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41 #include "gromacs/legacyheaders/typedefs.h"
42 #include "gromacs/legacyheaders/macros.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/pbcutil/pbc.h"
45 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/fileio/xvgr.h"
47 #include "gromacs/utility/futil.h"
48 #include "gromacs/fileio/tpxio.h"
49 #include "gromacs/fileio/trxio.h"
50 #include "gromacs/topology/index.h"
51 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/legacyheaders/nrnb.h"
53 #include "gromacs/math/units.h"
54 #include "gromacs/legacyheaders/coulomb.h"
55 #include "gromacs/legacyheaders/pme.h"
57 #include "gromacs/fileio/matio.h"
58 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/utility/fatalerror.h"
63 static void clust_size(const char *ndx, const char *trx, const char *xpm,
64 const char *xpmw, const char *ncl, const char *acl,
65 const char *mcl, const char *histo, const char *tempf,
66 const char *mcn, gmx_bool bMol, gmx_bool bPBC, const char *tpr,
67 real cut, int nskip, int nlevels,
68 t_rgb rmid, t_rgb rhi, int ndf,
69 const output_env_t oenv)
71 FILE *fp, *gp, *hp, *tp;
72 atom_id *index = NULL;
75 rvec *x = NULL, *v = NULL, dx;
79 gmx_bool bSame, bTPRwarn = TRUE;
83 gmx_mtop_t *mtop = NULL;
86 gmx_mtop_atomlookup_t alook;
88 int version, generation, ii, jj, nsame;
90 /* Cluster size distribution (matrix) */
91 real **cs_dist = NULL;
92 real tf, dx2, cut2, *t_x = NULL, *t_y, cmid, cmax, cav, ekin;
93 int i, j, k, ai, aj, ak, ci, cj, nframe, nclust, n_x, n_y, max_size = 0;
94 int *clust_index, *clust_size, max_clust_size, max_clust_ind, nav, nhisto;
95 t_rgb rlo = { 1.0, 1.0, 1.0 };
97 clear_trxframe(&fr, TRUE);
98 sprintf(timebuf, "Time (%s)", output_env_get_time_unit(oenv));
99 tf = output_env_get_time_factor(oenv);
100 fp = xvgropen(ncl, "Number of clusters", timebuf, "N", oenv);
101 gp = xvgropen(acl, "Average cluster size", timebuf, "#molecules", oenv);
102 hp = xvgropen(mcl, "Max cluster size", timebuf, "#molecules", oenv);
103 tp = xvgropen(tempf, "Temperature of largest cluster", timebuf, "T (K)",
106 if (!read_first_frame(oenv, &status, trx, &fr, TRX_NEED_X | TRX_READ_V))
117 read_tpxheader(tpr, &tpxh, TRUE, &version, &generation);
118 if (tpxh.natoms != natoms)
120 gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!",
121 tpxh.natoms, natoms);
123 ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, NULL, mtop);
131 tfac = ndf/(3.0*natoms);
138 printf("Using molecules rather than atoms. Not reading index file %s\n",
141 mols = &(mtop->mols);
143 /* Make dummy index */
146 for (i = 0; (i < nindex); i++)
150 gname = gmx_strdup("mols");
154 rd_index(ndx, 1, &nindex, &index, &gname);
157 alook = gmx_mtop_atomlookup_init(mtop);
159 snew(clust_index, nindex);
160 snew(clust_size, nindex);
165 for (i = 0; (i < nindex); i++)
173 if ((nskip == 0) || ((nskip > 0) && ((nframe % nskip) == 0)))
177 set_pbc(&pbc, ePBC, fr.box);
182 /* Put all atoms/molecules in their own cluster, with size 1 */
183 for (i = 0; (i < nindex); i++)
185 /* Cluster index is indexed with atom index number */
187 /* Cluster size is indexed with cluster number */
191 /* Loop over atoms */
192 for (i = 0; (i < nindex); i++)
197 /* Loop over atoms (only half a matrix) */
198 for (j = i+1; (j < nindex); j++)
202 /* If they are not in the same cluster already */
207 /* Compute distance */
211 for (ii = mols->index[ai]; !bSame && (ii < mols->index[ai+1]); ii++)
213 for (jj = mols->index[aj]; !bSame && (jj < mols->index[aj+1]); jj++)
217 pbc_dx(&pbc, x[ii], x[jj], dx);
221 rvec_sub(x[ii], x[jj], dx);
224 bSame = (dx2 < cut2);
232 pbc_dx(&pbc, x[ai], x[aj], dx);
236 rvec_sub(x[ai], x[aj], dx);
239 bSame = (dx2 < cut2);
241 /* If distance less than cut-off */
244 /* Merge clusters: check for all atoms whether they are in
245 * cluster cj and if so, put them in ci
247 for (k = 0; (k < nindex); k++)
249 if (clust_index[k] == cj)
251 if (clust_size[cj] <= 0)
253 gmx_fatal(FARGS, "negative cluster size %d for element %d",
267 t_x[n_x-1] = fr.time*tf;
268 srenew(cs_dist, n_x);
269 snew(cs_dist[n_x-1], nindex);
273 for (i = 0; (i < nindex); i++)
276 if (ci > max_clust_size)
284 cs_dist[n_x-1][ci-1] += 1.0;
285 max_size = max(max_size, ci);
293 fprintf(fp, "%14.6e %10d\n", fr.time, nclust);
296 fprintf(gp, "%14.6e %10.3f\n", fr.time, cav/nav);
298 fprintf(hp, "%14.6e %10d\n", fr.time, max_clust_size);
300 /* Analyse velocities, if present */
307 printf("You need a [TT].tpr[tt] file to analyse temperatures\n");
314 /* Loop over clusters and for each cluster compute 1/2 m v^2 */
315 if (max_clust_ind >= 0)
318 for (i = 0; (i < nindex); i++)
320 if (clust_index[i] == max_clust_ind)
323 gmx_mtop_atomnr_to_atom(alook, ai, &atom);
324 ekin += 0.5*atom->m*iprod(v[ai], v[ai]);
327 temp = (ekin*2.0)/(3.0*tfac*max_clust_size*BOLTZ);
328 fprintf(tp, "%10.3f %10.3f\n", fr.time, temp);
334 while (read_next_frame(oenv, status, &fr));
341 gmx_mtop_atomlookup_destroy(alook);
343 if (max_clust_ind >= 0)
345 fp = gmx_ffopen(mcn, "w");
346 fprintf(fp, "[ max_clust ]\n");
347 for (i = 0; (i < nindex); i++)
349 if (clust_index[i] == max_clust_ind)
353 for (j = mols->index[i]; (j < mols->index[i+1]); j++)
355 fprintf(fp, "%d\n", j+1);
360 fprintf(fp, "%d\n", index[i]+1);
367 /* Print the real distribution cluster-size/numer, averaged over the trajectory. */
368 fp = xvgropen(histo, "Cluster size distribution", "Cluster size", "()", oenv);
370 fprintf(fp, "%5d %8.3f\n", 0, 0.0);
371 for (j = 0; (j < max_size); j++)
374 for (i = 0; (i < n_x); i++)
376 nelem += cs_dist[i][j];
378 fprintf(fp, "%5d %8.3f\n", j+1, nelem/n_x);
379 nhisto += (int)((j+1)*nelem/n_x);
381 fprintf(fp, "%5d %8.3f\n", j+1, 0.0);
384 fprintf(stderr, "Total number of atoms in clusters = %d\n", nhisto);
386 /* Look for the smallest entry that is not zero
387 * This will make that zero is white, and not zero is coloured.
391 for (i = 0; (i < n_x); i++)
393 for (j = 0; (j < max_size); j++)
395 if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
397 cmid = cs_dist[i][j];
399 cmax = max(cs_dist[i][j], cmax);
402 fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
404 fp = gmx_ffopen(xpm, "w");
405 write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
406 n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
407 rlo, rmid, rhi, &nlevels);
411 for (i = 0; (i < n_x); i++)
413 for (j = 0; (j < max_size); j++)
415 cs_dist[i][j] *= (j+1);
416 if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
418 cmid = cs_dist[i][j];
420 cmax = max(cs_dist[i][j], cmax);
423 fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
424 fp = gmx_ffopen(xpmw, "w");
425 write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
426 "Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
427 rlo, rmid, rhi, &nlevels);
435 int gmx_clustsize(int argc, char *argv[])
437 const char *desc[] = {
438 "[THISMODULE] computes the size distributions of molecular/atomic clusters in",
439 "the gas phase. The output is given in the form of an [TT].xpm[tt] file.",
440 "The total number of clusters is written to an [TT].xvg[tt] file.[PAR]",
441 "When the [TT]-mol[tt] option is given clusters will be made out of",
442 "molecules rather than atoms, which allows clustering of large molecules.",
443 "In this case an index file would still contain atom numbers",
444 "or your calculation will die with a SEGV.[PAR]",
445 "When velocities are present in your trajectory, the temperature of",
446 "the largest cluster will be printed in a separate [TT].xvg[tt] file assuming",
447 "that the particles are free to move. If you are using constraints,",
448 "please correct the temperature. For instance water simulated with SHAKE",
449 "or SETTLE will yield a temperature that is 1.5 times too low. You can",
450 "compensate for this with the [TT]-ndf[tt] option. Remember to take the removal",
451 "of center of mass motion into account.[PAR]",
452 "The [TT]-mc[tt] option will produce an index file containing the",
453 "atom numbers of the largest cluster."
456 static real cutoff = 0.35;
457 static int nskip = 0;
458 static int nlevels = 20;
460 static gmx_bool bMol = FALSE;
461 static gmx_bool bPBC = TRUE;
462 static rvec rlo = { 1.0, 1.0, 0.0 };
463 static rvec rhi = { 0.0, 0.0, 1.0 };
468 { "-cut", FALSE, etREAL, {&cutoff},
469 "Largest distance (nm) to be considered in a cluster" },
470 { "-mol", FALSE, etBOOL, {&bMol},
471 "Cluster molecules rather than atoms (needs [TT].tpr[tt] file)" },
472 { "-pbc", FALSE, etBOOL, {&bPBC},
473 "Use periodic boundary conditions" },
474 { "-nskip", FALSE, etINT, {&nskip},
475 "Number of frames to skip between writing" },
476 { "-nlevels", FALSE, etINT, {&nlevels},
477 "Number of levels of grey in [TT].xpm[tt] output" },
478 { "-ndf", FALSE, etINT, {&ndf},
479 "Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used." },
480 { "-rgblo", FALSE, etRVEC, {rlo},
481 "RGB values for the color of the lowest occupied cluster size" },
482 { "-rgbhi", FALSE, etRVEC, {rhi},
483 "RGB values for the color of the highest occupied cluster size" }
485 #define NPA asize(pa)
486 const char *fnNDX, *fnTPR;
491 { efTRX, "-f", NULL, ffREAD },
492 { efTPR, NULL, NULL, ffOPTRD },
493 { efNDX, NULL, NULL, ffOPTRD },
494 { efXPM, "-o", "csize", ffWRITE },
495 { efXPM, "-ow", "csizew", ffWRITE },
496 { efXVG, "-nc", "nclust", ffWRITE },
497 { efXVG, "-mc", "maxclust", ffWRITE },
498 { efXVG, "-ac", "avclust", ffWRITE },
499 { efXVG, "-hc", "histo-clust", ffWRITE },
500 { efXVG, "-temp", "temp", ffOPTWR },
501 { efNDX, "-mcn", "maxclust", ffOPTWR }
503 #define NFILE asize(fnm)
505 if (!parse_common_args(&argc, argv,
506 PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
507 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
512 fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
513 rgblo.r = rlo[XX], rgblo.g = rlo[YY], rgblo.b = rlo[ZZ];
514 rgbhi.r = rhi[XX], rgbhi.g = rhi[YY], rgbhi.b = rhi[ZZ];
516 fnTPR = ftp2fn_null(efTPR, NFILE, fnm);
519 gmx_fatal(FARGS, "You need a tpr file for the -mol option");
522 clust_size(fnNDX, ftp2fn(efTRX, NFILE, fnm), opt2fn("-o", NFILE, fnm),
523 opt2fn("-ow", NFILE, fnm),
524 opt2fn("-nc", NFILE, fnm), opt2fn("-ac", NFILE, fnm),
525 opt2fn("-mc", NFILE, fnm), opt2fn("-hc", NFILE, fnm),
526 opt2fn("-temp", NFILE, fnm), opt2fn("-mcn", NFILE, fnm),
528 cutoff, nskip, nlevels, rgblo, rgbhi, ndf, oenv);