src/gromacs/gmxana/gmx_hydorder.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014,2015, 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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  34  */
  35
  36 #include "gmxpre.h"
  37
  38 #include <cmath>
  39 #include <cstring>
  40
  41 #include "gromacs/commandline/pargs.h"
  42 #include "gromacs/fileio/confio.h"
  43 #include "gromacs/fileio/matio.h"
  44 #include "gromacs/fileio/trxio.h"
  45 #include "gromacs/fileio/xvgr.h"
  46 #include "gromacs/gmxana/binsearch.h"
  47 #include "gromacs/gmxana/gmx_ana.h"
  48 #include "gromacs/gmxana/gstat.h"
  49 #include "gromacs/gmxana/powerspect.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52 #include "gromacs/pbcutil/rmpbc.h"
  53 #include "gromacs/topology/index.h"
  54 #include "gromacs/topology/topology.h"
  55 #include "gromacs/utility/arraysize.h"
  56 #include "gromacs/utility/cstringutil.h"
  57 #include "gromacs/utility/fatalerror.h"
  58 #include "gromacs/utility/futil.h"
  59 #include "gromacs/utility/gmxassert.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] = std::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 = static_cast<int>(std::round((1+x[i][XX]/box[XX][XX])*nslicex)) % nslicex;
 236         slindex_y = static_cast<int>(std::round((1+x[i][YY]/box[YY][YY])*nslicey)) % nslicey;
 237         slindex_z = static_cast<int>(std::round((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                                        gmx_output_env_t *oenv)
 278 {
 279     FILE         *fpsg   = NULL, *fpsk = NULL;
 280     t_topology    top;
 281     int           ePBC;
 282     t_trxstatus  *status;
 283     int           natoms;
 284     real          t;
 285     rvec         *xtop, *x;
 286     matrix        box;
 287     real          sg, sk, sgintf;
 288     atom_id     **index   = NULL;
 289     char        **grpname = NULL;
 290     int           i, j, k, n, *isize, ng, nslicez, framenr;
 291     real       ***sg_grid = NULL, ***sk_grid = NULL, ***sg_fravg = NULL, ***sk_fravg = NULL, ****sk_4d = NULL, ****sg_4d = NULL;
 292     int          *perm;
 293     int           ndx1, ndx2;
 294     int           bins;
 295     const real    onehalf = 1.0/2.0;
 296     /* real   ***intfpos[2]; pointers to arrays of two interface positions zcoord(framenr,xbin,ybin): intfpos[interface_index][t][nslicey*x+y]
 297      * i.e 1D Row-major order in (t,x,y) */
 298
 299
 300     read_tps_conf(fnTPS, &top, &ePBC, &xtop, NULL, box, FALSE);
 301
 302     *nslicex = static_cast<int>(box[XX][XX]/binw + onehalf); /*Calculate slicenr from binwidth*/
 303     *nslicey = static_cast<int>(box[YY][YY]/binw + onehalf);
 304     nslicez  = static_cast<int>(box[ZZ][ZZ]/binw +  onehalf);
 305
 306
 307
 308     ng = 1;
 309     /* get index groups */
 310     printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
 311     snew(grpname, ng);
 312     snew(index, ng);
 313     snew(isize, ng);
 314     get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
 315
 316     /* Analyze trajectory */
 317     natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
 318     if (natoms > top.atoms.nr)
 319     {
 320         gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
 321                   top.atoms.nr, natoms);
 322     }
 323     check_index(NULL, ng, index[0], NULL, natoms);
 324
 325
 326     /*Prepare structures for temporary storage of frame info*/
 327     snew(sg_grid, *nslicex);
 328     snew(sk_grid, *nslicex);
 329     for (i = 0; i < *nslicex; i++)
 330     {
 331         snew(sg_grid[i], *nslicey);
 332         snew(sk_grid[i], *nslicey);
 333         for (j = 0; j < *nslicey; j++)
 334         {
 335             snew(sg_grid[i][j], nslicez);
 336             snew(sk_grid[i][j], nslicez);
 337         }
 338     }
 339
 340     sg_4d    = NULL;
 341     sk_4d    = NULL;
 342     *nframes = 0;
 343     framenr  = 0;
 344
 345 /* Loop over frames*/
 346     do
 347     {
 348         /*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
 349         if (framenr%tblock == 0)
 350         {
 351             srenew(sk_4d, *nframes+1);
 352             srenew(sg_4d, *nframes+1);
 353             snew(sg_fravg, *nslicex);
 354             snew(sk_fravg, *nslicex);
 355             for (i = 0; i < *nslicex; i++)
 356             {
 357                 snew(sg_fravg[i], *nslicey);
 358                 snew(sk_fravg[i], *nslicey);
 359                 for (j = 0; j < *nslicey; j++)
 360                 {
 361                     snew(sg_fravg[i][j], nslicez);
 362                     snew(sk_fravg[i][j], nslicez);
 363                 }
 364             }
 365         }
 366
 367         find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0],
 368                               &sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
 369         GMX_RELEASE_ASSERT(sk_fravg != NULL, "Trying to dereference NULL sk_fravg pointer");
 370         for (i = 0; i < *nslicex; i++)
 371         {
 372             for (j = 0; j < *nslicey; j++)
 373             {
 374                 for (k = 0; k < nslicez; k++)
 375                 {
 376                     sk_fravg[i][j][k] += sk_grid[i][j][k]/tblock;
 377                     sg_fravg[i][j][k] += sg_grid[i][j][k]/tblock;
 378                 }
 379             }
 380         }
 381
 382         framenr++;
 383
 384         if (framenr%tblock == 0)
 385         {
 386             GMX_RELEASE_ASSERT(sk_4d != NULL, "Trying to dereference NULL sk_4d pointer");
 387             sk_4d[*nframes] = sk_fravg;
 388             sg_4d[*nframes] = sg_fravg;
 389             (*nframes)++;
 390         }
 391
 392     }
 393     while (read_next_x(oenv, status, &t, x, box));
 394     close_trj(status);
 395
 396     sfree(grpname);
 397     sfree(index);
 398     sfree(isize);
 399
 400     /*Debugging for printing out the entire order parameter meshes.*/
 401     if (debug)
 402     {
 403         fpsg = xvgropen("sg_ang_mesh", "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
 404         fpsk = xvgropen("sk_dist_mesh", "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
 405         for (n = 0; n < (*nframes); n++)
 406         {
 407             fprintf(fpsg, "%i\n", n);
 408             fprintf(fpsk, "%i\n", n);
 409             for (i = 0; (i < *nslicex); i++)
 410             {
 411                 for (j = 0; j < *nslicey; j++)
 412                 {
 413                     for (k = 0; k < nslicez; k++)
 414                     {
 415                         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]);
 416                         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]);
 417                     }
 418                 }
 419             }
 420         }
 421         xvgrclose(fpsg);
 422         xvgrclose(fpsk);
 423     }
 424
 425
 426     /* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
 427
 428     /*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
 429     sgintf = 0.5*(sgang1+sgang2);
 430
 431
 432     /*Allocate memory for interface arrays; */
 433     snew((*intfpos), 2);
 434     snew((*intfpos)[0], *nframes);
 435     snew((*intfpos)[1], *nframes);
 436
 437     bins = (*nslicex)*(*nslicey);
 438
 439
 440     snew(perm, nslicez);  /*permutation array for sorting along normal coordinate*/
 441
 442
 443     for (n = 0; n < *nframes; n++)
 444     {
 445         snew((*intfpos)[0][n], bins);
 446         snew((*intfpos)[1][n], bins);
 447         for (i = 0; i < *nslicex; i++)
 448         {
 449             for (j = 0; j < *nslicey; j++)
 450             {
 451                 rangeArray(perm, nslicez); /*reset permutation array to identity*/
 452                 /*Binsearch returns 2 bin-numbers where the order param is  <= setpoint sgintf*/
 453                 ndx1 = start_binsearch(sg_4d[n][i][j], perm, 0, nslicez/2-1, sgintf, 1);
 454                 ndx2 = start_binsearch(sg_4d[n][i][j], perm, nslicez/2, nslicez-1, sgintf, -1);
 455                 /*Use linear interpolation to smooth out the interface position*/
 456
 457                 /*left interface (0)*/
 458                 /*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){
 459                    pos=( (sgintf-sg_4d[n][i][j][perm[ndx1]])*perm[ndx1+1]+(sg_4d[n][i][j][perm[ndx1+1]]-sgintf)*perm[ndx1 ])*/
 460                 (*intfpos)[0][n][j+*nslicey*i] = (perm[ndx1]+onehalf)*binw;
 461                 /*right interface (1)*/
 462                 /*alpha=(sgintf-sg_4d[n][i][j][perm[ndx2]])/(sg_4d[n][i][j][perm[ndx2]+1]-sg_4d[n][i][j][perm[ndx2]]);*/
 463                 /*(*intfpos)[1][n][j+*nslicey*i]=((1-alpha)*perm[ndx2]+alpha*(perm[ndx2]+1)+onehalf)*box[ZZ][ZZ]/nslicez;*/
 464                 (*intfpos)[1][n][j+*nslicey*i] = (perm[ndx2]+onehalf)*binw;
 465             }
 466         }
 467     }
 468
 469
 470     sfree(sk_4d);
 471     sfree(sg_4d);
 472 }
 473
 474 static void writesurftoxpms(real ***surf, int tblocks, int xbins, int ybins, real bw, char **outfiles, int maplevels )
 475 {
 476
 477     char   numbuf[8];
 478     int    n, i, j;
 479     real **profile1, **profile2;
 480     real   max1, max2, min1, min2, *xticks, *yticks;
 481     t_rgb  lo = {1, 1, 1};
 482     t_rgb  hi = {0, 0, 0};
 483     FILE  *xpmfile1, *xpmfile2;
 484
 485 /*Prepare xpm structures for output*/
 486
 487 /*Allocate memory to tick's and matrices*/
 488     snew (xticks, xbins+1);
 489     snew (yticks, ybins+1);
 490
 491     profile1 = mk_matrix(xbins, ybins, FALSE);
 492     profile2 = mk_matrix(xbins, ybins, FALSE);
 493
 494     for (i = 0; i < xbins+1; i++)
 495     {
 496         xticks[i] += bw;
 497     }
 498     for (j = 0; j < ybins+1; j++)
 499     {
 500         yticks[j] += bw;
 501     }
 502
 503     xpmfile1 = gmx_ffopen(outfiles[0], "w");
 504     xpmfile2 = gmx_ffopen(outfiles[1], "w");
 505
 506     max1 = max2 = 0.0;
 507     min1 = min2 = 1000.00;
 508
 509     for (n = 0; n < tblocks; n++)
 510     {
 511         sprintf(numbuf, "%5d", n);
 512         /*Filling matrices for inclusion in xpm-files*/
 513         for (i = 0; i < xbins; i++)
 514         {
 515             for (j = 0; j < ybins; j++)
 516             {
 517                 profile1[i][j] = (surf[0][n][j+ybins*i]);
 518                 profile2[i][j] = (surf[1][n][j+ybins*i]);
 519                 /*Finding max and min values*/
 520                 if (profile1[i][j] > max1)
 521                 {
 522                     max1 = profile1[i][j];
 523                 }
 524                 if (profile1[i][j] < min1)
 525                 {
 526                     min1 = profile1[i][j];
 527                 }
 528                 if (profile2[i][j] > max2)
 529                 {
 530                     max2 = profile2[i][j];
 531                 }
 532                 if (profile2[i][j] < min2)
 533                 {
 534                     min2 = profile2[i][j];
 535                 }
 536             }
 537         }
 538
 539         write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
 540         write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
 541     }
 542
 543     gmx_ffclose(xpmfile1);
 544     gmx_ffclose(xpmfile2);
 545
 546
 547
 548     sfree(profile1);
 549     sfree(profile2);
 550     sfree(xticks);
 551     sfree(yticks);
 552 }
 553
 554
 555 static void writeraw(real ***surf, int tblocks, int xbins, int ybins, char **fnms)
 556 {
 557     FILE *raw1, *raw2;
 558     int   i, j, n;
 559
 560     raw1 = gmx_ffopen(fnms[0], "w");
 561     raw2 = gmx_ffopen(fnms[1], "w");
 562     fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 563     fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 564     for (n = 0; n < tblocks; n++)
 565     {
 566         fprintf(raw1, "%5d\n", n);
 567         fprintf(raw2, "%5d\n", n);
 568         for (i = 0; i < xbins; i++)
 569         {
 570             for (j = 0; j < ybins; j++)
 571             {
 572                 fprintf(raw1, "%i  %i  %8.5f\n", i, j, (surf[0][n][j+ybins*i]));
 573                 fprintf(raw2, "%i  %i  %8.5f\n", i, j, (surf[1][n][j+ybins*i]));
 574             }
 575         }
 576     }
 577
 578     gmx_ffclose(raw1);
 579     gmx_ffclose(raw2);
 580 }
 581
 582
 583
 584 int gmx_hydorder(int argc, char *argv[])
 585 {
 586     static const char *desc[] = {
 587         "[THISMODULE] computes the tetrahedrality order parameters around a ",
 588         "given atom. Both angle an distance order parameters are calculated. See",
 589         "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
 590         "for more details.[PAR]"
 591         "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
 592         "with 2 phases in the box gives the user the option to define a 2D interface in time",
 593         "separating the faces by specifying parameters [TT]-sgang1[tt] and",
 594         "[TT]-sgang2[tt] (it is important to select these judiciously)."
 595     };
 596
 597     int                axis      = 0;
 598     static int         nsttblock = 1;
 599     static int         nlevels   = 100;
 600     static real        binwidth  = 1.0; /* binwidth in mesh           */
 601     static real        sg1       = 1;
 602     static real        sg2       = 1;   /* order parameters for bulk phases */
 603     static gmx_bool    bFourier  = FALSE;
 604     static gmx_bool    bRawOut   = FALSE;
 605     int                frames, xslices, yslices; /* Dimensions of interface arrays*/
 606     real            ***intfpos;                  /* Interface arrays (intfnr,t,xy) -potentially large */
 607     static const char *normal_axis[] = { NULL, "z", "x", "y", NULL };
 608
 609     t_pargs            pa[] = {
 610         { "-d",   FALSE, etENUM, {normal_axis},
 611           "Direction of the normal on the membrane" },
 612         { "-bw",  FALSE, etREAL, {&binwidth},
 613           "Binwidth of box mesh" },
 614         { "-sgang1", FALSE, etREAL, {&sg1},
 615           "tetrahedral angle parameter in Phase 1 (bulk)" },
 616         { "-sgang2", FALSE, etREAL, {&sg2},
 617           "tetrahedral angle parameter in Phase 2 (bulk)" },
 618         { "-tblock", FALSE, etINT, {&nsttblock},
 619           "Number of frames in one time-block average"},
 620         { "-nlevel", FALSE, etINT, {&nlevels},
 621           "Number of Height levels in 2D - XPixMaps"}
 622     };
 623
 624     t_filenm           fnm[] = {                      /* files for g_order    */
 625         { efTRX, "-f", NULL,  ffREAD },               /* trajectory file              */
 626         { efNDX, "-n", NULL,  ffREAD },               /* index file           */
 627         { efTPR, "-s", NULL,  ffREAD },               /* topology file                */
 628         { efXPM, "-o", "intf",  ffWRMULT},            /* XPM- surface maps      */
 629         { efOUT, "-or", "raw", ffOPTWRMULT },         /* xvgr output file           */
 630         { efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
 631     };
 632 #define NFILE asize(fnm)
 633
 634     /*Filenames*/
 635     const char       *ndxfnm, *tpsfnm, *trxfnm;
 636     char            **spectra, **intfn, **raw;
 637     int               nfspect, nfxpm, nfraw;
 638     gmx_output_env_t *oenv;
 639
 640     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 641                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
 642     {
 643         return 0;
 644     }
 645     bFourier = opt2bSet("-Spect", NFILE, fnm);
 646     bRawOut  = opt2bSet("-or", NFILE, fnm);
 647
 648     if (binwidth < 0.0)
 649     {
 650         gmx_fatal(FARGS, "Can not have binwidth < 0");
 651     }
 652
 653     ndxfnm = ftp2fn(efNDX, NFILE, fnm);
 654     tpsfnm = ftp2fn(efTPR, NFILE, fnm);
 655     trxfnm = ftp2fn(efTRX, NFILE, fnm);
 656
 657     /* Calculate axis */
 658     GMX_RELEASE_ASSERT(normal_axis[0] != NULL, "Option setting inconsistency; normal_axis[0] is NULL");
 659     if (std::strcmp(normal_axis[0], "x") == 0)
 660     {
 661         axis = XX;
 662     }
 663     else if (std::strcmp(normal_axis[0], "y") == 0)
 664     {
 665         axis = YY;
 666     }
 667     else if (std::strcmp(normal_axis[0], "z") == 0)
 668     {
 669         axis = ZZ;
 670     }
 671     else
 672     {
 673         gmx_fatal(FARGS, "Invalid axis, use x, y or z");
 674     }
 675
 676     switch (axis)
 677     {
 678         case 0:
 679             fprintf(stderr, "Taking x axis as normal to the membrane\n");
 680             break;
 681         case 1:
 682             fprintf(stderr, "Taking y axis as normal to the membrane\n");
 683             break;
 684         case 2:
 685             fprintf(stderr, "Taking z axis as normal to the membrane\n");
 686             break;
 687     }
 688
 689     /* tetraheder order parameter */
 690     /* If either of the options is set we compute both */
 691     nfxpm = opt2fns(&intfn, "-o", NFILE, fnm);
 692     if (nfxpm != 2)
 693     {
 694         gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
 695     }
 696     calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
 697     writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
 698
 699     if (bFourier)
 700     {
 701         nfspect = opt2fns(&spectra, "-Spect", NFILE, fnm);
 702         if (nfspect != 2)
 703         {
 704             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfspect);
 705         }
 706         powerspectavg(intfpos, frames, xslices, yslices, spectra);
 707     }
 708
 709     if (bRawOut)
 710     {
 711         nfraw = opt2fns(&raw, "-or", NFILE, fnm);
 712         if (nfraw != 2)
 713         {
 714             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfraw);
 715         }
 716         writeraw(intfpos, frames, xslices, yslices, raw);
 717     }
 718
 719     return 0;
 720 }