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44 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/fileio/xvgr.h"
51 #include "gromacs/utility/futil.h"
53 #include "gromacs/fileio/tpxio.h"
54 #include "gromacs/fileio/trxio.h"
55 #include "gromacs/fileio/matio.h"
56 #include "binsearch.h"
57 #include "powerspect.h"
59 #include "gromacs/utility/fatalerror.h"
61 /* Print name of first atom in all groups in index file */
62 static void print_types(atom_id index[], atom_id a[], int ngrps,
63 char *groups[], t_topology *top)
67 fprintf(stderr, "Using following groups: \n");
68 for (i = 0; i < ngrps; i++)
70 fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
71 groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
73 fprintf(stderr, "\n");
76 static void check_length(real length, int a, int b)
80 fprintf(stderr, "WARNING: distance between atoms %d and "
81 "%d > 0.3 nm (%f). Index file might be corrupt.\n",
86 static void find_tetra_order_grid(t_topology top, int ePBC,
87 int natoms, matrix box,
88 rvec x[], int maxidx, atom_id index[],
89 real *sgmean, real *skmean,
90 int nslicex, int nslicey, int nslicez,
91 real ***sggrid, real ***skgrid)
93 int ix, jx, i, j, k, l, n, *nn[4];
94 rvec dx, rj, rk, urk, urj;
95 real cost, cost2, *sgmol, *skmol, rmean, rmean2, r2, box2, *r_nn[4];
97 int slindex_x, slindex_y, slindex_z;
99 real onethird = 1.0/3.0;
102 /* dmat = init_mat(maxidx, FALSE); */
104 box2 = box[XX][XX] * box[XX][XX];
106 /* Initialize expanded sl_count array */
107 snew(sl_count, nslicex);
108 for (i = 0; i < nslicex; i++)
110 snew(sl_count[i], nslicey);
111 for (j = 0; j < nslicey; j++)
113 snew(sl_count[i][j], nslicez);
118 for (i = 0; (i < 4); i++)
120 snew(r_nn[i], natoms);
123 for (j = 0; (j < natoms); j++)
132 /* Must init pbc every step because of pressure coupling */
133 set_pbc(&pbc, ePBC, box);
134 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
135 gmx_rmpbc(gpbc, natoms, box, x);
140 for (i = 0; (i < maxidx); i++)
141 { /* loop over index file */
143 for (j = 0; (j < maxidx); j++)
153 pbc_dx(&pbc, x[ix], x[jx], dx);
156 /* set_mat_entry(dmat,i,j,r2); */
158 /* determine the nearest neighbours */
161 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
162 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
163 r_nn[1][i] = r_nn[0][i]; nn[1][i] = nn[0][i];
164 r_nn[0][i] = r2; nn[0][i] = j;
166 else if (r2 < r_nn[1][i])
168 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
169 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
170 r_nn[1][i] = r2; nn[1][i] = j;
172 else if (r2 < r_nn[2][i])
174 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
175 r_nn[2][i] = r2; nn[2][i] = j;
177 else if (r2 < r_nn[3][i])
179 r_nn[3][i] = r2; nn[3][i] = j;
184 /* calculate mean distance between nearest neighbours */
186 for (j = 0; (j < 4); j++)
188 r_nn[j][i] = sqrt(r_nn[j][i]);
197 /* Chau1998a eqn 3 */
198 /* angular part tetrahedrality order parameter per atom */
199 for (j = 0; (j < 3); j++)
201 for (k = j+1; (k < 4); k++)
203 pbc_dx(&pbc, x[ix], x[index[nn[k][i]]], rk);
204 pbc_dx(&pbc, x[ix], x[index[nn[j][i]]], rj);
209 cost = iprod(urk, urj) + onethird;
217 /* normalize sgmol between 0.0 and 1.0 */
218 sgmol[i] = 3*sgmol[i]/32;
221 /* distance part tetrahedrality order parameter per atom */
222 rmean2 = 4 * 3 * rmean * rmean;
223 for (j = 0; (j < 4); j++)
225 skmol[i] += (rmean - r_nn[j][i]) * (rmean - r_nn[j][i]) / rmean2;
226 /* printf("%d %f (%f %f %f %f) \n",
227 i, skmol[i], rmean, rmean2, r_nn[j][i], (rmean - r_nn[j][i]) );
233 /* Compute sliced stuff in x y z*/
234 slindex_x = gmx_nint((1+x[i][XX]/box[XX][XX])*nslicex) % nslicex;
235 slindex_y = gmx_nint((1+x[i][YY]/box[YY][YY])*nslicey) % nslicey;
236 slindex_z = gmx_nint((1+x[i][ZZ]/box[ZZ][ZZ])*nslicez) % nslicez;
237 sggrid[slindex_x][slindex_y][slindex_z] += sgmol[i];
238 skgrid[slindex_x][slindex_y][slindex_z] += skmol[i];
239 (sl_count[slindex_x][slindex_y][slindex_z])++;
240 } /* loop over entries in index file */
245 for (i = 0; (i < nslicex); i++)
247 for (j = 0; j < nslicey; j++)
249 for (k = 0; k < nslicez; k++)
251 if (sl_count[i][j][k] > 0)
253 sggrid[i][j][k] /= sl_count[i][j][k];
254 skgrid[i][j][k] /= sl_count[i][j][k];
263 for (i = 0; (i < 4); i++)
270 /*Determines interface from tetrahedral order parameter in box with specified binwidth. */
271 /*Outputs interface positions(bins), the number of timeframes, and the number of surface-mesh points in xy*/
273 static void calc_tetra_order_interface(const char *fnNDX, const char *fnTPS, const char *fnTRX, real binw, int tblock,
274 int *nframes, int *nslicex, int *nslicey,
275 real sgang1, real sgang2, real ****intfpos,
278 FILE *fpsg = NULL, *fpsk = NULL;
279 char *sgslfn = "sg_ang_mesh"; /* Hardcoded filenames for debugging*/
280 char *skslfn = "sk_dist_mesh";
283 char title[STRLEN], subtitle[STRLEN];
289 real sg, sk, sgintf, pos;
290 atom_id **index = NULL;
291 char **grpname = NULL;
292 int i, j, k, n, *isize, ng, nslicez, framenr;
293 real ***sg_grid = NULL, ***sk_grid = NULL, ***sg_fravg = NULL, ***sk_fravg = NULL, ****sk_4d = NULL, ****sg_4d = NULL;
297 const real onehalf = 1.0/2.0;
298 /* real ***intfpos[2]; pointers to arrays of two interface positions zcoord(framenr,xbin,ybin): intfpos[interface_index][t][nslicey*x+y]
299 * i.e 1D Row-major order in (t,x,y) */
302 read_tps_conf(fnTPS, title, &top, &ePBC, &xtop, NULL, box, FALSE);
304 *nslicex = (int)(box[XX][XX]/binw + onehalf); /*Calculate slicenr from binwidth*/
305 *nslicey = (int)(box[YY][YY]/binw + onehalf);
306 nslicez = (int)(box[ZZ][ZZ]/binw + onehalf);
311 /* get index groups */
312 printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
316 get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
318 /* Analyze trajectory */
319 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
320 if (natoms > top.atoms.nr)
322 gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
323 top.atoms.nr, natoms);
325 check_index(NULL, ng, index[0], NULL, natoms);
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++)
333 snew(sg_grid[i], *nslicey);
334 snew(sk_grid[i], *nslicey);
335 for (j = 0; j < *nslicey; j++)
337 snew(sg_grid[i][j], nslicez);
338 snew(sk_grid[i][j], nslicez);
347 /* Loop over frames*/
350 /*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
351 if (framenr%tblock == 0)
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++)
359 snew(sg_fravg[i], *nslicey);
360 snew(sk_fravg[i], *nslicey);
361 for (j = 0; j < *nslicey; j++)
363 snew(sg_fravg[i][j], nslicez);
364 snew(sk_fravg[i][j], nslicez);
369 find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0],
370 &sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
371 for (i = 0; i < *nslicex; i++)
373 for (j = 0; j < *nslicey; j++)
375 for (k = 0; k < nslicez; k++)
377 sk_fravg[i][j][k] += sk_grid[i][j][k]/tblock;
378 sg_fravg[i][j][k] += sg_grid[i][j][k]/tblock;
385 if (framenr%tblock == 0)
387 sk_4d[*nframes] = sk_fravg;
388 sg_4d[*nframes] = sg_fravg;
393 while (read_next_x(oenv, status, &t, x, box));
400 /*Debugging for printing out the entire order parameter meshes.*/
403 fpsg = xvgropen(sgslfn, "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
404 fpsk = xvgropen(skslfn, "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
405 for (n = 0; n < (*nframes); n++)
407 fprintf(fpsg, "%i\n", n);
408 fprintf(fpsk, "%i\n", n);
409 for (i = 0; (i < *nslicex); i++)
411 for (j = 0; j < *nslicey; j++)
413 for (k = 0; k < nslicez; k++)
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]);
426 /* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
428 /*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
429 sgintf = 0.5*(sgang1+sgang2);
432 /*Allocate memory for interface arrays; */
434 snew((*intfpos)[0], *nframes);
435 snew((*intfpos)[1], *nframes);
437 bins = (*nslicex)*(*nslicey);
440 snew(perm, nslicez); /*permutation array for sorting along normal coordinate*/
443 for (n = 0; n < *nframes; n++)
445 snew((*intfpos)[0][n], bins);
446 snew((*intfpos)[1][n], bins);
447 for (i = 0; i < *nslicex; i++)
449 for (j = 0; j < *nslicey; j++)
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*/
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;
479 static void writesurftoxpms(real ***surf, int tblocks, int xbins, int ybins, real bw, char **outfiles, int maplevels )
484 real **profile1, **profile2;
485 real max1, max2, min1, min2, *xticks, *yticks;
486 t_rgb lo = {1, 1, 1};
487 t_rgb hi = {0, 0, 0};
488 FILE *xpmfile1, *xpmfile2;
490 /*Prepare xpm structures for output*/
492 /*Allocate memory to tick's and matrices*/
493 snew (xticks, xbins+1);
494 snew (yticks, ybins+1);
496 profile1 = mk_matrix(xbins, ybins, FALSE);
497 profile2 = mk_matrix(xbins, ybins, FALSE);
499 for (i = 0; i < xbins+1; i++)
503 for (j = 0; j < ybins+1; j++)
508 xpmfile1 = gmx_ffopen(outfiles[0], "w");
509 xpmfile2 = gmx_ffopen(outfiles[1], "w");
512 min1 = min2 = 1000.00;
514 for (n = 0; n < tblocks; n++)
516 sprintf(numbuf, "%5d", n);
517 /*Filling matrices for inclusion in xpm-files*/
518 for (i = 0; i < xbins; i++)
520 for (j = 0; j < ybins; j++)
522 profile1[i][j] = (surf[0][n][j+ybins*i]);
523 profile2[i][j] = (surf[1][n][j+ybins*i]);
524 /*Finding max and min values*/
525 if (profile1[i][j] > max1)
527 max1 = profile1[i][j];
529 if (profile1[i][j] < min1)
531 min1 = profile1[i][j];
533 if (profile2[i][j] > max2)
535 max2 = profile2[i][j];
537 if (profile2[i][j] < min2)
539 min2 = profile2[i][j];
544 write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
545 write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
548 gmx_ffclose(xpmfile1);
549 gmx_ffclose(xpmfile2);
560 static void writeraw(real ***surf, int tblocks, int xbins, int ybins, char **fnms)
565 raw1 = gmx_ffopen(fnms[0], "w");
566 raw2 = gmx_ffopen(fnms[1], "w");
567 fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
568 fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
569 for (n = 0; n < tblocks; n++)
571 fprintf(raw1, "%5d\n", n);
572 fprintf(raw2, "%5d\n", n);
573 for (i = 0; i < xbins; i++)
575 for (j = 0; j < ybins; j++)
577 fprintf(raw1, "%i %i %8.5f\n", i, j, (surf[0][n][j+ybins*i]));
578 fprintf(raw2, "%i %i %8.5f\n", i, j, (surf[1][n][j+ybins*i]));
589 int gmx_hydorder(int argc, char *argv[])
591 static const char *desc[] = {
592 "[THISMODULE] computes the tetrahedrality order parameters around a ",
593 "given atom. Both angle an distance order parameters are calculated. See",
594 "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
595 "for more details.[PAR]"
596 "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
597 "with 2 phases in the box gives the user the option to define a 2D interface in time",
598 "separating the faces by specifying parameters [TT]-sgang1[tt] and",
599 "[TT]-sgang2[tt] (it is important to select these judiciously)."
603 static int nsttblock = 1;
604 static int nlevels = 100;
605 static real binwidth = 1.0; /* binwidth in mesh */
607 static real sg2 = 1; /* order parameters for bulk phases */
608 static gmx_bool bFourier = FALSE;
609 static gmx_bool bRawOut = FALSE;
610 int frames, xslices, yslices; /* Dimensions of interface arrays*/
611 real ***intfpos; /* Interface arrays (intfnr,t,xy) -potentially large */
612 static char *normal_axis[] = { NULL, "z", "x", "y", NULL };
615 { "-d", FALSE, etENUM, {normal_axis},
616 "Direction of the normal on the membrane" },
617 { "-bw", FALSE, etREAL, {&binwidth},
618 "Binwidth of box mesh" },
619 { "-sgang1", FALSE, etREAL, {&sg1},
620 "tetrahedral angle parameter in Phase 1 (bulk)" },
621 { "-sgang2", FALSE, etREAL, {&sg2},
622 "tetrahedral angle parameter in Phase 2 (bulk)" },
623 { "-tblock", FALSE, etINT, {&nsttblock},
624 "Number of frames in one time-block average"},
625 { "-nlevel", FALSE, etINT, {&nlevels},
626 "Number of Height levels in 2D - XPixMaps"}
629 t_filenm fnm[] = { /* files for g_order */
630 { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
631 { efNDX, "-n", NULL, ffREAD }, /* index file */
632 { efTPX, "-s", NULL, ffREAD }, /* topology file */
633 { efXPM, "-o", "intf", ffWRMULT}, /* XPM- surface maps */
634 { efOUT, "-or", "raw", ffOPTWRMULT }, /* xvgr output file */
635 { efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
637 #define NFILE asize(fnm)
640 const char *ndxfnm, *tpsfnm, *trxfnm;
641 char **spectra, **intfn, **raw;
642 int nfspect, nfxpm, nfraw;
645 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
646 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
650 bFourier = opt2bSet("-Spect", NFILE, fnm);
651 bRawOut = opt2bSet("-or", NFILE, fnm);
655 gmx_fatal(FARGS, "Can not have binwidth < 0");
658 ndxfnm = ftp2fn(efNDX, NFILE, fnm);
659 tpsfnm = ftp2fn(efTPX, NFILE, fnm);
660 trxfnm = ftp2fn(efTRX, NFILE, fnm);
663 if (strcmp(normal_axis[0], "x") == 0)
667 else if (strcmp(normal_axis[0], "y") == 0)
671 else if (strcmp(normal_axis[0], "z") == 0)
677 gmx_fatal(FARGS, "Invalid axis, use x, y or z");
683 fprintf(stderr, "Taking x axis as normal to the membrane\n");
686 fprintf(stderr, "Taking y axis as normal to the membrane\n");
689 fprintf(stderr, "Taking z axis as normal to the membrane\n");
693 /* tetraheder order parameter */
694 /* If either of the options is set we compute both */
695 nfxpm = opt2fns(&intfn, "-o", NFILE, fnm);
698 gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
700 calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
701 writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
705 nfspect = opt2fns(&spectra, "-Spect", NFILE, fnm);
708 gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfspect);
710 powerspectavg(intfpos, frames, xslices, yslices, spectra);
715 nfraw = opt2fns(&raw, "-or", NFILE, fnm);
718 gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfraw);
720 writeraw(intfpos, frames, xslices, yslices, raw);