src/gromacs/gmxana/gmx_mindist.cpp

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstdlib>
  41 #include <cstring>
  42
  43 #include <algorithm>
  44
  45 #include "gromacs/commandline/pargs.h"
  46 #include "gromacs/commandline/viewit.h"
  47 #include "gromacs/fileio/confio.h"
  48 #include "gromacs/fileio/trxio.h"
  49 #include "gromacs/fileio/xvgr.h"
  50 #include "gromacs/gmxana/gmx_ana.h"
  51 #include "gromacs/math/functions.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/mdtypes/md_enums.h"
  54 #include "gromacs/pbcutil/pbc.h"
  55 #include "gromacs/pbcutil/rmpbc.h"
  56 #include "gromacs/topology/index.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/arraysize.h"
  59 #include "gromacs/utility/cstringutil.h"
  60 #include "gromacs/utility/fatalerror.h"
  61 #include "gromacs/utility/futil.h"
  62 #include "gromacs/utility/gmxassert.h"
  63 #include "gromacs/utility/smalloc.h"
  64
  65
  66 static void periodic_dist(int ePBC,
  67                           matrix box, rvec x[], int n, int index[],
  68                           real *rmin, real *rmax, int *min_ind)
  69 {
  70 #define NSHIFT_MAX 26
  71     int  nsz, nshift, sx, sy, sz, i, j, s;
  72     real sqr_box, r2min, r2max, r2;
  73     rvec shift[NSHIFT_MAX], d0, d;
  74
  75     sqr_box = std::min(norm2(box[XX]), norm2(box[YY]));
  76     if (ePBC == epbcXYZ)
  77     {
  78         sqr_box = std::min(sqr_box, norm2(box[ZZ]));
  79         nsz     = 1;
  80     }
  81     else if (ePBC == epbcXY)
  82     {
  83         nsz = 0;
  84     }
  85     else
  86     {
  87         gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist",
  88                   epbc_names[ePBC]);
  89         nsz = 0; /* Keep compilers quiet */
  90     }
  91
  92     nshift = 0;
  93     for (sz = -nsz; sz <= nsz; sz++)
  94     {
  95         for (sy = -1; sy <= 1; sy++)
  96         {
  97             for (sx = -1; sx <= 1; sx++)
  98             {
  99                 if (sx != 0 || sy != 0 || sz != 0)
 100                 {
 101                     for (i = 0; i < DIM; i++)
 102                     {
 103                         shift[nshift][i] =
 104                             sx*box[XX][i] + sy*box[YY][i] + sz*box[ZZ][i];
 105                     }
 106                     nshift++;
 107                 }
 108             }
 109         }
 110     }
 111
 112     r2min = sqr_box;
 113     r2max = 0;
 114
 115     for (i = 0; i < n; i++)
 116     {
 117         for (j = i+1; j < n; j++)
 118         {
 119             rvec_sub(x[index[i]], x[index[j]], d0);
 120             r2 = norm2(d0);
 121             if (r2 > r2max)
 122             {
 123                 r2max = r2;
 124             }
 125             for (s = 0; s < nshift; s++)
 126             {
 127                 rvec_add(d0, shift[s], d);
 128                 r2 = norm2(d);
 129                 if (r2 < r2min)
 130                 {
 131                     r2min      = r2;
 132                     min_ind[0] = i;
 133                     min_ind[1] = j;
 134                 }
 135             }
 136         }
 137     }
 138
 139     *rmin = std::sqrt(r2min);
 140     *rmax = std::sqrt(r2max);
 141 }
 142
 143 static void periodic_mindist_plot(const char *trxfn, const char *outfn,
 144                                   const t_topology *top, int ePBC,
 145                                   int n, int index[], gmx_bool bSplit,
 146                                   const gmx_output_env_t *oenv)
 147 {
 148     FILE        *out;
 149     const char  *leg[5] = { "min per.", "max int.", "box1", "box2", "box3" };
 150     t_trxstatus *status;
 151     real         t;
 152     rvec        *x;
 153     matrix       box;
 154     int          natoms, ind_min[2] = {0, 0}, ind_mini = 0, ind_minj = 0;
 155     real         rmin, rmax, rmint, tmint;
 156     gmx_bool     bFirst;
 157     gmx_rmpbc_t  gpbc = nullptr;
 158
 159     natoms = read_first_x(oenv, &status, trxfn, &t, &x, box);
 160
 161     check_index(nullptr, n, index, nullptr, natoms);
 162
 163     out = xvgropen(outfn, "Minimum distance to periodic image",
 164                    output_env_get_time_label(oenv), "Distance (nm)", oenv);
 165     if (output_env_get_print_xvgr_codes(oenv))
 166     {
 167         fprintf(out, "@ subtitle \"and maximum internal distance\"\n");
 168     }
 169     xvgr_legend(out, 5, leg, oenv);
 170
 171     rmint = box[XX][XX];
 172     tmint = 0;
 173
 174     if (nullptr != top)
 175     {
 176         gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
 177     }
 178
 179     bFirst = TRUE;
 180     do
 181     {
 182         if (nullptr != top)
 183         {
 184             gmx_rmpbc(gpbc, natoms, box, x);
 185         }
 186
 187         periodic_dist(ePBC, box, x, n, index, &rmin, &rmax, ind_min);
 188         if (rmin < rmint)
 189         {
 190             rmint    = rmin;
 191             tmint    = t;
 192             ind_mini = ind_min[0];
 193             ind_minj = ind_min[1];
 194         }
 195         if (bSplit && !bFirst && std::abs(t/output_env_get_time_factor(oenv)) < 1e-5)
 196         {
 197             fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 198         }
 199         fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
 200                 output_env_conv_time(oenv, t), rmin, rmax, norm(box[0]), norm(box[1]), norm(box[2]));
 201         bFirst = FALSE;
 202     }
 203     while (read_next_x(oenv, status, &t, x, box));
 204
 205     if (nullptr != top)
 206     {
 207         gmx_rmpbc_done(gpbc);
 208     }
 209
 210     xvgrclose(out);
 211
 212     fprintf(stdout,
 213             "\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
 214             "between atoms %d and %d\n",
 215             rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv).c_str(),
 216             index[ind_mini]+1, index[ind_minj]+1);
 217 }
 218
 219 static void calc_dist(real rcut, gmx_bool bPBC, int ePBC, matrix box, rvec x[],
 220                       int nx1, int nx2, int index1[], int index2[],
 221                       gmx_bool bGroup,
 222                       real *rmin, real *rmax, int *nmin, int *nmax,
 223                       int *ixmin, int *jxmin, int *ixmax, int *jxmax)
 224 {
 225     int      i, j, i0 = 0, j1;
 226     int      ix, jx;
 227     int     *index3;
 228     rvec     dx;
 229     real     r2, rmin2, rmax2, rcut2;
 230     t_pbc    pbc;
 231     int      nmin_j, nmax_j;
 232
 233     *ixmin = -1;
 234     *jxmin = -1;
 235     *ixmax = -1;
 236     *jxmax = -1;
 237     *nmin  = 0;
 238     *nmax  = 0;
 239
 240     rcut2 = gmx::square(rcut);
 241
 242     /* Must init pbc every step because of pressure coupling */
 243     if (bPBC)
 244     {
 245         set_pbc(&pbc, ePBC, box);
 246     }
 247     if (index2)
 248     {
 249         i0     = 0;
 250         j1     = nx2;
 251         index3 = index2;
 252     }
 253     else
 254     {
 255         j1     = nx1;
 256         index3 = index1;
 257     }
 258
 259     rmin2 = 1e12;
 260     rmax2 = -1e12;
 261
 262     for (j = 0; (j < j1); j++)
 263     {
 264         jx = index3[j];
 265         if (index2 == nullptr)
 266         {
 267             i0 = j + 1;
 268         }
 269         nmin_j = 0;
 270         nmax_j = 0;
 271         for (i = i0; (i < nx1); i++)
 272         {
 273             ix = index1[i];
 274             if (ix != jx)
 275             {
 276                 if (bPBC)
 277                 {
 278                     pbc_dx(&pbc, x[ix], x[jx], dx);
 279                 }
 280                 else
 281                 {
 282                     rvec_sub(x[ix], x[jx], dx);
 283                 }
 284                 r2 = iprod(dx, dx);
 285                 if (r2 < rmin2)
 286                 {
 287                     rmin2  = r2;
 288                     *ixmin = ix;
 289                     *jxmin = jx;
 290                 }
 291                 if (r2 > rmax2)
 292                 {
 293                     rmax2  = r2;
 294                     *ixmax = ix;
 295                     *jxmax = jx;
 296                 }
 297                 if (r2 <= rcut2)
 298                 {
 299                     nmin_j++;
 300                 }
 301                 else
 302                 {
 303                     nmax_j++;
 304                 }
 305             }
 306         }
 307         if (bGroup)
 308         {
 309             if (nmin_j > 0)
 310             {
 311                 (*nmin)++;
 312             }
 313             if (nmax_j > 0)
 314             {
 315                 (*nmax)++;
 316             }
 317         }
 318         else
 319         {
 320             *nmin += nmin_j;
 321             *nmax += nmax_j;
 322         }
 323     }
 324     *rmin = std::sqrt(rmin2);
 325     *rmax = std::sqrt(rmax2);
 326 }
 327
 328 void dist_plot(const char *fn, const char *afile, const char *dfile,
 329                const char *nfile, const char *rfile, const char *xfile,
 330                real rcut, gmx_bool bMat, const t_atoms *atoms,
 331                int ng, int *index[], int gnx[], char *grpn[], gmx_bool bSplit,
 332                gmx_bool bMin, int nres, int *residue, gmx_bool bPBC, int ePBC,
 333                gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
 334                const gmx_output_env_t *oenv)
 335 {
 336     FILE            *atm, *dist, *num;
 337     t_trxstatus     *trxout;
 338     char             buf[256];
 339     char           **leg;
 340     real             t, dmin, dmax, **mindres = nullptr, **maxdres = nullptr;
 341     int              nmin, nmax;
 342     t_trxstatus     *status;
 343     int              i = -1, j, k;
 344     int              min2, max2, min1r, min2r, max1r, max2r;
 345     int              min1 = 0;
 346     int              max1 = 0;
 347     int              oindex[2];
 348     rvec            *x0;
 349     matrix           box;
 350     gmx_bool         bFirst;
 351     FILE            *respertime = nullptr;
 352
 353     if (read_first_x(oenv, &status, fn, &t, &x0, box) == 0)
 354     {
 355         gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
 356     }
 357
 358     sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
 359     dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
 360     sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
 361     num    = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : nullptr;
 362     atm    = afile ? gmx_ffopen(afile, "w") : nullptr;
 363     trxout = xfile ? open_trx(xfile, "w") : nullptr;
 364
 365     if (bMat)
 366     {
 367         if (ng == 1)
 368         {
 369             snew(leg, 1);
 370             sprintf(buf, "Internal in %s", grpn[0]);
 371             leg[0] = gmx_strdup(buf);
 372             xvgr_legend(dist, 0, (const char**)leg, oenv);
 373             if (num)
 374             {
 375                 xvgr_legend(num, 0, (const char**)leg, oenv);
 376             }
 377         }
 378         else
 379         {
 380             snew(leg, (ng*(ng-1))/2);
 381             for (i = j = 0; (i < ng-1); i++)
 382             {
 383                 for (k = i+1; (k < ng); k++, j++)
 384                 {
 385                     sprintf(buf, "%s-%s", grpn[i], grpn[k]);
 386                     leg[j] = gmx_strdup(buf);
 387                 }
 388             }
 389             xvgr_legend(dist, j, (const char**)leg, oenv);
 390             if (num)
 391             {
 392                 xvgr_legend(num, j, (const char**)leg, oenv);
 393             }
 394         }
 395     }
 396     else
 397     {
 398         snew(leg, ng-1);
 399         for (i = 0; (i < ng-1); i++)
 400         {
 401             sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
 402             leg[i] = gmx_strdup(buf);
 403         }
 404         xvgr_legend(dist, ng-1, (const char**)leg, oenv);
 405         if (num)
 406         {
 407             xvgr_legend(num, ng-1, (const char**)leg, oenv);
 408         }
 409     }
 410
 411     if (bEachResEachTime)
 412     {
 413         sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
 414         respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
 415         xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
 416         if (bPrintResName && output_env_get_print_xvgr_codes(oenv) )
 417         {
 418             fprintf(respertime, "# ");
 419
 420             for (j = 0; j < nres; j++)
 421             {
 422                 fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
 423             }
 424             fprintf(respertime, "\n");
 425         }
 426
 427     }
 428
 429     if (nres)
 430     {
 431         snew(mindres, ng-1);
 432         snew(maxdres, ng-1);
 433         for (i = 1; i < ng; i++)
 434         {
 435             snew(mindres[i-1], nres);
 436             snew(maxdres[i-1], nres);
 437             for (j = 0; j < nres; j++)
 438             {
 439                 mindres[i-1][j] = 1e6;
 440             }
 441             /* maxdres[*][*] is already 0 */
 442         }
 443     }
 444     bFirst = TRUE;
 445     do
 446     {
 447         if (bSplit && !bFirst && std::abs(t/output_env_get_time_factor(oenv)) < 1e-5)
 448         {
 449             fprintf(dist, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 450             if (num)
 451             {
 452                 fprintf(num, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 453             }
 454             if (atm)
 455             {
 456                 fprintf(atm, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 457             }
 458         }
 459         fprintf(dist, "%12e", output_env_conv_time(oenv, t));
 460         if (num)
 461         {
 462             fprintf(num, "%12e", output_env_conv_time(oenv, t));
 463         }
 464
 465         if (bMat)
 466         {
 467             if (ng == 1)
 468             {
 469                 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[0], index[0], index[0], bGroup,
 470                           &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
 471                 fprintf(dist, "  %12e", bMin ? dmin : dmax);
 472                 if (num)
 473                 {
 474                     fprintf(num, "  %8d", bMin ? nmin : nmax);
 475                 }
 476             }
 477             else
 478             {
 479                 for (i = 0; (i < ng-1); i++)
 480                 {
 481                     for (k = i+1; (k < ng); k++)
 482                     {
 483                         calc_dist(rcut, bPBC, ePBC, box, x0, gnx[i], gnx[k], index[i], index[k],
 484                                   bGroup, &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
 485                         fprintf(dist, "  %12e", bMin ? dmin : dmax);
 486                         if (num)
 487                         {
 488                             fprintf(num, "  %8d", bMin ? nmin : nmax);
 489                         }
 490                     }
 491                 }
 492             }
 493         }
 494         else
 495         {
 496             for (i = 1; (i < ng); i++)
 497             {
 498                 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[i], index[0], index[i], bGroup,
 499                           &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
 500                 fprintf(dist, "  %12e", bMin ? dmin : dmax);
 501                 if (num)
 502                 {
 503                     fprintf(num, "  %8d", bMin ? nmin : nmax);
 504                 }
 505                 if (nres)
 506                 {
 507                     for (j = 0; j < nres; j++)
 508                     {
 509                         calc_dist(rcut, bPBC, ePBC, box, x0, residue[j+1]-residue[j], gnx[i],
 510                                   &(index[0][residue[j]]), index[i], bGroup,
 511                                   &dmin, &dmax, &nmin, &nmax, &min1r, &min2r, &max1r, &max2r);
 512                         mindres[i-1][j] = std::min(mindres[i-1][j], dmin);
 513                         maxdres[i-1][j] = std::max(maxdres[i-1][j], dmax);
 514                     }
 515                 }
 516             }
 517         }
 518         fprintf(dist, "\n");
 519         if (num)
 520         {
 521             fprintf(num, "\n");
 522         }
 523         if ( (bMin ? min1 : max1) != -1)
 524         {
 525             if (atm)
 526             {
 527                 fprintf(atm, "%12e  %12d  %12d\n",
 528                         output_env_conv_time(oenv, t), 1+(bMin ? min1 : max1),
 529                         1+(bMin ? min2 : max2));
 530             }
 531         }
 532
 533         if (trxout)
 534         {
 535             oindex[0] = bMin ? min1 : max1;
 536             oindex[1] = bMin ? min2 : max2;
 537             write_trx(trxout, 2, oindex, atoms, i, t, box, x0, nullptr, nullptr);
 538         }
 539         bFirst = FALSE;
 540         /*dmin should be minimum distance for residue and group*/
 541         if (bEachResEachTime)
 542         {
 543             fprintf(respertime, "%12e", t);
 544             for (i = 1; i < ng; i++)
 545             {
 546                 for (j = 0; j < nres; j++)
 547                 {
 548                     fprintf(respertime, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
 549                     /*reset distances for next time point*/
 550                     mindres[i-1][j] = 1e6;
 551                     maxdres[i-1][j] = 0;
 552                 }
 553             }
 554             fprintf(respertime, "\n");
 555         }
 556     }
 557     while (read_next_x(oenv, status, &t, x0, box));
 558
 559     close_trx(status);
 560     xvgrclose(dist);
 561     if (num)
 562     {
 563         xvgrclose(num);
 564     }
 565     if (atm)
 566     {
 567         gmx_ffclose(atm);
 568     }
 569     if (trxout)
 570     {
 571         close_trx(trxout);
 572     }
 573     if (respertime)
 574     {
 575         xvgrclose(respertime);
 576     }
 577
 578     if (nres && !bEachResEachTime)
 579     {
 580         FILE *res;
 581
 582         sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
 583         res = xvgropen(rfile, buf, "Residue (#)", "Distance (nm)", oenv);
 584         xvgr_legend(res, ng-1, (const char**)leg, oenv);
 585         for (j = 0; j < nres; j++)
 586         {
 587             fprintf(res, "%4d", j+1);
 588             for (i = 1; i < ng; i++)
 589             {
 590                 fprintf(res, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
 591             }
 592             fprintf(res, "\n");
 593         }
 594         xvgrclose(res);
 595     }
 596
 597     sfree(x0);
 598 }
 599
 600 int find_residues(const t_atoms *atoms, int n, int index[], int **resindex)
 601 {
 602     int  i;
 603     int  nres      = 0, resnr, presnr = 0;
 604     bool presFound = false;
 605     int *residx;
 606
 607     /* build index of first atom numbers for each residue */
 608     snew(residx, atoms->nres+1);
 609     for (i = 0; i < n; i++)
 610     {
 611         resnr = atoms->atom[index[i]].resind;
 612         if (!presFound || resnr != presnr)
 613         {
 614             residx[nres] = i;
 615             nres++;
 616             presnr    = resnr;
 617             presFound = true;
 618         }
 619     }
 620     if (debug)
 621     {
 622         printf("Found %d residues out of %d (%d/%d atoms)\n",
 623                nres, atoms->nres, atoms->nr, n);
 624     }
 625     srenew(residx, nres+1);
 626     /* mark end of last residue */
 627     residx[nres] = n;
 628     *resindex    = residx;
 629     return nres;
 630 }
 631
 632 void dump_res(FILE *out, int nres, int *resindex, int index[])
 633 {
 634     int i, j;
 635
 636     for (i = 0; i < nres-1; i++)
 637     {
 638         fprintf(out, "Res %d (%d):", i, resindex[i+1]-resindex[i]);
 639         for (j = resindex[i]; j < resindex[i+1]; j++)
 640         {
 641             fprintf(out, " %d(%d)", j, index[j]);
 642         }
 643         fprintf(out, "\n");
 644     }
 645 }
 646
 647 int gmx_mindist(int argc, char *argv[])
 648 {
 649     const char       *desc[] = {
 650         "[THISMODULE] computes the distance between one group and a number of",
 651         "other groups. Both the minimum distance",
 652         "(between any pair of atoms from the respective groups)",
 653         "and the number of contacts within a given",
 654         "distance are written to two separate output files.",
 655         "With the [TT]-group[tt] option a contact of an atom in another group",
 656         "with multiple atoms in the first group is counted as one contact",
 657         "instead of as multiple contacts.",
 658         "With [TT]-or[tt], minimum distances to each residue in the first",
 659         "group are determined and plotted as a function of residue number.[PAR]",
 660         "With option [TT]-pi[tt] the minimum distance of a group to its",
 661         "periodic image is plotted. This is useful for checking if a protein",
 662         "has seen its periodic image during a simulation. Only one shift in",
 663         "each direction is considered, giving a total of 26 shifts.",
 664         "It also plots the maximum distance within the group and the lengths",
 665         "of the three box vectors.[PAR]",
 666         "Also [gmx-distance] and [gmx-pairdist] calculate distances."
 667     };
 668
 669     static gmx_bool   bMat             = FALSE, bPI = FALSE, bSplit = FALSE, bMax = FALSE, bPBC = TRUE;
 670     static gmx_bool   bGroup           = FALSE;
 671     static real       rcutoff          = 0.6;
 672     static int        ng               = 1;
 673     static gmx_bool   bEachResEachTime = FALSE, bPrintResName = FALSE;
 674     t_pargs           pa[]             = {
 675         { "-matrix", FALSE, etBOOL, {&bMat},
 676           "Calculate half a matrix of group-group distances" },
 677         { "-max",    FALSE, etBOOL, {&bMax},
 678           "Calculate *maximum* distance instead of minimum" },
 679         { "-d",      FALSE, etREAL, {&rcutoff},
 680           "Distance for contacts" },
 681         { "-group",      FALSE, etBOOL, {&bGroup},
 682           "Count contacts with multiple atoms in the first group as one" },
 683         { "-pi",     FALSE, etBOOL, {&bPI},
 684           "Calculate minimum distance with periodic images" },
 685         { "-split",  FALSE, etBOOL, {&bSplit},
 686           "Split graph where time is zero" },
 687         { "-ng",       FALSE, etINT, {&ng},
 688           "Number of secondary groups to compute distance to a central group" },
 689         { "-pbc",    FALSE, etBOOL, {&bPBC},
 690           "Take periodic boundary conditions into account" },
 691         { "-respertime",  FALSE, etBOOL, {&bEachResEachTime},
 692           "When writing per-residue distances, write distance for each time point" },
 693         { "-printresname",  FALSE, etBOOL, {&bPrintResName},
 694           "Write residue names" }
 695     };
 696     gmx_output_env_t *oenv;
 697     t_topology       *top  = nullptr;
 698     int               ePBC = -1;
 699     rvec             *x;
 700     matrix            box;
 701     gmx_bool          bTop = FALSE;
 702
 703     int               i, nres = 0;
 704     const char       *trxfnm, *tpsfnm, *ndxfnm, *distfnm, *numfnm, *atmfnm, *oxfnm, *resfnm;
 705     char            **grpname;
 706     int              *gnx;
 707     int             **index, *residues = nullptr;
 708     t_filenm          fnm[] = {
 709         { efTRX, "-f",  nullptr,      ffREAD },
 710         { efTPS,  nullptr, nullptr,      ffOPTRD },
 711         { efNDX,  nullptr, nullptr,      ffOPTRD },
 712         { efXVG, "-od", "mindist",  ffWRITE },
 713         { efXVG, "-on", "numcont",  ffOPTWR },
 714         { efOUT, "-o", "atm-pair", ffOPTWR },
 715         { efTRO, "-ox", "mindist",  ffOPTWR },
 716         { efXVG, "-or", "mindistres", ffOPTWR }
 717     };
 718 #define NFILE asize(fnm)
 719
 720     if (!parse_common_args(&argc, argv,
 721                            PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
 722                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 723     {
 724         return 0;
 725     }
 726
 727     trxfnm  = ftp2fn(efTRX, NFILE, fnm);
 728     ndxfnm  = ftp2fn_null(efNDX, NFILE, fnm);
 729     distfnm = opt2fn("-od", NFILE, fnm);
 730     numfnm  = opt2fn_null("-on", NFILE, fnm);
 731     atmfnm  = ftp2fn_null(efOUT, NFILE, fnm);
 732     oxfnm   = opt2fn_null("-ox", NFILE, fnm);
 733     resfnm  = opt2fn_null("-or", NFILE, fnm);
 734     if (bPI || resfnm != nullptr)
 735     {
 736         /* We need a tps file */
 737         tpsfnm = ftp2fn(efTPS, NFILE, fnm);
 738     }
 739     else
 740     {
 741         tpsfnm = ftp2fn_null(efTPS, NFILE, fnm);
 742     }
 743
 744     if (!tpsfnm && !ndxfnm)
 745     {
 746         gmx_fatal(FARGS, "You have to specify either the index file or a tpr file");
 747     }
 748
 749     if (bPI)
 750     {
 751         ng = 1;
 752         fprintf(stderr, "Choose a group for distance calculation\n");
 753     }
 754     else if (!bMat)
 755     {
 756         ng++;
 757     }
 758
 759     snew(gnx, ng);
 760     snew(index, ng);
 761     snew(grpname, ng);
 762
 763     if (tpsfnm || resfnm || !ndxfnm)
 764     {
 765         snew(top, 1);
 766         bTop = read_tps_conf(tpsfnm, top, &ePBC, &x, nullptr, box, FALSE);
 767         if (bPI && !bTop)
 768         {
 769             printf("\nWARNING: Without a run input file a trajectory with broken molecules will not give the correct periodic image distance\n\n");
 770         }
 771     }
 772     get_index(top ? &(top->atoms) : nullptr, ndxfnm, ng, gnx, index, grpname);
 773
 774     if (bMat && (ng == 1))
 775     {
 776         ng = gnx[0];
 777         printf("Special case: making distance matrix between all atoms in group %s\n",
 778                grpname[0]);
 779         srenew(gnx, ng);
 780         srenew(index, ng);
 781         srenew(grpname, ng);
 782         for (i = 1; (i < ng); i++)
 783         {
 784             gnx[i]      = 1;
 785             grpname[i]  = grpname[0];
 786             snew(index[i], 1);
 787             index[i][0] = index[0][i];
 788         }
 789         gnx[0] = 1;
 790     }
 791
 792     if (resfnm)
 793     {
 794         GMX_RELEASE_ASSERT(top != nullptr, "top pointer cannot be NULL when finding residues");
 795         nres = find_residues(&(top->atoms), gnx[0], index[0], &residues);
 796
 797         if (debug)
 798         {
 799             dump_res(debug, nres, residues, index[0]);
 800         }
 801     }
 802
 803     if (bPI)
 804     {
 805         periodic_mindist_plot(trxfnm, distfnm, top, ePBC, gnx[0], index[0], bSplit, oenv);
 806     }
 807     else
 808     {
 809         dist_plot(trxfnm, atmfnm, distfnm, numfnm, resfnm, oxfnm,
 810                   rcutoff, bMat, top ? &(top->atoms) : nullptr,
 811                   ng, index, gnx, grpname, bSplit, !bMax, nres, residues, bPBC, ePBC,
 812                   bGroup, bEachResEachTime, bPrintResName, oenv);
 813     }
 814
 815     do_view(oenv, distfnm, "-nxy");
 816     if (!bPI)
 817     {
 818         do_view(oenv, numfnm, "-nxy");
 819     }
 820
 821     return 0;
 822 }