From 3a52686eb02334c843e2c2063699cdaab7b8e3e0 Mon Sep 17 00:00:00 2001 From: Erik Lindahl Date: Thu, 12 Jun 2014 00:24:32 +0200 Subject: [PATCH] Removed undocumented -map and -mdata options from g_sham. Both options and code were completely undocumented, and nobody seemed interested in helping document them for the last two years, so for now they are gone. Fixes #812. Change-Id: I4d60cf3d58da89d76a4461cdc2e75f031676d2c9 --- src/gromacs/gmxana/gmx_sham.c | 94 ++++------------------------------- 1 file changed, 9 insertions(+), 85 deletions(-) diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c index 9d670c4897..911fdbff0f 100644 --- a/src/gromacs/gmxana/gmx_sham.c +++ b/src/gromacs/gmxana/gmx_sham.c @@ -411,25 +411,24 @@ static void pick_minima(const char *logfile, int *ibox, int ndim, int len, real static void do_sham(const char *fn, const char *ndx, const char *xpmP, const char *xpm, const char *xpm2, - const char *xpm3, const char *xpm4, const char *pdb, + const char *xpm3, const char *pdb, const char *logf, int n, int neig, real **eig, gmx_bool bGE, int nenerT, real **enerT, - int nmap, real *mapindex, real **map, real Tref, real pmax, real gmax, real *emin, real *emax, int nlevels, real pmin, - const char *mname, int *idim, int *ibox, + int *idim, int *ibox, gmx_bool bXmin, real *xmin, gmx_bool bXmax, real *xmax) { FILE *fp; real *min_eig, *max_eig; real *axis_x, *axis_y, *axis_z, *axis = NULL; double *P; - real **PP, *W, *E, **WW, **EE, *S, **SS, *M, **MM, *bE; + real **PP, *W, *E, **WW, **EE, *S, **SS, *M, *bE; rvec xxx; char *buf; - double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax, Minf; + double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax; real *delta; int i, j, k, imin, len, index, d, *nbin, *bindex, bi; int *nxyz, maxbox; @@ -701,45 +700,7 @@ static void do_sham(const char *fn, const char *ndx, axis[j] = min_eig[i] + j/bfac[i]; } } - if (map) - { - snew(M, len); - snew(MM, maxbox*maxbox); - for (i = 0; (i < ibox[0]); i++) - { - MM[i] = &(M[i*ibox[1]]); - } - Mmin = 1e8; - Mmax = -1e8; - for (i = 0; (i < nmap); i++) - { - Mmin = min(Mmin, map[0][i]); - Mmax = max(Mmax, map[0][i]); - } - Minf = Mmax*1.05; - for (i = 0; (i < len); i++) - { - M[i] = Minf; - } - for (i = 0; (i < nmap); i++) - { - index = gmx_nint(mapindex[i]); - if (index >= len) - { - gmx_fatal(FARGS, "Number of bins in file from -mdata option does not correspond to current analysis"); - } - if (P[index] != 0) - { - M[index] = map[0][i]; - } - } - } - else - { - MM = NULL; - Minf = NOTSET; - } pick_minima(logf, ibox, neig, len, W); if (gmax <= 0) { @@ -778,13 +739,6 @@ static void do_sham(const char *fn, const char *ndx, write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1], axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels); gmx_ffclose(fp); - if (map) - { - fp = gmx_ffopen(xpm4, "w"); - write_xpm(fp, flags, "Custom Landscape", mname, "PC1", "PC2", - ibox[0], ibox[1], axis_x, axis_y, MM, 0, Minf, rlo, rhi, &nlevels); - gmx_ffclose(fp); - } } else if (neig == 3) { @@ -811,10 +765,6 @@ static void do_sham(const char *fn, const char *ndx, } gmx_ffclose(fp); write_xplor("out.xplor", W, ibox, min_eig, max_eig); - if (map) - { - write_xplor("user.xplor", M, ibox, min_eig, max_eig); - } nxyz[XX] = imin/(ibox[1]*ibox[2]); nxyz[YY] = (imin-nxyz[XX]*ibox[1]*ibox[2])/ibox[2]; nxyz[ZZ] = imin % ibox[2]; @@ -859,11 +809,6 @@ static void do_sham(const char *fn, const char *ndx, gmx_ffclose(fp); sfree(buf); } - if (map) - { - sfree(MM); - sfree(M); - } } static void ehisto(const char *fh, int n, real **enerT, const output_env_t oenv) @@ -975,7 +920,6 @@ int gmx_sham(int argc, char *argv[]) static rvec nrbox = {32, 32, 32}; static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1}; static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25; - static const char *mname = ""; t_pargs pa[] = { { "-time", FALSE, etBOOL, {&bHaveT}, "Expect a time in the input" }, @@ -1013,14 +957,12 @@ int gmx_sham(int argc, char *argv[]) "Maximum enthalpy in output, default is calculate" }, { "-nlevels", FALSE, etINT, {&nlevels}, "Number of levels for energy landscape" }, - { "-mname", FALSE, etSTR, {&mname}, - "Legend label for the custom landscape" }, }; #define NPA asize(pa) FILE *out; - int n, e_n, d_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox; - real **val, **et_val, **dt_val, *t, *e_t, e_dt, d_dt, *d_t, dt, tot, error; + int n, e_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox; + real **val, **et_val, *t, *e_t, e_dt, d_dt, dt, tot, error; real *rmin, *rmax; double *av, *sig, cum1, cum2, cum3, cum4, db; const char *fn_ge, *fn_ene; @@ -1038,9 +980,7 @@ int gmx_sham(int argc, char *argv[]) { efXPM, "-ls", "gibbs", ffOPTWR }, { efXPM, "-lsh", "enthalpy", ffOPTWR }, { efXPM, "-lss", "entropy", ffOPTWR }, - { efXPM, "-map", "map", ffOPTWR }, { efPDB, "-ls3", "gibbs3", ffOPTWR }, - { efXVG, "-mdata", "mapdata", ffOPTRD }, { efLOG, "-g", "shamlog", ffOPTWR } }; #define NFILE asize(fnm) @@ -1100,22 +1040,6 @@ int gmx_sham(int argc, char *argv[]) et_val = NULL; } - if (opt2fn_null("-mdata", NFILE, fnm) != NULL) - { - dt_val = read_xvg_time(opt2fn("-mdata", NFILE, fnm), bHaveT, - FALSE, tb, FALSE, te, - nsets_in, &d_nset, &d_n, &d_dt, &d_t); - if (d_nset != 1) - { - gmx_fatal(FARGS, "Can only handle one mapping data column in %s", - opt2fn("-mdata", NFILE, fnm)); - } - } - else - { - dt_val = NULL; - } - if (fn_ene && et_val) { ehisto(opt2fn("-histo", NFILE, fnm), e_n, et_val, oenv); @@ -1157,14 +1081,14 @@ int gmx_sham(int argc, char *argv[]) do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm), opt2fn("-lp", NFILE, fnm), opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm), - opt2fn("-lss", NFILE, fnm), opt2fn("-map", NFILE, fnm), + opt2fn("-lss", NFILE, fnm), opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm), - n, nset, val, fn_ge != NULL, e_nset, et_val, d_n, d_t, dt_val, Tref, + n, nset, val, fn_ge != NULL, e_nset, et_val, Tref, pmax, gmax, opt2parg_bSet("-emin", NPA, pa) ? &emin : NULL, opt2parg_bSet("-emax", NPA, pa) ? &emax : NULL, nlevels, pmin, - mname, idim, ibox, + idim, ibox, opt2parg_bSet("-xmin", NPA, pa), rmin, opt2parg_bSet("-xmax", NPA, pa), rmax); -- 2.22.0