TestOpenCLMonteCarloAnisotropicBarostat.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 OpenCL implementation of MonteCarloAnisotropicBarostat.
 */

#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

static OpenCLPlatform platform;

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);
    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));
    }
    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
    system.addForce(barostat);
    
    // Test it for three different temperatures.
    
    for (int i = 0; i < 3; i++) {
        barostat->setTemperature(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;
        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 expected = (numParticles+1)*BOLTZ*temp[i]/pressureInMD;
        ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
    }
}

void testIdealGasAxis(int axis) {
    // Test scaling just one axis.
    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);
    const bool scaleX = (axis == 0);
    const bool scaleY = (axis == 1);
    const bool scaleZ = (axis == 2);
    double boxX;
    double boxY;
    double boxZ;
    
    // 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));
    }
    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency, scaleX, scaleY, scaleZ);
    system.addForce(barostat);
    
    // Test it for three different temperatures.
    
    for (int i = 0; i < 3; i++) {
        barostat->setTemperature(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;
        for (int j = 0; j < steps; ++j) {
            Vec3 box[3];
            context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
	    boxX = box[0][0];
	    boxY = box[1][1];
	    boxZ = box[2][2];
            volume += box[0][0]*box[1][1]*box[2][2];
            integrator.step(frequency);
        }
        volume /= steps;
        double expected = (numParticles+1)*BOLTZ*temp[i]/pressureInMD;
        ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
	if (!scaleX) {
	  ASSERT(boxX == initialLength);
	}
	if (!scaleY) {
	  ASSERT(boxY == 0.5*initialLength);
	}
	if (!scaleZ) {
	  ASSERT(boxZ == 2*initialLength);
	}
    }
}

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);
    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, 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 testIce() {
    const int numMolecules = 432;
    const int frequency = 10;
    const int steps = 400;
    const double temp = 273.15;
    const double pressure = 3;
    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(2.7042, 0, 0), Vec3(0, 2.3419, 0), Vec3(0, 0, 2.2080));
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setUseDispersionCorrection(true);
    for (int i = 0; i < numMolecules; ++i) {
      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);
      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);
    }
    vector<Vec3> positions(system.getNumParticles());
    #include "ice_ih.dat"
    system.addForce(nonbonded);
    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, 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(0.913, density, 0.02);
}

int main(int argc, char* argv[]) {
    try {
        if (argc > 1)
            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
        testChangingBoxSize();
        testIdealGas();
        testIdealGasAxis(0);
        testIdealGasAxis(1);
        testIdealGasAxis(2);
        testRandomSeed();
        testIce();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}