src/gromacs/gmxana/gmx_hydorder.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
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  13  *
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  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41 #include <string.h>
  42
  43 #include "typedefs.h"
  44 #include "macros.h"
  45 #include "gstat.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/pbcutil/pbc.h"
  48 #include "gromacs/utility/futil.h"
  49 #include "index.h"
  50 #include "gromacs/fileio/tpxio.h"
  51 #include "gromacs/fileio/trxio.h"
  52 #include "binsearch.h"
  53 #include "powerspect.h"
  54
  55 #include "gromacs/commandline/pargs.h"
  56 #include "gromacs/fileio/matio.h"
  57 #include "gromacs/fileio/xvgr.h"
  58 #include "gromacs/pbcutil/rmpbc.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 /* Print name of first atom in all groups in index file */
  63 static void print_types(atom_id index[], atom_id a[], int ngrps,
  64                         char *groups[], t_topology *top)
  65 {
  66     int i;
  67
  68     fprintf(stderr, "Using following groups: \n");
  69     for (i = 0; i < ngrps; i++)
  70     {
  71         fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
  72                 groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
  73     }
  74     fprintf(stderr, "\n");
  75 }
  76
  77 static void check_length(real length, int a, int b)
  78 {
  79     if (length > 0.3)
  80     {
  81         fprintf(stderr, "WARNING: distance between atoms %d and "
  82                 "%d > 0.3 nm (%f). Index file might be corrupt.\n",
  83                 a, b, length);
  84     }
  85 }
  86
  87 static void find_tetra_order_grid(t_topology top, int ePBC,
  88                                   int natoms, matrix box,
  89                                   rvec x[], int maxidx, atom_id index[],
  90                                   real *sgmean, real *skmean,
  91                                   int nslicex, int nslicey, int nslicez,
  92                                   real ***sggrid, real ***skgrid)
  93 {
  94     int         ix, jx, i, j, k, l, n, *nn[4];
  95     rvec        dx, rj, rk, urk, urj;
  96     real        cost, cost2, *sgmol, *skmol, rmean, rmean2, r2, box2, *r_nn[4];
  97     t_pbc       pbc;
  98     int         slindex_x, slindex_y, slindex_z;
  99     int      ***sl_count;
 100     real        onethird = 1.0/3.0;
 101     gmx_rmpbc_t gpbc;
 102
 103     /*  dmat = init_mat(maxidx, FALSE); */
 104
 105     box2 = box[XX][XX] * box[XX][XX];
 106
 107     /* Initialize expanded sl_count array */
 108     snew(sl_count, nslicex);
 109     for (i = 0; i < nslicex; i++)
 110     {
 111         snew(sl_count[i], nslicey);
 112         for (j = 0; j < nslicey; j++)
 113         {
 114             snew(sl_count[i][j], nslicez);
 115         }
 116     }
 117
 118
 119     for (i = 0; (i < 4); i++)
 120     {
 121         snew(r_nn[i], natoms);
 122         snew(nn[i], natoms);
 123
 124         for (j = 0; (j < natoms); j++)
 125         {
 126             r_nn[i][j] = box2;
 127         }
 128     }
 129
 130     snew(sgmol, maxidx);
 131     snew(skmol, maxidx);
 132
 133     /* Must init pbc every step because of pressure coupling */
 134     set_pbc(&pbc, ePBC, box);
 135     gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 136     gmx_rmpbc(gpbc, natoms, box, x);
 137
 138     *sgmean = 0.0;
 139     *skmean = 0.0;
 140     l       = 0;
 141     for (i = 0; (i < maxidx); i++)
 142     {   /* loop over index file */
 143         ix = index[i];
 144         for (j = 0; (j < maxidx); j++)
 145         {
 146
 147             if (i == j)
 148             {
 149                 continue;
 150             }
 151
 152             jx = index[j];
 153
 154             pbc_dx(&pbc, x[ix], x[jx], dx);
 155             r2 = iprod(dx, dx);
 156
 157             /* set_mat_entry(dmat,i,j,r2); */
 158
 159             /* determine the nearest neighbours */
 160             if (r2 < r_nn[0][i])
 161             {
 162                 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
 163                 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
 164                 r_nn[1][i] = r_nn[0][i]; nn[1][i] = nn[0][i];
 165                 r_nn[0][i] = r2;         nn[0][i] = j;
 166             }
 167             else if (r2 < r_nn[1][i])
 168             {
 169                 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
 170                 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
 171                 r_nn[1][i] = r2;         nn[1][i] = j;
 172             }
 173             else if (r2 < r_nn[2][i])
 174             {
 175                 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
 176                 r_nn[2][i] = r2;         nn[2][i] = j;
 177             }
 178             else if (r2 < r_nn[3][i])
 179             {
 180                 r_nn[3][i] = r2;         nn[3][i] = j;
 181             }
 182         }
 183
 184
 185         /* calculate mean distance between nearest neighbours */
 186         rmean = 0;
 187         for (j = 0; (j < 4); j++)
 188         {
 189             r_nn[j][i] = sqrt(r_nn[j][i]);
 190             rmean     += r_nn[j][i];
 191         }
 192         rmean /= 4;
 193
 194         n        = 0;
 195         sgmol[i] = 0.0;
 196         skmol[i] = 0.0;
 197
 198         /* Chau1998a eqn 3 */
 199         /* angular part tetrahedrality order parameter per atom */
 200         for (j = 0; (j < 3); j++)
 201         {
 202             for (k = j+1; (k < 4); k++)
 203             {
 204                 pbc_dx(&pbc, x[ix], x[index[nn[k][i]]], rk);
 205                 pbc_dx(&pbc, x[ix], x[index[nn[j][i]]], rj);
 206
 207                 unitv(rk, urk);
 208                 unitv(rj, urj);
 209
 210                 cost  = iprod(urk, urj) + onethird;
 211                 cost2 = cost * cost;
 212
 213                 sgmol[i] += cost2;
 214                 l++;
 215                 n++;
 216             }
 217         }
 218         /* normalize sgmol between 0.0 and 1.0 */
 219         sgmol[i] = 3*sgmol[i]/32;
 220         *sgmean += sgmol[i];
 221
 222         /* distance part tetrahedrality order parameter per atom */
 223         rmean2 = 4 * 3 * rmean * rmean;
 224         for (j = 0; (j < 4); j++)
 225         {
 226             skmol[i] += (rmean - r_nn[j][i]) * (rmean - r_nn[j][i]) / rmean2;
 227             /*      printf("%d %f (%f %f %f %f) \n",
 228                     i, skmol[i], rmean, rmean2, r_nn[j][i], (rmean - r_nn[j][i]) );
 229              */
 230         }
 231
 232         *skmean += skmol[i];
 233
 234         /* Compute sliced stuff in x y z*/
 235         slindex_x = gmx_nint((1+x[i][XX]/box[XX][XX])*nslicex) % nslicex;
 236         slindex_y = gmx_nint((1+x[i][YY]/box[YY][YY])*nslicey) % nslicey;
 237         slindex_z = gmx_nint((1+x[i][ZZ]/box[ZZ][ZZ])*nslicez) % nslicez;
 238         sggrid[slindex_x][slindex_y][slindex_z] += sgmol[i];
 239         skgrid[slindex_x][slindex_y][slindex_z] += skmol[i];
 240         (sl_count[slindex_x][slindex_y][slindex_z])++;
 241     } /* loop over entries in index file */
 242
 243     *sgmean /= maxidx;
 244     *skmean /= maxidx;
 245
 246     for (i = 0; (i < nslicex); i++)
 247     {
 248         for (j = 0; j < nslicey; j++)
 249         {
 250             for (k = 0; k < nslicez; k++)
 251             {
 252                 if (sl_count[i][j][k] > 0)
 253                 {
 254                     sggrid[i][j][k] /= sl_count[i][j][k];
 255                     skgrid[i][j][k] /= sl_count[i][j][k];
 256                 }
 257             }
 258         }
 259     }
 260
 261     sfree(sl_count);
 262     sfree(sgmol);
 263     sfree(skmol);
 264     for (i = 0; (i < 4); i++)
 265     {
 266         sfree(r_nn[i]);
 267         sfree(nn[i]);
 268     }
 269 }
 270
 271 /*Determines interface from tetrahedral order parameter in box with specified binwidth.  */
 272 /*Outputs interface positions(bins), the number of timeframes, and the number of surface-mesh points in xy*/
 273
 274 static void calc_tetra_order_interface(const char *fnNDX, const char *fnTPS, const char *fnTRX, real binw, int tblock,
 275                                        int *nframes,  int *nslicex, int *nslicey,
 276                                        real sgang1, real sgang2, real ****intfpos,
 277                                        output_env_t oenv)
 278 {
 279     FILE         *fpsg   = NULL, *fpsk = NULL;
 280     char         *sgslfn = "sg_ang_mesh";  /* Hardcoded filenames for debugging*/
 281     char         *skslfn = "sk_dist_mesh";
 282     t_topology    top;
 283     int           ePBC;
 284     char          title[STRLEN], subtitle[STRLEN];
 285     t_trxstatus  *status;
 286     int           natoms;
 287     real          t;
 288     rvec         *xtop, *x;
 289     matrix        box;
 290     real          sg, sk, sgintf, pos;
 291     atom_id     **index   = NULL;
 292     char        **grpname = NULL;
 293     int           i, j, k, n, *isize, ng, nslicez, framenr;
 294     real       ***sg_grid = NULL, ***sk_grid = NULL, ***sg_fravg = NULL, ***sk_fravg = NULL, ****sk_4d = NULL, ****sg_4d = NULL;
 295     int          *perm;
 296     int           ndx1, ndx2;
 297     int           bins;
 298     const real    onehalf = 1.0/2.0;
 299     /* real   ***intfpos[2]; pointers to arrays of two interface positions zcoord(framenr,xbin,ybin): intfpos[interface_index][t][nslicey*x+y]
 300      * i.e 1D Row-major order in (t,x,y) */
 301
 302
 303     read_tps_conf(fnTPS, title, &top, &ePBC, &xtop, NULL, box, FALSE);
 304
 305     *nslicex = (int)(box[XX][XX]/binw + onehalf); /*Calculate slicenr from binwidth*/
 306     *nslicey = (int)(box[YY][YY]/binw + onehalf);
 307     nslicez  = (int)(box[ZZ][ZZ]/binw +  onehalf);
 308
 309
 310
 311     ng = 1;
 312     /* get index groups */
 313     printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
 314     snew(grpname, ng);
 315     snew(index, ng);
 316     snew(isize, ng);
 317     get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
 318
 319     /* Analyze trajectory */
 320     natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
 321     if (natoms > top.atoms.nr)
 322     {
 323         gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
 324                   top.atoms.nr, natoms);
 325     }
 326     check_index(NULL, ng, index[0], NULL, natoms);
 327
 328
 329     /*Prepare structures for temporary storage of frame info*/
 330     snew(sg_grid, *nslicex);
 331     snew(sk_grid, *nslicex);
 332     for (i = 0; i < *nslicex; i++)
 333     {
 334         snew(sg_grid[i], *nslicey);
 335         snew(sk_grid[i], *nslicey);
 336         for (j = 0; j < *nslicey; j++)
 337         {
 338             snew(sg_grid[i][j], nslicez);
 339             snew(sk_grid[i][j], nslicez);
 340         }
 341     }
 342
 343     sg_4d    = NULL;
 344     sk_4d    = NULL;
 345     *nframes = 0;
 346     framenr  = 0;
 347
 348 /* Loop over frames*/
 349     do
 350     {
 351         /*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
 352         if (framenr%tblock == 0)
 353         {
 354             srenew(sk_4d, *nframes+1);
 355             srenew(sg_4d, *nframes+1);
 356             snew(sg_fravg, *nslicex);
 357             snew(sk_fravg, *nslicex);
 358             for (i = 0; i < *nslicex; i++)
 359             {
 360                 snew(sg_fravg[i], *nslicey);
 361                 snew(sk_fravg[i], *nslicey);
 362                 for (j = 0; j < *nslicey; j++)
 363                 {
 364                     snew(sg_fravg[i][j], nslicez);
 365                     snew(sk_fravg[i][j], nslicez);
 366                 }
 367             }
 368         }
 369
 370         find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0],
 371                               &sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
 372         for (i = 0; i < *nslicex; i++)
 373         {
 374             for (j = 0; j < *nslicey; j++)
 375             {
 376                 for (k = 0; k < nslicez; k++)
 377                 {
 378                     sk_fravg[i][j][k] += sk_grid[i][j][k]/tblock;
 379                     sg_fravg[i][j][k] += sg_grid[i][j][k]/tblock;
 380                 }
 381             }
 382         }
 383
 384         framenr++;
 385
 386         if (framenr%tblock == 0)
 387         {
 388             sk_4d[*nframes] = sk_fravg;
 389             sg_4d[*nframes] = sg_fravg;
 390             (*nframes)++;
 391         }
 392
 393     }
 394     while (read_next_x(oenv, status, &t, x, box));
 395     close_trj(status);
 396
 397     sfree(grpname);
 398     sfree(index);
 399     sfree(isize);
 400
 401     /*Debugging for printing out the entire order parameter meshes.*/
 402     if (debug)
 403     {
 404         fpsg = xvgropen(sgslfn, "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
 405         fpsk = xvgropen(skslfn, "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
 406         for (n = 0; n < (*nframes); n++)
 407         {
 408             fprintf(fpsg, "%i\n", n);
 409             fprintf(fpsk, "%i\n", n);
 410             for (i = 0; (i < *nslicex); i++)
 411             {
 412                 for (j = 0; j < *nslicey; j++)
 413                 {
 414                     for (k = 0; k < nslicez; k++)
 415                     {
 416                         fprintf(fpsg, "%4f  %4f  %4f  %8f\n", (i+0.5)*box[XX][XX]/(*nslicex), (j+0.5)*box[YY][YY]/(*nslicey), (k+0.5)*box[ZZ][ZZ]/nslicez, sg_4d[n][i][j][k]);
 417                         fprintf(fpsk, "%4f  %4f  %4f  %8f\n", (i+0.5)*box[XX][XX]/(*nslicex), (j+0.5)*box[YY][YY]/(*nslicey), (k+0.5)*box[ZZ][ZZ]/nslicez, sk_4d[n][i][j][k]);
 418                     }
 419                 }
 420             }
 421         }
 422         xvgrclose(fpsg);
 423         xvgrclose(fpsk);
 424     }
 425
 426
 427     /* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
 428
 429     /*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
 430     sgintf = 0.5*(sgang1+sgang2);
 431
 432
 433     /*Allocate memory for interface arrays; */
 434     snew((*intfpos), 2);
 435     snew((*intfpos)[0], *nframes);
 436     snew((*intfpos)[1], *nframes);
 437
 438     bins = (*nslicex)*(*nslicey);
 439
 440
 441     snew(perm, nslicez);  /*permutation array for sorting along normal coordinate*/
 442
 443
 444     for (n = 0; n < *nframes; n++)
 445     {
 446         snew((*intfpos)[0][n], bins);
 447         snew((*intfpos)[1][n], bins);
 448         for (i = 0; i < *nslicex; i++)
 449         {
 450             for (j = 0; j < *nslicey; j++)
 451             {
 452                 rangeArray(perm, nslicez); /*reset permutation array to identity*/
 453                 /*Binsearch returns 2 bin-numbers where the order param is  <= setpoint sgintf*/
 454                 ndx1 = start_binsearch(sg_4d[n][i][j], perm, 0, nslicez/2-1, sgintf, 1);
 455                 ndx2 = start_binsearch(sg_4d[n][i][j], perm, nslicez/2, nslicez-1, sgintf, -1);
 456                 /*Use linear interpolation to smooth out the interface position*/
 457
 458                 /*left interface (0)*/
 459                 /*if((sg_4d[n][i][j][perm[ndx1+1]]-sg_4d[n][i][j][perm[ndx1]])/sg_4d[n][i][j][perm[ndx1]] > 0.01){
 460                    pos=( (sgintf-sg_4d[n][i][j][perm[ndx1]])*perm[ndx1+1]+(sg_4d[n][i][j][perm[ndx1+1]]-sgintf)*perm[ndx1 ])*/
 461                 (*intfpos)[0][n][j+*nslicey*i] = (perm[ndx1]+onehalf)*binw;
 462                 /*right interface (1)*/
 463                 /*alpha=(sgintf-sg_4d[n][i][j][perm[ndx2]])/(sg_4d[n][i][j][perm[ndx2]+1]-sg_4d[n][i][j][perm[ndx2]]);*/
 464                 /*(*intfpos)[1][n][j+*nslicey*i]=((1-alpha)*perm[ndx2]+alpha*(perm[ndx2]+1)+onehalf)*box[ZZ][ZZ]/nslicez;*/
 465                 (*intfpos)[1][n][j+*nslicey*i] = (perm[ndx2]+onehalf)*binw;
 466             }
 467         }
 468     }
 469
 470
 471     /*sfree(perm);*/
 472     sfree(sk_4d);
 473     sfree(sg_4d);
 474     /*sfree(sg_grid);*/
 475     /*sfree(sk_grid);*/
 476
 477
 478 }
 479
 480 static void writesurftoxpms(real ***surf, int tblocks, int xbins, int ybins, real bw, char **outfiles, int maplevels )
 481 {
 482
 483     char   numbuf[8];
 484     int    n, i, j;
 485     real **profile1, **profile2;
 486     real   max1, max2, min1, min2, *xticks, *yticks;
 487     t_rgb  lo = {1, 1, 1};
 488     t_rgb  hi = {0, 0, 0};
 489     FILE  *xpmfile1, *xpmfile2;
 490
 491 /*Prepare xpm structures for output*/
 492
 493 /*Allocate memory to tick's and matrices*/
 494     snew (xticks, xbins+1);
 495     snew (yticks, ybins+1);
 496
 497     profile1 = mk_matrix(xbins, ybins, FALSE);
 498     profile2 = mk_matrix(xbins, ybins, FALSE);
 499
 500     for (i = 0; i < xbins+1; i++)
 501     {
 502         xticks[i] += bw;
 503     }
 504     for (j = 0; j < ybins+1; j++)
 505     {
 506         yticks[j] += bw;
 507     }
 508
 509     xpmfile1 = gmx_ffopen(outfiles[0], "w");
 510     xpmfile2 = gmx_ffopen(outfiles[1], "w");
 511
 512     max1 = max2 = 0.0;
 513     min1 = min2 = 1000.00;
 514
 515     for (n = 0; n < tblocks; n++)
 516     {
 517         sprintf(numbuf, "%5d", n);
 518         /*Filling matrices for inclusion in xpm-files*/
 519         for (i = 0; i < xbins; i++)
 520         {
 521             for (j = 0; j < ybins; j++)
 522             {
 523                 profile1[i][j] = (surf[0][n][j+ybins*i]);
 524                 profile2[i][j] = (surf[1][n][j+ybins*i]);
 525                 /*Finding max and min values*/
 526                 if (profile1[i][j] > max1)
 527                 {
 528                     max1 = profile1[i][j];
 529                 }
 530                 if (profile1[i][j] < min1)
 531                 {
 532                     min1 = profile1[i][j];
 533                 }
 534                 if (profile2[i][j] > max2)
 535                 {
 536                     max2 = profile2[i][j];
 537                 }
 538                 if (profile2[i][j] < min2)
 539                 {
 540                     min2 = profile2[i][j];
 541                 }
 542             }
 543         }
 544
 545         write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
 546         write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
 547     }
 548
 549     gmx_ffclose(xpmfile1);
 550     gmx_ffclose(xpmfile2);
 551
 552
 553
 554     sfree(profile1);
 555     sfree(profile2);
 556     sfree(xticks);
 557     sfree(yticks);
 558 }
 559
 560
 561 static void writeraw(real ***surf, int tblocks, int xbins, int ybins, char **fnms)
 562 {
 563     FILE *raw1, *raw2;
 564     int   i, j, n;
 565
 566     raw1 = gmx_ffopen(fnms[0], "w");
 567     raw2 = gmx_ffopen(fnms[1], "w");
 568     fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 569     fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 570     for (n = 0; n < tblocks; n++)
 571     {
 572         fprintf(raw1, "%5d\n", n);
 573         fprintf(raw2, "%5d\n", n);
 574         for (i = 0; i < xbins; i++)
 575         {
 576             for (j = 0; j < ybins; j++)
 577             {
 578                 fprintf(raw1, "%i  %i  %8.5f\n", i, j, (surf[0][n][j+ybins*i]));
 579                 fprintf(raw2, "%i  %i  %8.5f\n", i, j, (surf[1][n][j+ybins*i]));
 580             }
 581         }
 582     }
 583
 584     gmx_ffclose(raw1);
 585     gmx_ffclose(raw2);
 586 }
 587
 588
 589
 590 int gmx_hydorder(int argc, char *argv[])
 591 {
 592     static const char *desc[] = {
 593         "[THISMODULE] computes the tetrahedrality order parameters around a ",
 594         "given atom. Both angle an distance order parameters are calculated. See",
 595         "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
 596         "for more details.[PAR]"
 597         "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
 598         "with 2 phases in the box gives the user the option to define a 2D interface in time",
 599         "separating the faces by specifying parameters [TT]-sgang1[tt] and",
 600         "[TT]-sgang2[tt] (it is important to select these judiciously)."
 601     };
 602
 603     int                axis      = 0;
 604     static int         nsttblock = 1;
 605     static int         nlevels   = 100;
 606     static real        binwidth  = 1.0; /* binwidth in mesh           */
 607     static real        sg1       = 1;
 608     static real        sg2       = 1;   /* order parameters for bulk phases */
 609     static gmx_bool    bFourier  = FALSE;
 610     static gmx_bool    bRawOut   = FALSE;
 611     int                frames, xslices, yslices; /* Dimensions of interface arrays*/
 612     real            ***intfpos;                  /* Interface arrays (intfnr,t,xy) -potentially large */
 613     static char       *normal_axis[] = { NULL, "z", "x", "y", NULL };
 614
 615     t_pargs            pa[] = {
 616         { "-d",   FALSE, etENUM, {normal_axis},
 617           "Direction of the normal on the membrane" },
 618         { "-bw",  FALSE, etREAL, {&binwidth},
 619           "Binwidth of box mesh" },
 620         { "-sgang1", FALSE, etREAL, {&sg1},
 621           "tetrahedral angle parameter in Phase 1 (bulk)" },
 622         { "-sgang2", FALSE, etREAL, {&sg2},
 623           "tetrahedral angle parameter in Phase 2 (bulk)" },
 624         { "-tblock", FALSE, etINT, {&nsttblock},
 625           "Number of frames in one time-block average"},
 626         { "-nlevel", FALSE, etINT, {&nlevels},
 627           "Number of Height levels in 2D - XPixMaps"}
 628     };
 629
 630     t_filenm           fnm[] = {                      /* files for g_order    */
 631         { efTRX, "-f", NULL,  ffREAD },               /* trajectory file              */
 632         { efNDX, "-n", NULL,  ffREAD },               /* index file           */
 633         { efTPX, "-s", NULL,  ffREAD },               /* topology file                */
 634         { efXPM, "-o", "intf",  ffWRMULT},            /* XPM- surface maps      */
 635         { efOUT, "-or", "raw", ffOPTWRMULT },         /* xvgr output file           */
 636         { efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
 637     };
 638 #define NFILE asize(fnm)
 639
 640     /*Filenames*/
 641     const char  *ndxfnm, *tpsfnm, *trxfnm;
 642     char       **spectra, **intfn, **raw;
 643     int          nfspect, nfxpm, nfraw;
 644     output_env_t oenv;
 645
 646     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 647                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
 648     {
 649         return 0;
 650     }
 651     bFourier = opt2bSet("-Spect", NFILE, fnm);
 652     bRawOut  = opt2bSet("-or", NFILE, fnm);
 653
 654     if (binwidth < 0.0)
 655     {
 656         gmx_fatal(FARGS, "Can not have binwidth < 0");
 657     }
 658
 659     ndxfnm = ftp2fn(efNDX, NFILE, fnm);
 660     tpsfnm = ftp2fn(efTPX, NFILE, fnm);
 661     trxfnm = ftp2fn(efTRX, NFILE, fnm);
 662
 663     /* Calculate axis */
 664     if (strcmp(normal_axis[0], "x") == 0)
 665     {
 666         axis = XX;
 667     }
 668     else if (strcmp(normal_axis[0], "y") == 0)
 669     {
 670         axis = YY;
 671     }
 672     else if (strcmp(normal_axis[0], "z") == 0)
 673     {
 674         axis = ZZ;
 675     }
 676     else
 677     {
 678         gmx_fatal(FARGS, "Invalid axis, use x, y or z");
 679     }
 680
 681     switch (axis)
 682     {
 683         case 0:
 684             fprintf(stderr, "Taking x axis as normal to the membrane\n");
 685             break;
 686         case 1:
 687             fprintf(stderr, "Taking y axis as normal to the membrane\n");
 688             break;
 689         case 2:
 690             fprintf(stderr, "Taking z axis as normal to the membrane\n");
 691             break;
 692     }
 693
 694     /* tetraheder order parameter */
 695     /* If either of the options is set we compute both */
 696     nfxpm = opt2fns(&intfn, "-o", NFILE, fnm);
 697     if (nfxpm != 2)
 698     {
 699         gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
 700     }
 701     calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
 702     writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
 703
 704     if (bFourier)
 705     {
 706         nfspect = opt2fns(&spectra, "-Spect", NFILE, fnm);
 707         if (nfspect != 2)
 708         {
 709             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfspect);
 710         }
 711         powerspectavg(intfpos, frames, xslices, yslices, spectra);
 712     }
 713
 714     if (bRawOut)
 715     {
 716         nfraw = opt2fns(&raw, "-or", NFILE, fnm);
 717         if (nfraw != 2)
 718         {
 719             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfraw);
 720         }
 721         writeraw(intfpos, frames, xslices, yslices, raw);
 722     }
 723
 724     return 0;
 725 }