Move symtab.* to topology/

[gromacs.git] / src / gromacs / gmxana / gmx_clustsize.c

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2007, The GROMACS development team.
 * Copyright (c) 2013,2014, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>

#include "typedefs.h"
#include "macros.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/utility/futil.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "calcgrid.h"
#include "nrnb.h"
#include "gromacs/math/units.h"
#include "coulomb.h"
#include "pme.h"
#include "gstat.h"
#include "gromacs/fileio/matio.h"
#include "mtop_util.h"
#include "gmx_ana.h"

#include "gromacs/utility/fatalerror.h"

static void clust_size(const char *ndx, const char *trx, const char *xpm,
                       const char *xpmw, const char *ncl, const char *acl,
                       const char *mcl, const char *histo, const char *tempf,
                       const char *mcn, gmx_bool bMol, gmx_bool bPBC, const char *tpr,
                       real cut, int nskip, int nlevels,
                       t_rgb rmid, t_rgb rhi, int ndf,
                       const output_env_t oenv)
{
    FILE                 *fp, *gp, *hp, *tp;
    atom_id              *index = NULL;
    int                   nindex, natoms;
    t_trxstatus          *status;
    rvec                 *x = NULL, *v = NULL, dx;
    t_pbc                 pbc;
    char                 *gname;
    char                  timebuf[32];
    gmx_bool              bSame, bTPRwarn = TRUE;
    /* Topology stuff */
    t_trxframe            fr;
    t_tpxheader           tpxh;
    gmx_mtop_t           *mtop = NULL;
    int                   ePBC = -1;
    t_block              *mols = NULL;
    gmx_mtop_atomlookup_t alook;
    t_atom               *atom;
    int                   version, generation, ii, jj, nsame;
    real                  temp, tfac;
    /* Cluster size distribution (matrix) */
    real                **cs_dist = NULL;
    real                  tf, dx2, cut2, *t_x = NULL, *t_y, cmid, cmax, cav, ekin;
    int                   i, j, k, ai, aj, ak, ci, cj, nframe, nclust, n_x, n_y, max_size = 0;
    int                  *clust_index, *clust_size, max_clust_size, max_clust_ind, nav, nhisto;
    t_rgb                 rlo = { 1.0, 1.0, 1.0 };

    clear_trxframe(&fr, TRUE);
    sprintf(timebuf, "Time (%s)", output_env_get_time_unit(oenv));
    tf     = output_env_get_time_factor(oenv);
    fp     = xvgropen(ncl, "Number of clusters", timebuf, "N", oenv);
    gp     = xvgropen(acl, "Average cluster size", timebuf, "#molecules", oenv);
    hp     = xvgropen(mcl, "Max cluster size", timebuf, "#molecules", oenv);
    tp     = xvgropen(tempf, "Temperature of largest cluster", timebuf, "T (K)",
                      oenv);

    if (!read_first_frame(oenv, &status, trx, &fr, TRX_NEED_X | TRX_READ_V))
    {
        gmx_file(trx);
    }

    natoms = fr.natoms;
    x      = fr.x;

    if (tpr)
    {
        snew(mtop, 1);
        read_tpxheader(tpr, &tpxh, TRUE, &version, &generation);
        if (tpxh.natoms != natoms)
        {
            gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!",
                      tpxh.natoms, natoms);
        }
        ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, NULL, mtop);
    }
    if (ndf <= -1)
    {
        tfac = 1;
    }
    else
    {
        tfac = ndf/(3.0*natoms);
    }

    if (bMol)
    {
        if (ndx)
        {
            printf("Using molecules rather than atoms. Not reading index file %s\n",
                   ndx);
        }
        mols = &(mtop->mols);

        /* Make dummy index */
        nindex = mols->nr;
        snew(index, nindex);
        for (i = 0; (i < nindex); i++)
        {
            index[i] = i;
        }
        gname = strdup("mols");
    }
    else
    {
        rd_index(ndx, 1, &nindex, &index, &gname);
    }

    alook = gmx_mtop_atomlookup_init(mtop);

    snew(clust_index, nindex);
    snew(clust_size, nindex);
    cut2   = cut*cut;
    nframe = 0;
    n_x    = 0;
    snew(t_y, nindex);
    for (i = 0; (i < nindex); i++)
    {
        t_y[i] = i+1;
    }
    max_clust_size = 1;
    max_clust_ind  = -1;
    do
    {
        if ((nskip == 0) || ((nskip > 0) && ((nframe % nskip) == 0)))
        {
            if (bPBC)
            {
                set_pbc(&pbc, ePBC, fr.box);
            }
            max_clust_size = 1;
            max_clust_ind  = -1;

            /* Put all atoms/molecules in their own cluster, with size 1 */
            for (i = 0; (i < nindex); i++)
            {
                /* Cluster index is indexed with atom index number */
                clust_index[i] = i;
                /* Cluster size is indexed with cluster number */
                clust_size[i]  = 1;
            }

            /* Loop over atoms */
            for (i = 0; (i < nindex); i++)
            {
                ai = index[i];
                ci = clust_index[i];

                /* Loop over atoms (only half a matrix) */
                for (j = i+1; (j < nindex); j++)
                {
                    cj = clust_index[j];

                    /* If they are not in the same cluster already */
                    if (ci != cj)
                    {
                        aj = index[j];

                        /* Compute distance */
                        if (bMol)
                        {
                            bSame = FALSE;
                            for (ii = mols->index[ai]; !bSame && (ii < mols->index[ai+1]); ii++)
                            {
                                for (jj = mols->index[aj]; !bSame && (jj < mols->index[aj+1]); jj++)
                                {
                                    if (bPBC)
                                    {
                                        pbc_dx(&pbc, x[ii], x[jj], dx);
                                    }
                                    else
                                    {
                                        rvec_sub(x[ii], x[jj], dx);
                                    }
                                    dx2   = iprod(dx, dx);
                                    bSame = (dx2 < cut2);
                                }
                            }
                        }
                        else
                        {
                            if (bPBC)
                            {
                                pbc_dx(&pbc, x[ai], x[aj], dx);
                            }
                            else
                            {
                                rvec_sub(x[ai], x[aj], dx);
                            }
                            dx2   = iprod(dx, dx);
                            bSame = (dx2 < cut2);
                        }
                        /* If distance less than cut-off */
                        if (bSame)
                        {
                            /* Merge clusters: check for all atoms whether they are in
                             * cluster cj and if so, put them in ci
                             */
                            for (k = 0; (k < nindex); k++)
                            {
                                if (clust_index[k] == cj)
                                {
                                    if (clust_size[cj] <= 0)
                                    {
                                        gmx_fatal(FARGS, "negative cluster size %d for element %d",
                                                  clust_size[cj], cj);
                                    }
                                    clust_size[cj]--;
                                    clust_index[k] = ci;
                                    clust_size[ci]++;
                                }
                            }
                        }
                    }
                }
            }
            n_x++;
            srenew(t_x, n_x);
            t_x[n_x-1] = fr.time*tf;
            srenew(cs_dist, n_x);
            snew(cs_dist[n_x-1], nindex);
            nclust = 0;
            cav    = 0;
            nav    = 0;
            for (i = 0; (i < nindex); i++)
            {
                ci = clust_size[i];
                if (ci > max_clust_size)
                {
                    max_clust_size = ci;
                    max_clust_ind  = i;
                }
                if (ci > 0)
                {
                    nclust++;
                    cs_dist[n_x-1][ci-1] += 1.0;
                    max_size              = max(max_size, ci);
                    if (ci > 1)
                    {
                        cav += ci;
                        nav++;
                    }
                }
            }
            fprintf(fp, "%14.6e  %10d\n", fr.time, nclust);
            if (nav > 0)
            {
                fprintf(gp, "%14.6e  %10.3f\n", fr.time, cav/nav);
            }
            fprintf(hp, "%14.6e  %10d\n", fr.time, max_clust_size);
        }
        /* Analyse velocities, if present */
        if (fr.bV)
        {
            if (!tpr)
            {
                if (bTPRwarn)
                {
                    printf("You need a [TT].tpr[tt] file to analyse temperatures\n");
                    bTPRwarn = FALSE;
                }
            }
            else
            {
                v = fr.v;
                /* Loop over clusters and for each cluster compute 1/2 m v^2 */
                if (max_clust_ind >= 0)
                {
                    ekin = 0;
                    for (i = 0; (i < nindex); i++)
                    {
                        if (clust_index[i] == max_clust_ind)
                        {
                            ai    = index[i];
                            gmx_mtop_atomnr_to_atom(alook, ai, &atom);
                            ekin += 0.5*atom->m*iprod(v[ai], v[ai]);
                        }
                    }
                    temp = (ekin*2.0)/(3.0*tfac*max_clust_size*BOLTZ);
                    fprintf(tp, "%10.3f  %10.3f\n", fr.time, temp);
                }
            }
        }
        nframe++;
    }
    while (read_next_frame(oenv, status, &fr));
    close_trx(status);
    gmx_ffclose(fp);
    gmx_ffclose(gp);
    gmx_ffclose(hp);
    gmx_ffclose(tp);

    gmx_mtop_atomlookup_destroy(alook);

    if (max_clust_ind >= 0)
    {
        fp = gmx_ffopen(mcn, "w");
        fprintf(fp, "[ max_clust ]\n");
        for (i = 0; (i < nindex); i++)
        {
            if (clust_index[i] == max_clust_ind)
            {
                if (bMol)
                {
                    for (j = mols->index[i]; (j < mols->index[i+1]); j++)
                    {
                        fprintf(fp, "%d\n", j+1);
                    }
                }
                else
                {
                    fprintf(fp, "%d\n", index[i]+1);
                }
            }
        }
        gmx_ffclose(fp);
    }

    /* Print the real distribution cluster-size/numer, averaged over the trajectory. */
    fp     = xvgropen(histo, "Cluster size distribution", "Cluster size", "()", oenv);
    nhisto = 0;
    fprintf(fp, "%5d  %8.3f\n", 0, 0.0);
    for (j = 0; (j < max_size); j++)
    {
        real nelem = 0;
        for (i = 0; (i < n_x); i++)
        {
            nelem += cs_dist[i][j];
        }
        fprintf(fp, "%5d  %8.3f\n", j+1, nelem/n_x);
        nhisto += (int)((j+1)*nelem/n_x);
    }
    fprintf(fp, "%5d  %8.3f\n", j+1, 0.0);
    gmx_ffclose(fp);

    fprintf(stderr, "Total number of atoms in clusters =  %d\n", nhisto);

    /* Look for the smallest entry that is not zero
     * This will make that zero is white, and not zero is coloured.
     */
    cmid = 100.0;
    cmax = 0.0;
    for (i = 0; (i < n_x); i++)
    {
        for (j = 0; (j < max_size); j++)
        {
            if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
            {
                cmid = cs_dist[i][j];
            }
            cmax = max(cs_dist[i][j], cmax);
        }
    }
    fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
    cmid = 1;
    fp   = gmx_ffopen(xpm, "w");
    write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
               n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
               rlo, rmid, rhi, &nlevels);
    gmx_ffclose(fp);
    cmid = 100.0;
    cmax = 0.0;
    for (i = 0; (i < n_x); i++)
    {
        for (j = 0; (j < max_size); j++)
        {
            cs_dist[i][j] *= (j+1);
            if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
            {
                cmid = cs_dist[i][j];
            }
            cmax = max(cs_dist[i][j], cmax);
        }
    }
    fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
    fp = gmx_ffopen(xpmw, "w");
    write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
               "Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
               rlo, rmid, rhi, &nlevels);
    gmx_ffclose(fp);

    sfree(clust_index);
    sfree(clust_size);
    sfree(index);
}

int gmx_clustsize(int argc, char *argv[])
{
    const char     *desc[] = {
        "[THISMODULE] computes the size distributions of molecular/atomic clusters in",
        "the gas phase. The output is given in the form of an [TT].xpm[tt] file.",
        "The total number of clusters is written to an [TT].xvg[tt] file.[PAR]",
        "When the [TT]-mol[tt] option is given clusters will be made out of",
        "molecules rather than atoms, which allows clustering of large molecules.",
        "In this case an index file would still contain atom numbers",
        "or your calculation will die with a SEGV.[PAR]",
        "When velocities are present in your trajectory, the temperature of",
        "the largest cluster will be printed in a separate [TT].xvg[tt] file assuming",
        "that the particles are free to move. If you are using constraints,",
        "please correct the temperature. For instance water simulated with SHAKE",
        "or SETTLE will yield a temperature that is 1.5 times too low. You can",
        "compensate for this with the [TT]-ndf[tt] option. Remember to take the removal",
        "of center of mass motion into account.[PAR]",
        "The [TT]-mc[tt] option will produce an index file containing the",
        "atom numbers of the largest cluster."
    };

    static real     cutoff   = 0.35;
    static int      nskip    = 0;
    static int      nlevels  = 20;
    static int      ndf      = -1;
    static gmx_bool bMol     = FALSE;
    static gmx_bool bPBC     = TRUE;
    static rvec     rlo      = { 1.0, 1.0, 0.0 };
    static rvec     rhi      = { 0.0, 0.0, 1.0 };

    output_env_t    oenv;

    t_pargs         pa[] = {
        { "-cut",      FALSE, etREAL, {&cutoff},
          "Largest distance (nm) to be considered in a cluster" },
        { "-mol",      FALSE, etBOOL, {&bMol},
          "Cluster molecules rather than atoms (needs [TT].tpr[tt] file)" },
        { "-pbc",      FALSE, etBOOL, {&bPBC},
          "Use periodic boundary conditions" },
        { "-nskip",    FALSE, etINT,  {&nskip},
          "Number of frames to skip between writing" },
        { "-nlevels",  FALSE, etINT,  {&nlevels},
          "Number of levels of grey in [TT].xpm[tt] output" },
        { "-ndf",      FALSE, etINT,  {&ndf},
          "Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used." },
        { "-rgblo",    FALSE, etRVEC, {rlo},
          "RGB values for the color of the lowest occupied cluster size" },
        { "-rgbhi",    FALSE, etRVEC, {rhi},
          "RGB values for the color of the highest occupied cluster size" }
    };
#define NPA asize(pa)
    const char     *fnNDX, *fnTPR;
    gmx_bool        bSQ, bRDF;
    t_rgb           rgblo, rgbhi;

    t_filenm        fnm[] = {
        { efTRX, "-f",  NULL,         ffREAD  },
        { efTPR, NULL,  NULL,         ffOPTRD },
        { efNDX, NULL,  NULL,         ffOPTRD },
        { efXPM, "-o", "csize",       ffWRITE },
        { efXPM, "-ow", "csizew",      ffWRITE },
        { efXVG, "-nc", "nclust",      ffWRITE },
        { efXVG, "-mc", "maxclust",    ffWRITE },
        { efXVG, "-ac", "avclust",     ffWRITE },
        { efXVG, "-hc", "histo-clust", ffWRITE },
        { efXVG, "-temp", "temp",     ffOPTWR },
        { efNDX, "-mcn", "maxclust", ffOPTWR }
    };
#define NFILE asize(fnm)

    if (!parse_common_args(&argc, argv,
                           PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
                           NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
    {
        return 0;
    }

    fnNDX   = ftp2fn_null(efNDX, NFILE, fnm);
    rgblo.r = rlo[XX], rgblo.g = rlo[YY], rgblo.b = rlo[ZZ];
    rgbhi.r = rhi[XX], rgbhi.g = rhi[YY], rgbhi.b = rhi[ZZ];

    fnTPR = ftp2fn_null(efTPR, NFILE, fnm);
    if (bMol && !fnTPR)
    {
        gmx_fatal(FARGS, "You need a tpr file for the -mol option");
    }

    clust_size(fnNDX, ftp2fn(efTRX, NFILE, fnm), opt2fn("-o", NFILE, fnm),
               opt2fn("-ow", NFILE, fnm),
               opt2fn("-nc", NFILE, fnm), opt2fn("-ac", NFILE, fnm),
               opt2fn("-mc", NFILE, fnm), opt2fn("-hc", NFILE, fnm),
               opt2fn("-temp", NFILE, fnm), opt2fn("-mcn", NFILE, fnm),
               bMol, bPBC, fnTPR,
               cutoff, nskip, nlevels, rgblo, rgbhi, ndf, oenv);

    return 0;
}