ReferenceMonteCarloBarostat.cpp

/* Portions copyright (c) 2010 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
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 * permit persons to whom the Software is furnished to do so, subject
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 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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#include <string.h>
#include <sstream>

#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceMonteCarloBarostat.h"

using namespace std;
using namespace OpenMM;

/**---------------------------------------------------------------------------------------

  Constructor

  --------------------------------------------------------------------------------------- */

ReferenceMonteCarloBarostat::ReferenceMonteCarloBarostat(int numAtoms, const vector<vector<int> >& molecules) : molecules(molecules) {
    savedAtomPositions[0].resize(numAtoms);
    savedAtomPositions[1].resize(numAtoms);
    savedAtomPositions[2].resize(numAtoms);
}

/**---------------------------------------------------------------------------------------

  Destructor

  --------------------------------------------------------------------------------------- */

ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat( ) {
}

/**---------------------------------------------------------------------------------------

  Apply the barostat at the start of a time step.

  @param atomPositions      atom positions
  @param boxSize            the periodic box dimensions
  @param scale              the factor by which to scale atom positions

  --------------------------------------------------------------------------------------- */

void ReferenceMonteCarloBarostat::applyBarostat(vector<RealVec>& atomPositions, const RealVec& boxSize, RealOpenMM scale) {
    int numAtoms = savedAtomPositions[0].size();
    for (int i = 0; i < numAtoms; i++)
        for (int j = 0; j < 3; j++)
            savedAtomPositions[j][i] = atomPositions[i][j];

    // Loop over molecules.

    for (int i = 0; i < (int) molecules.size(); i++) {
        // Find the molecule center.

        RealOpenMM pos[3] = {0, 0, 0};
        for (int j = 0; j < (int) molecules[i].size(); j++) {
            RealVec& atomPos = atomPositions[molecules[i][j]];
            pos[0] += atomPos[0];
            pos[1] += atomPos[1];
            pos[2] += atomPos[2];
        }
        pos[0] /= molecules[i].size();
        pos[1] /= molecules[i].size();
        pos[2] /= molecules[i].size();

        // Move it into the first periodic box.

        int xcell = (int) floor(pos[0]/boxSize[0]);
        int ycell = (int) floor(pos[1]/boxSize[1]);
        int zcell = (int) floor(pos[2]/boxSize[2]);
        RealOpenMM dx = xcell*boxSize[0];
        RealOpenMM dy = ycell*boxSize[1];
        RealOpenMM dz = zcell*boxSize[2];
        pos[0] -= dx;
        pos[1] -= dy;
        pos[2] -= dz;

        // Now scale the position of the molecule center.

        dx = pos[0]*(scale-1)-dx;
        dy = pos[1]*(scale-1)-dy;
        dz = pos[2]*(scale-1)-dz;
        for (int j = 0; j < (int) molecules[i].size(); j++) {
            RealVec& atomPos = atomPositions[molecules[i][j]];
            atomPos[0] += dx;
            atomPos[1] += dy;
            atomPos[2] += dz;
        }
    }
}

void ReferenceMonteCarloBarostat::applyBarostatXYZ(vector<RealVec>& atomPositions, const RealVec& boxSize, RealOpenMM scaleX, RealOpenMM scaleY, RealOpenMM scaleZ) {
    int numAtoms = savedAtomPositions[0].size();
    for (int i = 0; i < numAtoms; i++)
        for (int j = 0; j < 3; j++)
            savedAtomPositions[j][i] = atomPositions[i][j];

    // Loop over molecules.

    for (int i = 0; i < (int) molecules.size(); i++) {
        // Find the molecule center.

        RealOpenMM pos[3] = {0, 0, 0};
        for (int j = 0; j < (int) molecules[i].size(); j++) {
            RealVec& atomPos = atomPositions[molecules[i][j]];
            pos[0] += atomPos[0];
            pos[1] += atomPos[1];
            pos[2] += atomPos[2];
        }
        pos[0] /= molecules[i].size();
        pos[1] /= molecules[i].size();
        pos[2] /= molecules[i].size();

        // Move it into the first periodic box.

        int xcell = (int) floor(pos[0]/boxSize[0]);
        int ycell = (int) floor(pos[1]/boxSize[1]);
        int zcell = (int) floor(pos[2]/boxSize[2]);
        RealOpenMM dx = xcell*boxSize[0];
        RealOpenMM dy = ycell*boxSize[1];
        RealOpenMM dz = zcell*boxSize[2];
        pos[0] -= dx;
        pos[1] -= dy;
        pos[2] -= dz;

        // Now scale the position of the molecule center.

        dx = pos[0]*(scaleX-1)-dx;
        dy = pos[1]*(scaleY-1)-dy;
        dz = pos[2]*(scaleZ-1)-dz;
        for (int j = 0; j < (int) molecules[i].size(); j++) {
            RealVec& atomPos = atomPositions[molecules[i][j]];
            atomPos[0] += dx;
            atomPos[1] += dy;
            atomPos[2] += dz;
        }
    }
}

/**---------------------------------------------------------------------------------------

  Restore atom positions to what they were before applyBarostat() was called.

  @param atomPositions      atom positions

  --------------------------------------------------------------------------------------- */

void ReferenceMonteCarloBarostat::restorePositions(vector<RealVec>& atomPositions) {
    int numAtoms = savedAtomPositions[0].size();
    for (int i = 0; i < numAtoms; i++)
        for (int j = 0; j < 3; j++)
            atomPositions[i][j] = savedAtomPositions[j][i];
}