Updated selection documentation.

[gromacs/qmmm-gamess-us.git] / src / gmxlib / trajana / centerofmass.c

/*
 *
 *                This source code is part of
 *
 *                 G   R   O   M   A   C   S
 *
 *          GROningen MAchine for Chemical Simulations
 *
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2009, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
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 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
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 *
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/*! \internal \file
 * \brief Implementation of functions in centerofmass.h.
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <typedefs.h>
#include <pbc.h>
#include <vec.h>

#include <centerofmass.h>

/*!
 * \param[in]  top    Topology structure (unused, can be NULL).
 * \param[in]  x      Position vectors of all atoms.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index  Indices of atoms.
 * \param[out] xout   COG position for the indexed atoms.
 * \returns    0 on success.
 */
int
gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout)
{
    int                 m, j, ai;

    clear_rvec(xout);
    for (m = 0; m < nrefat; ++m)
    {
        ai = index[m];
        rvec_inc(xout, x[ai]);
    }
    svmul(1.0/nrefat, xout, xout);
    return 0;
}

/*!
 * \param[in]  top    Topology structure with masses.
 * \param[in]  x      Position vectors of all atoms.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index  Indices of atoms.
 * \param[out] xout   COM position for the indexed atoms.
 * \returns    0 on success, EINVAL if \p top is NULL.
 *
 * Works exactly as gmx_calc_cog() with the exception that a center of
 * mass are calculated, and hence a topology with masses is required.
 */
int
gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout)
{
    int                 m, j, ai;
    real                mass, mtot;

    if (!top)
    {
        gmx_incons("no masses available while mass weighting was requested");
        return EINVAL;
    }
    clear_rvec(xout);
    mtot = 0;
    for (m = 0; m < nrefat; ++m)
    {
        ai = index[m];
        mass = top->atoms.atom[ai].m;
        for (j = 0; j < DIM; ++j)
        {
            xout[j] += mass * x[ai][j];
        }
        mtot += mass;
    }
    svmul(1.0/mtot, xout, xout);
    return 0;
}

/*!
 * \param[in]  top   Topology structure with masses
 *   (can be NULL if \p bMASS==FALSE).
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index Indices of atoms.
 * \param[in]  bMass If TRUE, mass weighting is used.
 * \param[out] xout  COM/COG position for the indexed atoms.
 * \returns    0 on success, EINVAL if \p top is NULL and \p bMass is TRUE.
 *
 * Calls either gmx_calc_com() or gmx_calc_cog() depending on the value of
 * \p bMass.
 * Other parameters are passed unmodified to these functions.
 */
int
gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
          bool bMass, rvec xout)
{
    if (bMass)
    {
        return gmx_calc_com(top, x, nrefat, index, xout);
    }
    else
    {
        return gmx_calc_cog(top, x, nrefat, index, xout);
    }
}


/*!
 * \param[in]  top    Topology structure (unused, can be NULL).
 * \param[in]  x      Position vectors of all atoms.
 * \param[in]  pbc    Periodic boundary conditions structure.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index  Indices of atoms.
 * \param[out] xout   COG position for the indexed atoms.
 * \returns    0 on success.
 *
 * Works exactly as gmx_calc_com_pbc(), but calculates the center of geometry.
 */
int
gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                 int nrefat, atom_id index[], rvec xout)
{
    const real          tol = 1e-4;
    bool                bChanged;
    int                 m, j, ai, iter;
    rvec                dx, xtest;

    /* First simple calculation */
    gmx_calc_cog(top, x, nrefat, index, xout);
    /* Now check if any atom is more than half the box from the COM */
    if (pbc)
    {
        iter = 0;
        do
        {
            bChanged = FALSE;
            for (m = 0; m < nrefat; ++m)
            {
                ai = index[m];
                pbc_dx(pbc, x[ai], xout, dx);
                rvec_add(xout, dx, xtest);
                for (j = 0; j < DIM; ++j)
                {
                    if (fabs(xtest[j] - x[ai][j]) > tol)
                    {
                        /* Here we have used the wrong image for contributing to the COM */
                        xout[j] += (xtest[j] - x[ai][j]) / nrefat;
                        x[ai][j] = xtest[j];
                        bChanged = TRUE;
                    }
                }
            }
            iter++;
        }
        while (bChanged);
    }
    return 0;
}

/*!
 * \param[in]  top    Topology structure with masses.
 * \param[in]  x      Position vectors of all atoms.
 * \param[in]  pbc    Periodic boundary conditions structure.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index  Indices of atoms.
 * \param[out] xout   COM position for the indexed atoms.
 * \returns    0 on success, EINVAL if \p top is NULL.
 *
 * Works as gmx_calc_com(), but takes into account periodic boundary
 * conditions: If any atom is more than half the box from the COM,
 * it is wrapped around and a new COM is calculated. This is repeated
 * until no atoms violate the condition.
 *
 * Modified from src/tools/gmx_sorient.c in Gromacs distribution.
 */
int
gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                 int nrefat, atom_id index[], rvec xout)
{
    const real          tol = 1e-4;
    bool                bChanged;
    int                 m, j, ai, iter;
    real                mass, mtot;
    rvec                dx, xtest;

    if (!top)
    {
        gmx_incons("no masses available while mass weighting was requested");
        return EINVAL;
    }
    /* First simple calculation */
    clear_rvec(xout);
    mtot = 0;
    for (m = 0; m < nrefat; ++m)
    {
        ai = index[m];
        mass = top->atoms.atom[ai].m;
        for (j = 0; j < DIM; ++j)
        {
            xout[j] += mass * x[ai][j];
        }
        mtot += mass;
    }
    svmul(1.0/mtot, xout, xout);
    /* Now check if any atom is more than half the box from the COM */
    if (pbc)
    {
        iter = 0;
        do
        {
            bChanged = FALSE;
            for (m = 0; m < nrefat; ++m)
            {
                ai = index[m];
                mass = top->atoms.atom[ai].m / mtot;
                pbc_dx(pbc, x[ai], xout, dx);
                rvec_add(xout, dx, xtest);
                for (j = 0; j < DIM; ++j)
                {
                    if (fabs(xtest[j] - x[ai][j]) > tol)
                    {
                        /* Here we have used the wrong image for contributing to the COM */
                        xout[j] += mass * (xtest[j] - x[ai][j]);
                        x[ai][j] = xtest[j];
                        bChanged = TRUE;
                    }
                }
            }
            iter++;
        }
        while (bChanged);
    }
    return 0;
}

/*!
 * \param[in]  top   Topology structure with masses
 *   (can be NULL if \p bMASS==FALSE).
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  pbc    Periodic boundary conditions structure.
 * \param[in]  nrefat Number of atoms in the index.
 * \param[in]  index Indices of atoms.
 * \param[in]  bMass If TRUE, mass weighting is used.
 * \param[out] xout  COM/COG position for the indexed atoms.
 * \returns    0 on success, EINVAL if \p top is NULL and \p bMass is TRUE.
 *
 * Calls either gmx_calc_com() or gmx_calc_cog() depending on the value of
 * \p bMass.
 * Other parameters are passed unmodified to these functions.
 */
int
gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                  int nrefat, atom_id index[], bool bMass, rvec xout)
{
    if (bMass)
    {
        return gmx_calc_com_pbc(top, x, pbc, nrefat, index, xout);
    }
    else
    {
        return gmx_calc_cog_pbc(top, x, pbc, nrefat, index, xout);
    }
}


/*!
 * \param[in]  top   Topology structure (unused, can be NULL).
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  block t_block structure that divides \p index into blocks.
 * \param[in]  index Indices of atoms.
 * \param[out] xout  \p block->nr COG positions.
 * \returns    0 on success.
 */
int
gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block, atom_id index[],
                   rvec xout[])
{
    int                 b, i, ai;
    rvec                xb;

    for (b = 0; b < block->nr; ++b)
    {
        clear_rvec(xb);
        for (i = block->index[b]; i < block->index[b+1]; ++i)
        {
            ai = index[i];
            rvec_inc(xb, x[ai]);
        }
        svmul(1.0/(block->index[b+1] - block->index[b]), xb, xout[b]);
    }
    return 0;
}

/*!
 * \param[in]  top   Topology structure with masses.
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  block t_block structure that divides \p index into blocks.
 * \param[in]  index Indices of atoms.
 * \param[out] xout  \p block->nr COM positions.
 * \returns    0 on success, EINVAL if \p top is NULL.
 *
 * Works exactly as gmx_calc_cog_block() with the exception that centers of
 * mass are calculated, and hence a topology with masses is required.
 */
int
gmx_calc_com_block(t_topology *top, rvec x[], t_block *block, atom_id index[],
                   rvec xout[])
{
    int                 b, i, ai, d;
    rvec                xb;
    real                mass, mtot;

    if (!top)
    {
        gmx_incons("no masses available while mass weighting was requested");
        return EINVAL;
    }
    for (b = 0; b < block->nr; ++b)
    {
        clear_rvec(xb);
        mtot = 0;
        for (i = block->index[b]; i < block->index[b+1]; ++i)
        {
            ai = index[i];
            mass = top->atoms.atom[ai].m;
            for (d = 0; d < DIM; ++d)
            {
                xb[d] += mass * x[ai][d];
            }
            mtot += mass;
        }
        svmul(1.0/mtot, xb, xout[b]);
    }
    return 0;
}

/*!
 * \param[in]  top   Topology structure with masses
 *   (can be NULL if \p bMASS==FALSE).
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  block t_block structure that divides \p index into blocks.
 * \param[in]  index Indices of atoms.
 * \param[in]  bMass If TRUE, mass weighting is used.
 * \param[out] xout  \p block->nr COM/COG positions.
 * \returns    0 on success, EINVAL if \p top is NULL and \p bMass is TRUE.
 *
 * Calls either gmx_calc_com_block() or gmx_calc_cog_block() depending on the
 * value of \p bMass.
 * Other parameters are passed unmodified to these functions.
 */
int
gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block, atom_id index[],
                    bool bMass, rvec xout[])
{
    if (bMass)
    {
        return gmx_calc_com_block(top, x, block, index, xout);
    }
    else
    {
        return gmx_calc_cog_block(top, x, block, index, xout);
    }
}

/*!
 * \param[in]  top   Topology structure with masses
 *   (can be NULL if \p bMASS==FALSE).
 * \param[in]  x     Position vectors of all atoms.
 * \param[in]  block Blocks for calculation.
 * \param[in]  bMass If TRUE, mass weighting is used.
 * \param[out] xout  \p block->nr COM/COG positions.
 * \returns    0 on success, EINVAL if \p top is NULL and \p bMass is TRUE.
 *
 * Calls gmx_calc_comg_block(), converting the \p t_blocka structure into
 * a \p t_block and an index. Other parameters are passed unmodified.
 *
 * \attention
 * This function assumes that a pointer to \c t_blocka can be safely typecast
 * into \c t_block such that the index fields can still be referenced.
 * With the present Gromacs defitions of these types, this is the case,
 * but if the layout of these structures is changed, this may lead to strange
 * crashes.
 */
int
gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
                     bool bMass, rvec xout[])
{
    /* TODO: It would probably be better to do this without the type cast */
    return gmx_calc_comg_block(top, x, (t_block *)block, block->a, bMass, xout);
}