MonteCarloMembraneBarostatImpl.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        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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 * Authors: Peter Eastman, Lee-Ping Wang                                      *
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#include "openmm/internal/MonteCarloMembraneBarostatImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/Context.h"
#include "openmm/kernels.h"
#include "openmm/OpenMMException.h"
#include "SimTKOpenMMUtilities.h"
#include <cmath>
#include <vector>
#include <algorithm>

using namespace OpenMM;
using namespace std;

MonteCarloMembraneBarostatImpl::MonteCarloMembraneBarostatImpl(const MonteCarloMembraneBarostat& owner) : owner(owner), step(0) {
}

void MonteCarloMembraneBarostatImpl::initialize(ContextImpl& context) {
    if (!context.getSystem().usesPeriodicBoundaryConditions())
        throw OpenMMException("A barostat cannot be used with a non-periodic system");
    kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
    kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner, 3);
    Vec3 box[3];
    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
    double volume = box[0][0]*box[1][1]*box[2][2];
    for (int i=0; i<3; i++) {
        volumeScale[i] = 0.01*volume;
        numAttempted[i] = 0;
        numAccepted[i] = 0;
    }
    SimTKOpenMMUtilities::setRandomNumberSeed(owner.getRandomNumberSeed());
}

void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context, bool& forcesInvalid) {
    if (++step < owner.getFrequency() || owner.getFrequency() == 0)
        return;
    step = 0;
    
    // Compute the current potential energy.
    
    int groups = context.getIntegrator().getIntegrationForceGroups();
    double initialEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
    double pressure = context.getParameter(MonteCarloMembraneBarostat::Pressure())*(AVOGADRO*1e-25);
    double tension = context.getParameter(MonteCarloMembraneBarostat::SurfaceTension())*(AVOGADRO*1e-25);
    
    // Choose which axis to modify at random.
    int axis;
    while (true) {
        double rnd = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()*3.0;
        if (rnd < 1.0) {
            axis = 0;
            break;
        } else if (rnd < 2.0) {
            axis = (owner.getXYMode() == MonteCarloMembraneBarostat::XYIsotropic ? 0 : 1);
            break;
        } else if (owner.getZMode() == MonteCarloMembraneBarostat::ZFree) {
            axis = 2;
            break;
        }
    }
    
    // Modify the periodic box size.
    
    Vec3 box[3];
    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
    double volume = box[0][0]*box[1][1]*box[2][2];
    double deltaVolume = volumeScale[axis]*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
    double newVolume = volume+deltaVolume;
    Vec3 lengthScale(1.0, 1.0, 1.0);
    if ((axis == 0 || axis == 1) && owner.getXYMode() == MonteCarloMembraneBarostat::XYIsotropic)
        lengthScale[0] = lengthScale[1] = sqrt(newVolume/volume);
    else
        lengthScale[axis] = newVolume/volume;
    if (owner.getZMode() == MonteCarloMembraneBarostat::ConstantVolume) {
        lengthScale[2] = 1.0/(lengthScale[0]*lengthScale[1]);
        newVolume = volume;
        deltaVolume = 0;
    }
    double deltaArea = box[0][0]*lengthScale[0]*box[1][1]*lengthScale[1] - box[0][0]*box[1][1];
    kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
    context.getOwner().setPeriodicBoxVectors(Vec3(box[0][0]*lengthScale[0], box[0][1]*lengthScale[1], box[0][2]*lengthScale[2]),
                                             Vec3(box[1][0]*lengthScale[0], box[1][1]*lengthScale[1], box[1][2]*lengthScale[2]),
                                             Vec3(box[2][0]*lengthScale[0], box[2][1]*lengthScale[1], box[2][2]*lengthScale[2]));
    kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);

    // Compute the energy of the modified system.

    double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
    double kT = BOLTZ*context.getParameter(MonteCarloMembraneBarostat::Temperature());
    double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*log(newVolume/volume);
    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > exp(-w/kT)) {
        // Reject the step.
        
        context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
        kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
    }
    else {
        numAccepted[axis]++;
        forcesInvalid = true;
    }
    numAttempted[axis]++;
    if (numAttempted[axis] >= 10) {
        if (numAccepted[axis] < 0.25*numAttempted[axis]) {
            volumeScale[axis] /= 1.1;
            numAttempted[axis] = 0;
            numAccepted[axis] = 0;
        }
        else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
            volumeScale[axis] = min(volumeScale[axis]*1.1, volume*0.3);
            numAttempted[axis] = 0;
            numAccepted[axis] = 0;
        }
    }
}

map<string, double> MonteCarloMembraneBarostatImpl::getDefaultParameters() {
    map<string, double> parameters;
    parameters[MonteCarloMembraneBarostat::Pressure()] = getOwner().getDefaultPressure();
    parameters[MonteCarloMembraneBarostat::SurfaceTension()] = getOwner().getDefaultSurfaceTension();
    parameters[MonteCarloMembraneBarostat::Temperature()] = getOwner().getDefaultTemperature();
    return parameters;
}

vector<string> MonteCarloMembraneBarostatImpl::getKernelNames() {
    vector<string> names;
    names.push_back(ApplyMonteCarloBarostatKernel::Name());
    return names;
}

Vec3 MonteCarloMembraneBarostatImpl::computeCurrentPressure(ContextImpl& context) {
    Vec3 box[3];
    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
    double volume = box[0][0]*box[1][1]*box[2][2];
    double delta = 1e-3;
    int groups = context.getIntegrator().getIntegrationForceGroups();
    kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
    vector<double> ke;
    kernel.getAs<ApplyMonteCarloBarostatKernel>().computeKineticEnergy(context, ke);
    double deltaVolume = volume*2*delta;
    Vec3 pressure;

    // Compute the pressure along each axis.

    for (int axis = 0; axis < 3; axis++) {
        // Compute the first energy.

        Vec3 scale1(1, 1, 1);
        scale1[axis] = 1.0+delta;
        context.getOwner().setPeriodicBoxVectors(box[0]*scale1[0], box[1]*scale1[1], box[2]*scale1[2]);
        kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, scale1[0], scale1[1], scale1[2]);
        double energy1 = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();

        // Compute the second energy.

        Vec3 scale2(1, 1, 1);
        scale2[axis] = 1.0-delta;
        context.getOwner().setPeriodicBoxVectors(box[0]*scale2[0], box[1]*scale2[1], box[2]*scale2[2]);
        kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, scale2[0]/scale1[0], scale2[1]/scale1[1], scale2[2]/scale1[2]);
        double energy2 = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();

        // Reset the box shape.

        context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
        kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, 1/scale2[0], 1/scale2[1], 1/scale2[2]);

        // Compute the pressure.

        pressure[axis] = (2.0*ke[axis]/volume - (energy1-energy2)/deltaVolume)/(AVOGADRO*1e-25);
    }

    // Restore the context to its original state.

    kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
    return pressure;
}