstraint(firstParticle+1, firstParticle+2, dHH);
                nonbonded->addException(firstParticle, firstParticle+1, 0, 1, 0);
                nonbonded->addException(firstParticle, firstParticle+2, 0, 1, 0);
                nonbonded->addException(firstParticle+1, firstParticle+2, 0, 1, 0);
            }
        }
    }
    system.addForce(nonbonded);
    MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
    system.addForce(barostat);

    // Simulate it and see if the density matches the expected value (1 g/mL).

    LangevinIntegrator integrator(temp, 1.0, 0.002);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    integrator.step(2000);
    double volume = 0.0;
    for (int j = 0; j < steps; ++j) {
        Vec3 box[3];
        context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
        volume += box[0][0]*box[1][1]*box[2][2];
        integrator.step(frequency);
    }
    volume /= steps;
    double density = numMolecules*18/(AVOGADRO*volume*1e-21);
    ASSERT_USUALLY_EQUAL_TOL(1.0, density, 0.02);
}

void testLJPressure() {
    const int gridSize = 8;
    const int frequency = 10;
    const int steps = 1000;
    const double spacing = 1.2;
    const double temp = 150.0;
    const double pressure = 10.0;

    // Create a gas of LJ particles.  This is much more compressible than water, which means
    // the fluctuations in pressure are much smaller and it's easier to compute the average.

    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(gridSize*spacing, 0, 0), Vec3(0, gridSize*spacing, 0), Vec3(0, 0, gridSize*spacing));
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    vector<Vec3> positions;
    for (int i = 0; i < gridSize; ++i) {
        for (int j = 0; j < gridSize; ++j) {
            for (int k = 0; k < gridSize; ++k) {
                system.addParticle(1.0);
                nonbonded->addParticle(0.0, 1.0, 1.0);
                positions.push_back(Vec3(spacing*i, spacing*j, spacing*k));
            }
        }
    }
    system.addForce(nonbonded);
    MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
    system.addForce(barostat);

    // Simulate it and see if the average instantaneous pressure matches the heat bath pressure.

    LangevinIntegrator integrator(temp, 1.0, 0.01);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    integrator.step(1000);
    double avgPressure = 0.0;
    for (int j = 0; j < steps; ++j) {
        Vec3 box[3];
        context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
        avgPressure += barostat->computeCurrentPressure(context);
        integrator.step(frequency);
    }
    avgPressure /= steps;
    ASSERT_USUALLY_EQUAL_TOL(pressure, avgPressure, 0.1);
}

void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        initializeTests(argc, argv);
        testChangingBoxSize();
        testIdealGas();
        testMolecularGas();
        testRandomSeed();
        // Don't run testWater() or testLJPressure() here, because they're very slow on
        // Reference platform.  Individual platforms can run them from runPlatformTests().
        runPlatformTests();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}