Remove all unnecessary HAVE_CONFIG_H

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

/*
 * 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, 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
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 */
#include "config.h"

#include <math.h>
#include <stdio.h>
#include <string.h>

#include "gromacs/fileio/confio.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/units.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "txtdump.h"
#include "typedefs.h"
#include "gromacs/math/vec.h"
#include "gromacs/fileio/xvgr.h"
#include "viewit.h"
#include "gromacs/pbcutil/pbc.h"
#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"


#define NK  24
#define NPK 4

#define NKC  6
#define NKC0 4
int  kset_c[NKC+1] = { 0, 3, 9, 13, 16, 19, NK };

rvec v0[NK] = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}, {1, 1, 0}, {1, -1, 0}, {1, 0, 1}, {1, 0, -1}, {0, 1, 1}, {0, 1, -1}, {1, 1, 1}, {1, 1, -1}, {1, -1, 1}, {-1, 1, 1}, {2, 0, 0}, {0, 2, 0}, {0, 0, 2}, {3, 0, 0}, {0, 3, 0}, {0, 0, 3}, {4, 0, 0}, {0, 4, 0}, {0, 0, 4}};
rvec v1[NK] = {{0, 1, 0}, {0, 0, 1}, {1, 0, 0}, {0, 0, 1}, {0, 0, 1}, {0, 1, 0}, {0, 1, 0}, {1, 0, 0}, {1, 0, 0}, {1, -1, 0}, {1, -1, 0}, {1, 0, -1}, { 0, 1, -1}, {0, 1, 0}, {0, 0, 1}, {1, 0, 0}, {0, 1, 0}, {0, 0, 1}, {1, 0, 0}, {0, 1, 0}, {0, 0, 1}, {1, 0, 0}};
rvec v2[NK] = {{0, 0, 1}, {1, 0, 0}, {0, 1, 0}, {1, -1, 0}, {1, 1, 0}, {1, 0, -1}, {1, 0, 1}, {0, 1, -1}, {0, 1, 1}, {1, 1, -2}, {1, 1, 2}, {1, 2, 1}, { 2, 1, 1}, {0, 0, 1}, {1, 0, 0}, {0, 1, 0}, {0, 0, 1}, {1, 0, 0}, {0, 1, 0}, {0, 0, 1}, {1, 0, 0}, {0, 1, 0}};

static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac,
                         real rho, real wt, const char *fn_trans,
                         const char *fn_tca, const char *fn_tc,
                         const char *fn_tcf, const char *fn_cub,
                         const char *fn_vk, const output_env_t oenv)
{
    FILE  *fp, *fp_vk, *fp_cub = NULL;
    int    nk, ntc;
    real **tcaf, **tcafc = NULL, eta;
    int    i, j, k, kc;
    int    ncorr;
    real   fitparms[3], *sig;

    nk  = kset_c[nkc];
    ntc = nk*NPK;

    if (fn_trans)
    {
        fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)",
                      oenv);
        for (i = 0; i < nframes; i++)
        {
            fprintf(fp, "%g", i*dt);
            for (j = 0; j < ntc; j++)
            {
                fprintf(fp, " %g", tc[j][i]);
            }
            fprintf(fp, "\n");
        }
        gmx_ffclose(fp);
        do_view(oenv, fn_trans, "-nxy");
    }

    ncorr = (nframes+1)/2;
    if (ncorr > (int)(5*wt/dt+0.5))
    {
        ncorr = (int)(5*wt/dt+0.5)+1;
    }
    snew(tcaf, nk);
    for (k = 0; k < nk; k++)
    {
        snew(tcaf[k], ncorr);
    }
    if (fn_cub)
    {
        snew(tcafc, nkc);
        for (k = 0; k < nkc; k++)
        {
            snew(tcafc[k], ncorr);
        }
    }
    snew(sig, ncorr);
    for (i = 0; i < ncorr; i++)
    {
        sig[i] = exp(0.5*i*dt/wt);
    }

    low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions",
                    nframes, ntc, ncorr, tc, dt, eacNormal,
                    1, FALSE, FALSE, FALSE, 0, 0, 0);
    do_view(oenv, fn_tca, "-nxy");

    fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions",
                  "Time (ps)", "TCAF", oenv);
    for (i = 0; i < ncorr; i++)
    {
        kc = 0;
        fprintf(fp, "%g", i*dt);
        for (k = 0; k < nk; k++)
        {
            for (j = 0; j < NPK; j++)
            {
                tcaf[k][i] += tc[NPK*k+j][i];
            }
            if (fn_cub)
            {
                for (j = 0; j < NPK; j++)
                {
                    tcafc[kc][i] += tc[NPK*k+j][i];
                }
            }
            if (i == 0)
            {
                fprintf(fp, " %g", 1.0);
            }
            else
            {
                tcaf[k][i] /= tcaf[k][0];
                fprintf(fp, " %g", tcaf[k][i]);
            }
            if (k+1 == kset_c[kc+1])
            {
                kc++;
            }
        }
        fprintf(fp, "\n");
    }
    gmx_ffclose(fp);
    do_view(oenv, fn_tc, "-nxy");

    if (fn_cub)
    {
        fp_cub = xvgropen(fn_cub, "TCAFs and fits", "Time (ps)", "TCAF", oenv);
        for (kc = 0; kc < nkc; kc++)
        {
            fprintf(fp_cub, "%g %g\n", 0.0, 1.0);
            for (i = 1; i < ncorr; i++)
            {
                tcafc[kc][i] /= tcafc[kc][0];
                fprintf(fp_cub, "%g %g\n", i*dt, tcafc[kc][i]);
            }
            fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
            tcafc[kc][0] = 1.0;
        }
    }

    fp_vk = xvgropen(fn_vk, "Fits", "k (nm\\S-1\\N)",
                     "\\8h\\4 (10\\S-3\\N kg m\\S-1\\N s\\S-1\\N)", oenv);
    if (output_env_get_print_xvgr_codes(oenv))
    {
        fprintf(fp_vk, "@    s0 symbol 2\n");
        fprintf(fp_vk, "@    s0 symbol color 1\n");
        fprintf(fp_vk, "@    s0 linestyle 0\n");
        if (fn_cub)
        {
            fprintf(fp_vk, "@    s1 symbol 3\n");
            fprintf(fp_vk, "@    s1 symbol color 2\n");
        }
    }
    fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
    for (k = 0; k < nk; k++)
    {
        tcaf[k][0]   = 1.0;
        fitparms[0]  = 1;
        fitparms[1]  = 1;
        do_lmfit(ncorr, tcaf[k], sig, dt, 0, 0, ncorr*dt,
                 oenv, bDebugMode(), effnVAC, fitparms, 0);
        eta = 1000*fitparms[1]*rho/
            (4*fitparms[0]*PICO*norm2(kfac[k])/(NANO*NANO));
        fprintf(stdout, "k %6.3f  tau %6.3f  eta %8.5f 10^-3 kg/(m s)\n",
                norm(kfac[k]), fitparms[0], eta);
        fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
        for (i = 0; i < ncorr; i++)
        {
            fprintf(fp, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
        }
        fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
    }
    gmx_ffclose(fp);
    do_view(oenv, fn_tcf, "-nxy");

    if (fn_cub)
    {
        fprintf(stdout, "Averaged over k-vectors:\n");
        fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
        for (k = 0; k < nkc; k++)
        {
            tcafc[k][0]  = 1.0;
            fitparms[0]  = 1;
            fitparms[1]  = 1;
            do_lmfit(ncorr, tcafc[k], sig, dt, 0, 0, ncorr*dt,
                     oenv, bDebugMode(), effnVAC, fitparms, 0);
            eta = 1000*fitparms[1]*rho/
                (4*fitparms[0]*PICO*norm2(kfac[kset_c[k]])/(NANO*NANO));
            fprintf(stdout,
                    "k %6.3f  tau %6.3f  Omega %6.3f  eta %8.5f 10^-3 kg/(m s)\n",
                    norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
            fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
            for (i = 0; i < ncorr; i++)
            {
                fprintf(fp_cub, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
            }
            fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
        }
        fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
        gmx_ffclose(fp_cub);
        do_view(oenv, fn_cub, "-nxy");
    }
    gmx_ffclose(fp_vk);
    do_view(oenv, fn_vk, "-nxy");
}


int gmx_tcaf(int argc, char *argv[])
{
    const char     *desc[] = {
        "[THISMODULE] computes tranverse current autocorrelations.",
        "These are used to estimate the shear viscosity, [GRK]eta[grk].",
        "For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.[PAR]",
        "Transverse currents are calculated using the",
        "k-vectors (1,0,0) and (2,0,0) each also in the [IT]y[it]- and [IT]z[it]-direction,",
        "(1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors",
        "are not independent) and (1,1,1) and the 3 other box diagonals (also",
        "not independent). For each k-vector the sine and cosine are used, in",
        "combination with the velocity in 2 perpendicular directions. This gives",
        "a total of 16*2*2=64 transverse currents. One autocorrelation is",
        "calculated fitted for each k-vector, which gives 16 TCAFs. Each of",
        "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W [SINH]Wv[sinh])[math],",
        "[MATH]v = -t/(2 [GRK]tau[grk])[math], [MATH]W = [SQRT]1 - 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k^2[sqrt][math], which gives 16 values of [GRK]tau[grk]",
        "and [GRK]eta[grk]. The fit weights decay exponentially with time constant [MATH]w[math] (given with [TT]-wt[tt]) as [MATH][EXP]-t/w[exp][math], and the TCAF and",
        "fit are calculated up to time [MATH]5*w[math].",
        "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], from which",
        "one can estimate the shear viscosity at k=0.[PAR]",
        "When the box is cubic, one can use the option [TT]-oc[tt], which",
        "averages the TCAFs over all k-vectors with the same length.",
        "This results in more accurate TCAFs.",
        "Both the cubic TCAFs and fits are written to [TT]-oc[tt]",
        "The cubic [GRK]eta[grk] estimates are also written to [TT]-ov[tt].[PAR]",
        "With option [TT]-mol[tt], the transverse current is determined of",
        "molecules instead of atoms. In this case, the index group should",
        "consist of molecule numbers instead of atom numbers.[PAR]",
        "The k-dependent viscosities in the [TT]-ov[tt] file should be",
        "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain the viscosity at",
        "infinite wavelength.[PAR]",
        "[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
        "The initial, non-exponential, part of the autocorrelation function",
        "is very important for obtaining a good fit."
    };

    static gmx_bool bMol = FALSE, bK34 = FALSE;
    static real     wt   = 5;
    t_pargs         pa[] = {
        { "-mol", FALSE, etBOOL, {&bMol},
          "Calculate TCAF of molecules" },
        { "-k34", FALSE, etBOOL, {&bK34},
          "Also use k=(3,0,0) and k=(4,0,0)" },
        { "-wt", FALSE, etREAL, {&wt},
          "Exponential decay time for the TCAF fit weights" }
    };

    t_topology      top;
    int             ePBC;
    t_trxframe      fr;
    matrix          box;
    gmx_bool        bTPS, bTop; /* ,bCubic; */
    int             gnx;
    atom_id        *index, *atndx = NULL, at;
    char           *grpname;
    char            title[256];
    real            t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
    t_trxstatus    *status;
    int             nframes, n_alloc, i, j, k, d;
    rvec            mv_mol, cm_mol, kfac[NK];
    int             nkc, nk, ntc;
    real          **c1, **tc;
    output_env_t    oenv;

#define NHISTO 360

    t_filenm  fnm[] = {
        { efTRN, "-f",    NULL,      ffREAD  },
        { efTPS, NULL,    NULL,      ffOPTRD },
        { efNDX, NULL,    NULL,      ffOPTRD },
        { efXVG, "-ot",  "transcur", ffOPTWR },
        { efXVG, "-oa",  "tcaf_all", ffWRITE },
        { efXVG, "-o",   "tcaf",     ffWRITE },
        { efXVG, "-of",  "tcaf_fit", ffWRITE },
        { efXVG, "-oc",  "tcaf_cub", ffOPTWR },
        { efXVG, "-ov",  "visc_k",   ffWRITE }
    };
#define NFILE asize(fnm)
    int       npargs;
    t_pargs  *ppa;

    npargs = asize(pa);
    ppa    = add_acf_pargs(&npargs, pa);

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

    bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
                         TRUE);
    get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);

    if (bMol)
    {
        if (!bTop)
        {
            gmx_fatal(FARGS, "Need a topology to determine the molecules");
        }
        atndx = top.mols.index;
    }

    if (bK34)
    {
        nkc = NKC;
    }
    else
    {
        nkc = NKC0;
    }
    nk  = kset_c[nkc];
    ntc = nk*NPK;

    sprintf(title, "Velocity Autocorrelation Function for %s", grpname);

    sysmass = 0;
    for (i = 0; i < nk; i++)
    {
        if (iprod(v0[i], v1[i]) != 0)
        {
            gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
        }
        if (iprod(v0[i], v2[i]) != 0)
        {
            gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
        }
        if (iprod(v1[i], v2[i]) != 0)
        {
            gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
        }
        unitv(v1[i], v1[i]);
        unitv(v2[i], v2[i]);
    }
    snew(tc, ntc);
    for (i = 0; i < top.atoms.nr; i++)
    {
        sysmass += top.atoms.atom[i].m;
    }

    read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr,
                     TRX_NEED_X | TRX_NEED_V);
    t0 = fr.time;

    n_alloc = 0;
    nframes = 0;
    rho     = 0;
    /* bCubic = TRUE; */
    do
    {
        /*
           bCubic = bCubic && !TRICLINIC(fr.box) &&
           fabs(fr.box[XX][XX]-fr.box[YY][YY]) < 0.001*fr.box[XX][XX] &&
           fabs(fr.box[XX][XX]-fr.box[ZZ][ZZ]) < 0.001*fr.box[XX][XX];
         */

        if (nframes >= n_alloc)
        {
            n_alloc += 100;
            for (i = 0; i < ntc; i++)
            {
                srenew(tc[i], n_alloc);
            }
        }

        rho += 1/det(fr.box);
        for (k = 0; k < nk; k++)
        {
            for (d = 0; d < DIM; d++)
            {
                kfac[k][d] = 2*M_PI*v0[k][d]/fr.box[d][d];
            }
        }
        for (i = 0; i < ntc; i++)
        {
            tc[i][nframes] = 0;
        }

        for (i = 0; i < gnx; i++)
        {
            if (bMol)
            {
                clear_rvec(mv_mol);
                clear_rvec(cm_mol);
                mtot = 0;
                for (j = 0; j < atndx[index[i]+1] - atndx[index[i]]; j++)
                {
                    at          = atndx[index[i]] + j;
                    m           = top.atoms.atom[at].m;
                    mv_mol[XX] += m*fr.v[at][XX];
                    mv_mol[YY] += m*fr.v[at][YY];
                    mv_mol[ZZ] += m*fr.v[at][ZZ];
                    cm_mol[XX] += m*fr.x[at][XX];
                    cm_mol[YY] += m*fr.x[at][YY];
                    cm_mol[ZZ] += m*fr.x[at][ZZ];
                    mtot       += m;
                }
                svmul(1.0/mtot, cm_mol, cm_mol);
            }
            else
            {
                svmul(top.atoms.atom[index[i]].m, fr.v[index[i]], mv_mol);
            }

            if (!bMol)
            {
                copy_rvec(fr.x[index[i]], cm_mol);
            }
            j = 0;
            for (k = 0; k < nk; k++)
            {
                sx              = sin(iprod(kfac[k], cm_mol));
                cx              = cos(iprod(kfac[k], cm_mol));
                tc[j][nframes] += sx*iprod(v1[k], mv_mol);
                j++;
                tc[j][nframes] += cx*iprod(v1[k], mv_mol);
                j++;
                tc[j][nframes] += sx*iprod(v2[k], mv_mol);
                j++;
                tc[j][nframes] += cx*iprod(v2[k], mv_mol);
                j++;
            }
        }

        t1 = fr.time;
        nframes++;
    }
    while (read_next_frame(oenv, status, &fr));
    close_trj(status);

    dt = (t1-t0)/(nframes-1);

    rho *= sysmass/nframes*AMU/(NANO*NANO*NANO);
    fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
    process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt,
                 opt2fn_null("-ot", NFILE, fnm),
                 opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm),
                 opt2fn("-of", NFILE, fnm), opt2fn_null("-oc", NFILE, fnm),
                 opt2fn("-ov", NFILE, fnm), oenv);

    return 0;
}