Remove continuation from convert_tpr

[gromacs.git] / src / gromacs / gmxana / gmx_angle.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015, 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
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 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
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 */
#include "gmxpre.h"

#include <cmath>
#include <cstring>

#include <algorithm>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"

static void dump_dih_trr(int nframes, int nangles, real **dih, const char *fn,
                         real *time)
{
    int              i, j, k, l, m, na;
    struct t_fileio *fio;
    rvec            *x;
    matrix           box = {{2, 0, 0}, {0, 2, 0}, {0, 0, 2}};

    na = (nangles*2);
    if ((na % 3) != 0)
    {
        na = 1+na/3;
    }
    else
    {
        na = na/3;
    }
    printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n",
           nangles, na);
    snew(x, na);
    fio = gmx_trr_open(fn, "w");
    for (i = 0; (i < nframes); i++)
    {
        k = l = 0;
        for (j = 0; (j < nangles); j++)
        {
            for (m = 0; (m < 2); m++)
            {
                // This is just because the compler and static-analyzer cannot
                // know that dih[j][i] is always valid. Since it occurs in the innermost
                // loop over angles and will only trigger on coding errors, we
                // only enable it for debug builds.
                GMX_ASSERT(dih != NULL && dih[j] != NULL, "Incorrect dihedral array data");
                x[k][l] = (m == 0) ? std::cos(dih[j][i]) : std::sin(dih[j][i]);
                l++;
                if (l == DIM)
                {
                    l = 0;
                    k++;
                }
            }
        }
        gmx_trr_write_frame(fio, i, time[i], 0, box, na, x, NULL, NULL);
    }
    gmx_trr_close(fio);
    sfree(x);
}

int gmx_g_angle(int argc, char *argv[])
{
    static const char *desc[] = {
        "[THISMODULE] computes the angle distribution for a number of angles",
        "or dihedrals.[PAR]",
        "With option [TT]-ov[tt], you can plot the average angle of",
        "a group of angles as a function of time. With the [TT]-all[tt] option,",
        "the first graph is the average and the rest are the individual angles.[PAR]",
        "With the [TT]-of[tt] option, [THISMODULE] also calculates the fraction of trans",
        "dihedrals (only for dihedrals) as function of time, but this is",
        "probably only fun for a select few.[PAR]",
        "With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
        "It should be noted that the index file must contain",
        "atom triplets for angles or atom quadruplets for dihedrals.",
        "If this is not the case, the program will crash.[PAR]",
        "With option [TT]-or[tt], a trajectory file is dumped containing cos and",
        "sin of selected dihedral angles, which subsequently can be used as",
        "input for a principal components analysis using [gmx-covar].[PAR]",
        "Option [TT]-ot[tt] plots when transitions occur between",
        "dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
        "records a histogram of the times between such transitions,",
        "assuming the input trajectory frames are equally spaced in time."
    };
    static const char *opt[]    = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
    static gmx_bool    bALL     = FALSE, bChandler = FALSE, bAverCorr = FALSE, bPBC = TRUE;
    static real        binwidth = 1;
    t_pargs            pa[]     = {
        { "-type", FALSE, etENUM, {opt},
          "Type of angle to analyse" },
        { "-all",    FALSE,  etBOOL, {&bALL},
          "Plot all angles separately in the averages file, in the order of appearance in the index file." },
        { "-binwidth", FALSE, etREAL, {&binwidth},
          "binwidth (degrees) for calculating the distribution" },
        { "-periodic", FALSE, etBOOL, {&bPBC},
          "Print dihedral angles modulo 360 degrees" },
        { "-chandler", FALSE,  etBOOL, {&bChandler},
          "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 or phi > 60." },
        { "-avercorr", FALSE,  etBOOL, {&bAverCorr},
          "Average the correlation functions for the individual angles/dihedrals" }
    };
    static const char *bugs[] = {
        "Counting transitions only works for dihedrals with multiplicity 3"
    };

    FILE              *out;
    real               dt;
    int                isize;
    int               *index;
    char              *grpname;
    real               maxang, S2, norm_fac, maxstat;
    unsigned long      mode;
    int                nframes, maxangstat, mult, *angstat;
    int                i, j, nangles, first, last;
    gmx_bool           bAver, bRb, bPeriodic,
                       bFrac,               /* calculate fraction too?  */
                       bTrans,              /* worry about transtions too? */
                       bCorr;               /* correlation function ? */
    real              aver, aver2, aversig; /* fraction trans dihedrals */
    double            tfrac = 0;
    char              title[256];
    real            **dih = NULL; /* mega array with all dih. angles at all times*/
    real             *time, *trans_frac, *aver_angle;
    t_filenm          fnm[] = {
        { efTRX, "-f", NULL,  ffREAD  },
        { efNDX, NULL, "angle",  ffREAD  },
        { efXVG, "-od", "angdist",  ffWRITE },
        { efXVG, "-ov", "angaver",  ffOPTWR },
        { efXVG, "-of", "dihfrac",  ffOPTWR },
        { efXVG, "-ot", "dihtrans", ffOPTWR },
        { efXVG, "-oh", "trhisto",  ffOPTWR },
        { efXVG, "-oc", "dihcorr",  ffOPTWR },
        { efTRR, "-or", NULL,       ffOPTWR }
    };
#define NFILE asize(fnm)
    int               npargs;
    t_pargs          *ppa;
    gmx_output_env_t *oenv;

    npargs = asize(pa);
    ppa    = add_acf_pargs(&npargs, pa);
    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
                           NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
                           &oenv))
    {
        return 0;
    }

    mult   = 4;
    maxang = 360.0;
    bRb    = FALSE;

    GMX_RELEASE_ASSERT(opt[0] != NULL, "Internal option inconsistency; opt[0]==NULL after processing");

    switch (opt[0][0])
    {
        case 'a':
            mult   = 3;
            maxang = 180.0;
            break;
        case 'd':
            break;
        case 'i':
            break;
        case 'r':
            bRb = TRUE;
            break;
    }

    if (opt2bSet("-or", NFILE, fnm))
    {
        if (mult != 4)
        {
            gmx_fatal(FARGS, "Can not combine angles with trr dump");
        }
        else
        {
            please_cite(stdout, "Mu2005a");
        }
    }

    /* Calculate bin size */
    maxangstat = static_cast<int>(maxang/binwidth+0.5);
    binwidth   = maxang/maxangstat;

    rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
    nangles = isize/mult;
    if ((isize % mult) != 0)
    {
        gmx_fatal(FARGS, "number of index elements not multiple of %d, "
                  "these can not be %s\n",
                  mult, (mult == 3) ? "angle triplets" : "dihedral quadruplets");
    }


    /* Check whether specific analysis has to be performed */
    bCorr  = opt2bSet("-oc", NFILE, fnm);
    bAver  = opt2bSet("-ov", NFILE, fnm);
    bTrans = opt2bSet("-ot", NFILE, fnm);
    bFrac  = opt2bSet("-of", NFILE, fnm);
    if (bTrans && opt[0][0] != 'd')
    {
        fprintf(stderr, "Option -ot should only accompany -type dihedral. Disabling -ot.\n");
        bTrans = FALSE;
    }

    if (bChandler && !bCorr)
    {
        bCorr = TRUE;
    }

    if (bFrac && !bRb)
    {
        fprintf(stderr, "Warning:"
                " calculating fractions as defined in this program\n"
                "makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
        bFrac = FALSE;
    }

    if ( (bTrans || bFrac || bCorr) && mult == 3)
    {
        gmx_fatal(FARGS, "Can only do transition, fraction or correlation\n"
                  "on dihedrals. Select -d\n");
    }

    /*
     * We need to know the nr of frames so we can allocate memory for an array
     * with all dihedral angles at all timesteps. Works for me.
     */
    if (bTrans || bCorr  || bALL || opt2bSet("-or", NFILE, fnm))
    {
        snew(dih, nangles);
    }

    snew(angstat, maxangstat);

    read_ang_dih(ftp2fn(efTRX, NFILE, fnm), (mult == 3),
                 bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm),
                 bRb, bPBC, maxangstat, angstat,
                 &nframes, &time, isize, index, &trans_frac, &aver_angle, dih,
                 oenv);

    dt = (time[nframes-1]-time[0])/(nframes-1);

    if (bAver)
    {
        sprintf(title, "Average Angle: %s", grpname);
        out = xvgropen(opt2fn("-ov", NFILE, fnm),
                       title, "Time (ps)", "Angle (degrees)", oenv);
        for (i = 0; (i < nframes); i++)
        {
            fprintf(out, "%10.5f  %8.3f", time[i], aver_angle[i]*RAD2DEG);
            if (bALL)
            {
                for (j = 0; (j < nangles); j++)
                {
                    if (bPBC)
                    {
                        real dd = dih[j][i];
                        fprintf(out, "  %8.3f", std::atan2(std::sin(dd), std::cos(dd))*RAD2DEG);
                    }
                    else
                    {
                        fprintf(out, "  %8.3f", dih[j][i]*RAD2DEG);
                    }
                }
            }
            fprintf(out, "\n");
        }
        xvgrclose(out);
    }
    if (opt2bSet("-or", NFILE, fnm))
    {
        dump_dih_trr(nframes, nangles, dih, opt2fn("-or", NFILE, fnm), time);
    }

    if (bFrac)
    {
        sprintf(title, "Trans fraction: %s", grpname);
        out = xvgropen(opt2fn("-of", NFILE, fnm),
                       title, "Time (ps)", "Fraction", oenv);
        tfrac = 0.0;
        for (i = 0; (i < nframes); i++)
        {
            fprintf(out, "%10.5f  %10.3f\n", time[i], trans_frac[i]);
            tfrac += trans_frac[i];
        }
        xvgrclose(out);

        tfrac /= nframes;
        fprintf(stderr, "Average trans fraction: %g\n", tfrac);
    }
    sfree(trans_frac);

    if (bTrans)
    {
        ana_dih_trans(opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm),
                      dih, nframes, nangles, grpname, time, bRb, oenv);
    }

    if (bCorr)
    {
        /* Autocorrelation function */
        if (nframes < 2)
        {
            fprintf(stderr, "Not enough frames for correlation function\n");
        }
        else
        {

            if (bChandler)
            {
                real     dval, sixty = DEG2RAD*60;
                gmx_bool bTest;

                for (i = 0; (i < nangles); i++)
                {
                    for (j = 0; (j < nframes); j++)
                    {
                        dval = dih[i][j];
                        if (bRb)
                        {
                            bTest = (dval > -sixty) && (dval < sixty);
                        }
                        else
                        {
                            bTest = (dval < -sixty) || (dval > sixty);
                        }
                        if (bTest)
                        {
                            dih[i][j] = dval-tfrac;
                        }
                        else
                        {
                            dih[i][j] = -tfrac;
                        }
                    }
                }
            }
            if (bChandler)
            {
                mode = eacNormal;
            }
            else
            {
                mode = eacCos;
            }
            do_autocorr(opt2fn("-oc", NFILE, fnm), oenv,
                        "Dihedral Autocorrelation Function",
                        nframes, nangles, dih, dt, mode, bAverCorr);
        }
    }


    /* Determine the non-zero part of the distribution */
    for (first = 0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
    {
        ;
    }
    for (last = maxangstat-1; (last > 0) && (angstat[last-1] == 0); last--)
    {
        ;
    }

    aver = aver2 = 0;
    for (i = 0; (i < nframes); i++)
    {
        aver  += RAD2DEG*aver_angle[i];
        aver2 += gmx::square(RAD2DEG*aver_angle[i]);
    }
    aver   /= nframes;
    aver2  /= nframes;
    aversig = std::sqrt(aver2-gmx::square(aver));
    printf("Found points in the range from %d to %d (max %d)\n",
           first, last, maxangstat);
    printf(" < angle >  = %g\n", aver);
    printf("< angle^2 > = %g\n", aver2);
    printf("Std. Dev.   = %g\n", aversig);

    if (mult == 3)
    {
        sprintf(title, "Angle Distribution: %s", grpname);
    }
    else
    {
        sprintf(title, "Dihedral Distribution: %s", grpname);

        calc_distribution_props(maxangstat, angstat, -180.0, 0, NULL, &S2);
        fprintf(stderr, "Order parameter S^2 = %g\n", S2);
    }

    bPeriodic = (mult == 4) && (first == 0) && (last == maxangstat-1);

    out = xvgropen(opt2fn("-od", NFILE, fnm), title, "Degrees", "", oenv);
    if (output_env_get_print_xvgr_codes(oenv))
    {
        fprintf(out, "@    subtitle \"average angle: %g\\So\\N\"\n", aver);
    }
    norm_fac = 1.0/(nangles*nframes*binwidth);
    if (bPeriodic)
    {
        maxstat = 0;
        for (i = first; (i <= last); i++)
        {
            maxstat = std::max(maxstat, angstat[i]*norm_fac);
        }
        if (output_env_get_print_xvgr_codes(oenv))
        {
            fprintf(out, "@with g0\n");
            fprintf(out, "@    world xmin -180\n");
            fprintf(out, "@    world xmax  180\n");
            fprintf(out, "@    world ymin 0\n");
            fprintf(out, "@    world ymax %g\n", maxstat*1.05);
            fprintf(out, "@    xaxis  tick major 60\n");
            fprintf(out, "@    xaxis  tick minor 30\n");
            fprintf(out, "@    yaxis  tick major 0.005\n");
            fprintf(out, "@    yaxis  tick minor 0.0025\n");
        }
    }
    for (i = first; (i <= last); i++)
    {
        fprintf(out, "%10g  %10f\n", i*binwidth+180.0-maxang, angstat[i]*norm_fac);
    }
    if (bPeriodic)
    {
        /* print first bin again as last one */
        fprintf(out, "%10g  %10f\n", 180.0, angstat[0]*norm_fac);
    }

    xvgrclose(out);

    do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
    if (bAver)
    {
        do_view(oenv, opt2fn("-ov", NFILE, fnm), "-nxy");
    }

    return 0;
}