src/gromacs/gmxana/gmx_hydorder.cpp

   1 /*
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   5  * Copyright (c) 2019,2020, by the GROMACS development team, led by
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  36
  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/fileio/confio.h"
  44 #include "gromacs/fileio/matio.h"
  45 #include "gromacs/fileio/trxio.h"
  46 #include "gromacs/fileio/xvgr.h"
  47 #include "gromacs/gmxana/binsearch.h"
  48 #include "gromacs/gmxana/gmx_ana.h"
  49 #include "gromacs/gmxana/gstat.h"
  50 #include "gromacs/gmxana/powerspect.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/pbcutil/pbc.h"
  53 #include "gromacs/pbcutil/rmpbc.h"
  54 #include "gromacs/topology/index.h"
  55 #include "gromacs/topology/topology.h"
  56 #include "gromacs/utility/arraysize.h"
  57 #include "gromacs/utility/cstringutil.h"
  58 #include "gromacs/utility/fatalerror.h"
  59 #include "gromacs/utility/futil.h"
  60 #include "gromacs/utility/gmxassert.h"
  61 #include "gromacs/utility/smalloc.h"
  62
  63 static void find_tetra_order_grid(t_topology top,
  64                                   PbcType    pbcType,
  65                                   int        natoms,
  66                                   matrix     box,
  67                                   rvec       x[],
  68                                   int        maxidx,
  69                                   const int  index[],
  70                                   real*      sgmean,
  71                                   real*      skmean,
  72                                   int        nslicex,
  73                                   int        nslicey,
  74                                   int        nslicez,
  75                                   real***    sggrid,
  76                                   real***    skgrid)
  77 {
  78     int         ix, jx, i, j, k, l, n, *nn[4];
  79     rvec        dx, rj, rk, urk, urj;
  80     real        cost, cost2, *sgmol, *skmol, rmean, rmean2, r2, box2, *r_nn[4];
  81     t_pbc       pbc;
  82     int         slindex_x, slindex_y, slindex_z;
  83     int***      sl_count;
  84     real        onethird = 1.0 / 3.0;
  85     gmx_rmpbc_t gpbc;
  86
  87     /*  dmat = init_mat(maxidx, FALSE); */
  88
  89     box2 = box[XX][XX] * box[XX][XX];
  90
  91     /* Initialize expanded sl_count array */
  92     snew(sl_count, nslicex);
  93     for (i = 0; i < nslicex; i++)
  94     {
  95         snew(sl_count[i], nslicey);
  96         for (j = 0; j < nslicey; j++)
  97         {
  98             snew(sl_count[i][j], nslicez);
  99         }
 100     }
 101
 102
 103     for (i = 0; (i < 4); i++)
 104     {
 105         snew(r_nn[i], natoms);
 106         snew(nn[i], natoms);
 107
 108         for (j = 0; (j < natoms); j++)
 109         {
 110             r_nn[i][j] = box2;
 111         }
 112     }
 113
 114     snew(sgmol, maxidx);
 115     snew(skmol, maxidx);
 116
 117     /* Must init pbc every step because of pressure coupling */
 118     set_pbc(&pbc, pbcType, box);
 119     gpbc = gmx_rmpbc_init(&top.idef, pbcType, natoms);
 120     gmx_rmpbc(gpbc, natoms, box, x);
 121
 122     *sgmean = 0.0;
 123     *skmean = 0.0;
 124     l       = 0;
 125     for (i = 0; (i < maxidx); i++)
 126     { /* loop over index file */
 127         ix = index[i];
 128         for (j = 0; (j < maxidx); j++)
 129         {
 130
 131             if (i == j)
 132             {
 133                 continue;
 134             }
 135
 136             jx = index[j];
 137
 138             pbc_dx(&pbc, x[ix], x[jx], dx);
 139             r2 = iprod(dx, dx);
 140
 141             /* set_mat_entry(dmat,i,j,r2); */
 142
 143             /* determine the nearest neighbours */
 144             if (r2 < r_nn[0][i])
 145             {
 146                 r_nn[3][i] = r_nn[2][i];
 147                 nn[3][i]   = nn[2][i];
 148                 r_nn[2][i] = r_nn[1][i];
 149                 nn[2][i]   = nn[1][i];
 150                 r_nn[1][i] = r_nn[0][i];
 151                 nn[1][i]   = nn[0][i];
 152                 r_nn[0][i] = r2;
 153                 nn[0][i]   = j;
 154             }
 155             else if (r2 < r_nn[1][i])
 156             {
 157                 r_nn[3][i] = r_nn[2][i];
 158                 nn[3][i]   = nn[2][i];
 159                 r_nn[2][i] = r_nn[1][i];
 160                 nn[2][i]   = nn[1][i];
 161                 r_nn[1][i] = r2;
 162                 nn[1][i]   = j;
 163             }
 164             else if (r2 < r_nn[2][i])
 165             {
 166                 r_nn[3][i] = r_nn[2][i];
 167                 nn[3][i]   = nn[2][i];
 168                 r_nn[2][i] = r2;
 169                 nn[2][i]   = j;
 170             }
 171             else if (r2 < r_nn[3][i])
 172             {
 173                 r_nn[3][i] = r2;
 174                 nn[3][i]   = j;
 175             }
 176         }
 177
 178
 179         /* calculate mean distance between nearest neighbours */
 180         rmean = 0;
 181         for (j = 0; (j < 4); j++)
 182         {
 183             r_nn[j][i] = std::sqrt(r_nn[j][i]);
 184             rmean += r_nn[j][i];
 185         }
 186         rmean /= 4;
 187
 188         n        = 0;
 189         sgmol[i] = 0.0;
 190         skmol[i] = 0.0;
 191
 192         /* Chau1998a eqn 3 */
 193         /* angular part tetrahedrality order parameter per atom */
 194         for (j = 0; (j < 3); j++)
 195         {
 196             for (k = j + 1; (k < 4); k++)
 197             {
 198                 pbc_dx(&pbc, x[ix], x[index[nn[k][i]]], rk);
 199                 pbc_dx(&pbc, x[ix], x[index[nn[j][i]]], rj);
 200
 201                 unitv(rk, urk);
 202                 unitv(rj, urj);
 203
 204                 cost  = iprod(urk, urj) + onethird;
 205                 cost2 = cost * cost;
 206
 207                 sgmol[i] += cost2;
 208                 l++;
 209                 n++;
 210             }
 211         }
 212         /* normalize sgmol between 0.0 and 1.0 */
 213         sgmol[i] = 3 * sgmol[i] / 32;
 214         *sgmean += sgmol[i];
 215
 216         /* distance part tetrahedrality order parameter per atom */
 217         rmean2 = 4 * 3 * rmean * rmean;
 218         for (j = 0; (j < 4); j++)
 219         {
 220             skmol[i] += (rmean - r_nn[j][i]) * (rmean - r_nn[j][i]) / rmean2;
 221             /*      printf("%d %f (%f %f %f %f) \n",
 222                     i, skmol[i], rmean, rmean2, r_nn[j][i], (rmean - r_nn[j][i]) );
 223              */
 224         }
 225
 226         *skmean += skmol[i];
 227
 228         /* Compute sliced stuff in x y z*/
 229         slindex_x = static_cast<int>(std::round((1 + x[i][XX] / box[XX][XX]) * nslicex)) % nslicex;
 230         slindex_y = static_cast<int>(std::round((1 + x[i][YY] / box[YY][YY]) * nslicey)) % nslicey;
 231         slindex_z = static_cast<int>(std::round((1 + x[i][ZZ] / box[ZZ][ZZ]) * nslicez)) % nslicez;
 232         sggrid[slindex_x][slindex_y][slindex_z] += sgmol[i];
 233         skgrid[slindex_x][slindex_y][slindex_z] += skmol[i];
 234         (sl_count[slindex_x][slindex_y][slindex_z])++;
 235     } /* loop over entries in index file */
 236
 237     *sgmean /= maxidx;
 238     *skmean /= maxidx;
 239
 240     for (i = 0; (i < nslicex); i++)
 241     {
 242         for (j = 0; j < nslicey; j++)
 243         {
 244             for (k = 0; k < nslicez; k++)
 245             {
 246                 if (sl_count[i][j][k] > 0)
 247                 {
 248                     sggrid[i][j][k] /= sl_count[i][j][k];
 249                     skgrid[i][j][k] /= sl_count[i][j][k];
 250                 }
 251             }
 252         }
 253     }
 254
 255     sfree(sl_count);
 256     sfree(sgmol);
 257     sfree(skmol);
 258     for (i = 0; (i < 4); i++)
 259     {
 260         sfree(r_nn[i]);
 261         sfree(nn[i]);
 262     }
 263 }
 264
 265 /*Determines interface from tetrahedral order parameter in box with specified binwidth.  */
 266 /*Outputs interface positions(bins), the number of timeframes, and the number of surface-mesh points in xy*/
 267
 268 static void calc_tetra_order_interface(const char*       fnNDX,
 269                                        const char*       fnTPS,
 270                                        const char*       fnTRX,
 271                                        real              binw,
 272                                        int               tblock,
 273                                        int*              nframes,
 274                                        int*              nslicex,
 275                                        int*              nslicey,
 276                                        real              sgang1,
 277                                        real              sgang2,
 278                                        real****          intfpos,
 279                                        gmx_output_env_t* oenv)
 280 {
 281     FILE *       fpsg = nullptr, *fpsk = nullptr;
 282     t_topology   top;
 283     PbcType      pbcType;
 284     t_trxstatus* status;
 285     int          natoms;
 286     real         t;
 287     rvec *       xtop, *x;
 288     matrix       box;
 289     real         sg, sk, sgintf;
 290     int**        index   = nullptr;
 291     char**       grpname = nullptr;
 292     int          i, j, k, n, *isize, ng, nslicez, framenr;
 293     real ***sg_grid = nullptr, ***sk_grid = nullptr, ***sg_fravg = nullptr, ***sk_fravg = nullptr,
 294          ****sk_4d = nullptr, ****sg_4d = nullptr;
 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, &top, &pbcType, &xtop, nullptr, box, FALSE);
 304
 305     *nslicex = static_cast<int>(box[XX][XX] / binw + onehalf); /*Calculate slicenr from binwidth*/
 306     *nslicey = static_cast<int>(box[YY][YY] / binw + onehalf);
 307     nslicez  = static_cast<int>(box[ZZ][ZZ] / binw + onehalf);
 308
 309
 310     ng = 1;
 311     /* get index groups */
 312     printf("Select the group that contains the atoms you want to use for the tetrahedrality order "
 313            "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)", top.atoms.nr, natoms);
 324     }
 325     check_index(nullptr, ng, index[0], nullptr, natoms);
 326
 327
 328     /*Prepare structures for temporary storage of frame info*/
 329     snew(sg_grid, *nslicex);
 330     snew(sk_grid, *nslicex);
 331     for (i = 0; i < *nslicex; i++)
 332     {
 333         snew(sg_grid[i], *nslicey);
 334         snew(sk_grid[i], *nslicey);
 335         for (j = 0; j < *nslicey; j++)
 336         {
 337             snew(sg_grid[i][j], nslicez);
 338             snew(sk_grid[i][j], nslicez);
 339         }
 340     }
 341
 342     sg_4d    = nullptr;
 343     sk_4d    = nullptr;
 344     *nframes = 0;
 345     framenr  = 0;
 346
 347     /* Loop over frames*/
 348     do
 349     {
 350         /*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
 351         if (framenr % tblock == 0)
 352         {
 353             srenew(sk_4d, *nframes + 1);
 354             srenew(sg_4d, *nframes + 1);
 355             snew(sg_fravg, *nslicex);
 356             snew(sk_fravg, *nslicex);
 357             for (i = 0; i < *nslicex; i++)
 358             {
 359                 snew(sg_fravg[i], *nslicey);
 360                 snew(sk_fravg[i], *nslicey);
 361                 for (j = 0; j < *nslicey; j++)
 362                 {
 363                     snew(sg_fravg[i][j], nslicez);
 364                     snew(sk_fravg[i][j], nslicez);
 365                 }
 366             }
 367         }
 368
 369         find_tetra_order_grid(top, pbcType, natoms, box, x, isize[0], index[0], &sg, &sk, *nslicex,
 370                               *nslicey, nslicez, sg_grid, sk_grid);
 371         GMX_RELEASE_ASSERT(sk_fravg != nullptr, "Trying to dereference NULL sk_fravg pointer");
 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             GMX_RELEASE_ASSERT(sk_4d != nullptr, "Trying to dereference NULL sk_4d pointer");
 389             sk_4d[*nframes] = sk_fravg;
 390             sg_4d[*nframes] = sg_fravg;
 391             (*nframes)++;
 392         }
 393
 394     } while (read_next_x(oenv, status, &t, x, box));
 395     close_trx(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("sg_ang_mesh", "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)",
 405                         "S\\sg\\N", oenv);
 406         fpsk = xvgropen("sk_dist_mesh", "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)",
 407                         "S\\sk\\N", oenv);
 408         for (n = 0; n < (*nframes); n++)
 409         {
 410             fprintf(fpsg, "%i\n", n);
 411             fprintf(fpsk, "%i\n", n);
 412             for (i = 0; (i < *nslicex); i++)
 413             {
 414                 for (j = 0; j < *nslicey; j++)
 415                 {
 416                     for (k = 0; k < nslicez; k++)
 417                     {
 418                         fprintf(fpsg, "%4f  %4f  %4f  %8f\n", (i + 0.5) * box[XX][XX] / (*nslicex),
 419                                 (j + 0.5) * box[YY][YY] / (*nslicey),
 420                                 (k + 0.5) * box[ZZ][ZZ] / nslicez, sg_4d[n][i][j][k]);
 421                         fprintf(fpsk, "%4f  %4f  %4f  %8f\n", (i + 0.5) * box[XX][XX] / (*nslicex),
 422                                 (j + 0.5) * box[YY][YY] / (*nslicey),
 423                                 (k + 0.5) * box[ZZ][ZZ] / nslicez, sk_4d[n][i][j][k]);
 424                     }
 425                 }
 426             }
 427         }
 428         xvgrclose(fpsg);
 429         xvgrclose(fpsk);
 430     }
 431
 432
 433     /* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
 434
 435     /*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
 436     sgintf = 0.5 * (sgang1 + sgang2);
 437
 438
 439     /*Allocate memory for interface arrays; */
 440     snew((*intfpos), 2);
 441     snew((*intfpos)[0], *nframes);
 442     snew((*intfpos)[1], *nframes);
 443
 444     bins = (*nslicex) * (*nslicey);
 445
 446
 447     snew(perm, nslicez); /*permutation array for sorting along normal coordinate*/
 448
 449
 450     for (n = 0; n < *nframes; n++)
 451     {
 452         snew((*intfpos)[0][n], bins);
 453         snew((*intfpos)[1][n], bins);
 454         for (i = 0; i < *nslicex; i++)
 455         {
 456             for (j = 0; j < *nslicey; j++)
 457             {
 458                 rangeArray(perm, nslicez); /*reset permutation array to identity*/
 459                 /*Binsearch returns 2 bin-numbers where the order param is  <= setpoint sgintf*/
 460                 ndx1 = start_binsearch(sg_4d[n][i][j], perm, 0, nslicez / 2 - 1, sgintf, 1);
 461                 ndx2 = start_binsearch(sg_4d[n][i][j], perm, nslicez / 2, nslicez - 1, sgintf, -1);
 462                 /*Use linear interpolation to smooth out the interface position*/
 463
 464                 /*left interface (0)*/
 465                 /*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){
 466                    pos=( (sgintf-sg_4d[n][i][j][perm[ndx1]])*perm[ndx1+1]+(sg_4d[n][i][j][perm[ndx1+1]]-sgintf)*perm[ndx1 ])*/
 467                 (*intfpos)[0][n][j + *nslicey * i] = (perm[ndx1] + onehalf) * binw;
 468                 /*right interface (1)*/
 469                 /*alpha=(sgintf-sg_4d[n][i][j][perm[ndx2]])/(sg_4d[n][i][j][perm[ndx2]+1]-sg_4d[n][i][j][perm[ndx2]]);*/
 470                 /*(*intfpos)[1][n][j+*nslicey*i]=((1-alpha)*perm[ndx2]+alpha*(perm[ndx2]+1)+onehalf)*box[ZZ][ZZ]/nslicez;*/
 471                 (*intfpos)[1][n][j + *nslicey * i] = (perm[ndx2] + onehalf) * binw;
 472             }
 473         }
 474     }
 475
 476
 477     sfree(sk_4d);
 478     sfree(sg_4d);
 479 }
 480
 481 static void writesurftoxpms(real***                          surf,
 482                             int                              tblocks,
 483                             int                              xbins,
 484                             int                              ybins,
 485                             real                             bw,
 486                             gmx::ArrayRef<const std::string> outfiles,
 487                             int                              maplevels)
 488 {
 489
 490     char   numbuf[STRLEN];
 491     int    n, i, j;
 492     real **profile1, **profile2;
 493     real   max1, max2, min1, min2, *xticks, *yticks;
 494     t_rgb  lo = { 1, 1, 1 };
 495     t_rgb  hi = { 0, 0, 0 };
 496     FILE * xpmfile1, *xpmfile2;
 497
 498     /*Prepare xpm structures for output*/
 499
 500     /*Allocate memory to tick's and matrices*/
 501     snew(xticks, xbins + 1);
 502     snew(yticks, ybins + 1);
 503
 504     profile1 = mk_matrix(xbins, ybins, FALSE);
 505     profile2 = mk_matrix(xbins, ybins, FALSE);
 506
 507     for (i = 0; i < xbins + 1; i++)
 508     {
 509         xticks[i] += bw;
 510     }
 511     for (j = 0; j < ybins + 1; j++)
 512     {
 513         yticks[j] += bw;
 514     }
 515
 516     xpmfile1 = gmx_ffopen(outfiles[0], "w");
 517     xpmfile2 = gmx_ffopen(outfiles[1], "w");
 518
 519     max1 = max2 = 0.0;
 520     min1 = min2 = 1000.00;
 521
 522     for (n = 0; n < tblocks; n++)
 523     {
 524         sprintf(numbuf, "%5d", n);
 525         /*Filling matrices for inclusion in xpm-files*/
 526         for (i = 0; i < xbins; i++)
 527         {
 528             for (j = 0; j < ybins; j++)
 529             {
 530                 profile1[i][j] = (surf[0][n][j + ybins * i]);
 531                 profile2[i][j] = (surf[1][n][j + ybins * i]);
 532                 /*Finding max and min values*/
 533                 if (profile1[i][j] > max1)
 534                 {
 535                     max1 = profile1[i][j];
 536                 }
 537                 if (profile1[i][j] < min1)
 538                 {
 539                     min1 = profile1[i][j];
 540                 }
 541                 if (profile2[i][j] > max2)
 542                 {
 543                     max2 = profile2[i][j];
 544                 }
 545                 if (profile2[i][j] < min2)
 546                 {
 547                     min2 = profile2[i][j];
 548                 }
 549             }
 550         }
 551
 552         write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
 553                   profile1, min1, max1, lo, hi, &maplevels);
 554         write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
 555                   profile2, min2, max2, lo, hi, &maplevels);
 556     }
 557
 558     gmx_ffclose(xpmfile1);
 559     gmx_ffclose(xpmfile2);
 560
 561
 562     sfree(profile1);
 563     sfree(profile2);
 564     sfree(xticks);
 565     sfree(yticks);
 566 }
 567
 568
 569 static void writeraw(real*** surf, int tblocks, int xbins, int ybins, gmx::ArrayRef<const std::string> fnms)
 570 {
 571     FILE *raw1, *raw2;
 572     int   i, j, n;
 573
 574     raw1 = gmx_ffopen(fnms[0], "w");
 575     raw2 = gmx_ffopen(fnms[1], "w");
 576     fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 577     fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
 578     for (n = 0; n < tblocks; n++)
 579     {
 580         fprintf(raw1, "%5d\n", n);
 581         fprintf(raw2, "%5d\n", n);
 582         for (i = 0; i < xbins; i++)
 583         {
 584             for (j = 0; j < ybins; j++)
 585             {
 586                 fprintf(raw1, "%i  %i  %8.5f\n", i, j, (surf[0][n][j + ybins * i]));
 587                 fprintf(raw2, "%i  %i  %8.5f\n", i, j, (surf[1][n][j + ybins * i]));
 588             }
 589         }
 590     }
 591
 592     gmx_ffclose(raw1);
 593     gmx_ffclose(raw2);
 594 }
 595
 596
 597 int gmx_hydorder(int argc, char* argv[])
 598 {
 599     static const char* desc[] = {
 600         "[THISMODULE] computes the tetrahedrality order parameters around a ",
 601         "given atom. Both angle an distance order parameters are calculated. See",
 602         "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
 603         "for more details.[PAR]",
 604         "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
 605         "with 2 phases in the box gives the user the option to define a 2D interface in time",
 606         "separating the faces by specifying parameters [TT]-sgang1[tt] and",
 607         "[TT]-sgang2[tt] (it is important to select these judiciously)."
 608     };
 609
 610     int                axis      = 0;
 611     static int         nsttblock = 1;
 612     static int         nlevels   = 100;
 613     static real        binwidth  = 1.0; /* binwidth in mesh           */
 614     static real        sg1       = 1;
 615     static real        sg2       = 1; /* order parameters for bulk phases */
 616     static gmx_bool    bFourier  = FALSE;
 617     static gmx_bool    bRawOut   = FALSE;
 618     int                frames, xslices, yslices; /* Dimensions of interface arrays*/
 619     real***            intfpos; /* Interface arrays (intfnr,t,xy) -potentially large */
 620     static const char* normal_axis[] = { nullptr, "z", "x", "y", nullptr };
 621
 622     t_pargs pa[] = {
 623         { "-d", FALSE, etENUM, { normal_axis }, "Direction of the normal on the membrane" },
 624         { "-bw", FALSE, etREAL, { &binwidth }, "Binwidth of box mesh" },
 625         { "-sgang1", FALSE, etREAL, { &sg1 }, "tetrahedral angle parameter in Phase 1 (bulk)" },
 626         { "-sgang2", FALSE, etREAL, { &sg2 }, "tetrahedral angle parameter in Phase 2 (bulk)" },
 627         { "-tblock", FALSE, etINT, { &nsttblock }, "Number of frames in one time-block average" },
 628         { "-nlevel", FALSE, etINT, { &nlevels }, "Number of Height levels in 2D - XPixMaps" }
 629     };
 630
 631     t_filenm fnm[] = {
 632         /* files for g_order    */
 633         { efTRX, "-f", nullptr, ffREAD },              /* trajectory file              */
 634         { efNDX, "-n", nullptr, ffREAD },              /* index file           */
 635         { efTPR, "-s", nullptr, ffREAD },              /* topology file                */
 636         { efXPM, "-o", "intf", ffWRMULT },             /* XPM- surface maps     */
 637         { efOUT, "-or", "raw", ffOPTWRMULT },          /* xvgr output file           */
 638         { efOUT, "-Spect", "intfspect", ffOPTWRMULT }, /* Fourier spectrum interfaces */
 639     };
 640 #define NFILE asize(fnm)
 641
 642     /*Filenames*/
 643     const char *      ndxfnm, *tpsfnm, *trxfnm;
 644     gmx_output_env_t* oenv;
 645
 646     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
 647                            asize(desc), desc, 0, nullptr, &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(efTPR, NFILE, fnm);
 661     trxfnm = ftp2fn(efTRX, NFILE, fnm);
 662
 663     /* Calculate axis */
 664     GMX_RELEASE_ASSERT(normal_axis[0] != nullptr,
 665                        "Option setting inconsistency; normal_axis[0] is NULL");
 666     if (std::strcmp(normal_axis[0], "x") == 0)
 667     {
 668         axis = XX;
 669     }
 670     else if (std::strcmp(normal_axis[0], "y") == 0)
 671     {
 672         axis = YY;
 673     }
 674     else if (std::strcmp(normal_axis[0], "z") == 0)
 675     {
 676         axis = ZZ;
 677     }
 678     else
 679     {
 680         gmx_fatal(FARGS, "Invalid axis, use x, y or z");
 681     }
 682
 683     switch (axis)
 684     {
 685         case 0: fprintf(stderr, "Taking x axis as normal to the membrane\n"); break;
 686         case 1: fprintf(stderr, "Taking y axis as normal to the membrane\n"); break;
 687         case 2: fprintf(stderr, "Taking z axis as normal to the membrane\n"); break;
 688     }
 689
 690     /* tetraheder order parameter */
 691     /* If either of the options is set we compute both */
 692     gmx::ArrayRef<const std::string> intfn = opt2fns("-o", NFILE, fnm);
 693     if (intfn.size() != 2)
 694     {
 695         gmx_fatal(FARGS, "No or not correct number (2) of output-files: %td", intfn.ssize());
 696     }
 697     calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices,
 698                                &yslices, sg1, sg2, &intfpos, oenv);
 699     writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
 700
 701     if (bFourier)
 702     {
 703         gmx::ArrayRef<const std::string> spectra = opt2fns("-Spect", NFILE, fnm);
 704         if (spectra.size() != 2)
 705         {
 706             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %td", spectra.ssize());
 707         }
 708         powerspectavg(intfpos, frames, xslices, yslices, spectra);
 709     }
 710
 711     if (bRawOut)
 712     {
 713         gmx::ArrayRef<const std::string> raw = opt2fns("-or", NFILE, fnm);
 714         if (raw.size() != 2)
 715         {
 716             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %td", raw.ssize());
 717         }
 718         writeraw(intfpos, frames, xslices, yslices, raw);
 719     }
 720
 721     return 0;
 722 }