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41 #include "gromacs/commandline/pargs.h"
42 #include "gromacs/fileio/matio.h"
43 #include "gromacs/fileio/tpxio.h"
44 #include "gromacs/fileio/trxio.h"
45 #include "gromacs/fileio/xvgr.h"
46 #include "gromacs/gmxana/correl.h"
47 #include "gromacs/gmxana/geminate.h"
48 #include "gromacs/gmxana/gmx_ana.h"
49 #include "gromacs/gmxana/gstat.h"
50 #include "gromacs/legacyheaders/copyrite.h"
51 #include "gromacs/legacyheaders/macros.h"
52 #include "gromacs/legacyheaders/txtdump.h"
53 #include "gromacs/legacyheaders/viewit.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/pbcutil/pbc.h"
57 #include "gromacs/topology/index.h"
58 #include "gromacs/utility/cstringutil.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/utility/gmxomp.h"
62 #include "gromacs/utility/smalloc.h"
66 /*#define HAVE_NN_LOOPS*/
68 typedef short int t_E;
71 typedef int t_hx[max_hx];
72 #define NRHXTYPES max_hx
73 const char *hxtypenames[NRHXTYPES] =
74 {"n-n", "n-n+1", "n-n+2", "n-n+3", "n-n+4", "n-n+5", "n-n>6"};
78 #define MASTER_THREAD_ONLY(threadNr) ((threadNr) == 0)
80 #define MASTER_THREAD_ONLY(threadNr) ((threadNr) == (threadNr))
83 /* -----------------------------------------*/
89 hbNo, hbDist, hbHB, hbNR, hbR2
92 noDA, ACC, DON, DA, INGROUP
95 NN_NULL, NN_NONE, NN_BINARY, NN_1_over_r3, NN_dipole, NN_NR
98 static const char *grpnames[grNR] = {"0", "1", "I" };
100 static gmx_bool bDebug = FALSE;
105 #define HB_YESINS HB_YES|HB_INS
109 #define ISHB(h) (((h) & 2) == 2)
110 #define ISDIST(h) (((h) & 1) == 1)
111 #define ISDIST2(h) (((h) & 4) == 4)
112 #define ISACC(h) (((h) & 1) == 1)
113 #define ISDON(h) (((h) & 2) == 2)
114 #define ISINGRP(h) (((h) & 4) == 4)
127 typedef int t_icell[grNR];
128 typedef atom_id h_id[MAXHYDRO];
131 int history[MAXHYDRO];
132 /* Has this hbond existed ever? If so as hbDist or hbHB or both.
133 * Result is stored as a bitmap (1 = hbDist) || (2 = hbHB)
135 /* Bitmask array which tells whether a hbond is present
136 * at a given time. Either of these may be NULL
138 int n0; /* First frame a HB was found */
139 int nframes, maxframes; /* Amount of frames in this hbond */
142 /* See Xu and Berne, JPCB 105 (2001), p. 11929. We define the
143 * function g(t) = [1-h(t)] H(t) where H(t) is one when the donor-
144 * acceptor distance is less than the user-specified distance (typically
151 atom_id *acc; /* Atom numbers of the acceptors */
152 int *grp; /* Group index */
153 int *aptr; /* Map atom number to acceptor index */
158 int *don; /* Atom numbers of the donors */
159 int *grp; /* Group index */
160 int *dptr; /* Map atom number to donor index */
161 int *nhydro; /* Number of hydrogens for each donor */
162 h_id *hydro; /* The atom numbers of the hydrogens */
163 h_id *nhbonds; /* The number of HBs per H at current */
166 /* Tune this to match memory requirements. It should be a signed integer type, e.g. signed char.*/
170 int len; /* The length of frame and p. */
171 int *frame; /* The frames at which transitio*/
176 /* Periodicity history. Used for the reversible geminate recombination. */
177 t_pShift **pHist; /* The periodicity of every hbond in t_hbdata->hbmap:
178 * pHist[d][a]. We can safely assume that the same
179 * periodic shift holds for all hydrogens of a da-pair.
181 * Nowadays it only stores TRANSITIONS, and not the shift at every frame.
182 * That saves a LOT of memory, an hopefully kills a mysterious bug where
183 * pHist gets contaminated. */
185 PSTYPE nper; /* The length of p2i */
186 ivec *p2i; /* Maps integer to periodic shift for a pair.*/
187 matrix P; /* Projection matrix to find the box shifts. */
188 int gemtype; /* enumerated type */
193 int *Etot; /* Total energy for each frame */
194 t_E ****E; /* Energy estimate for [d][a][h][frame-n0] */
198 gmx_bool bHBmap, bDAnr, bGem;
200 /* The following arrays are nframes long */
201 int nframes, max_frames, maxhydro;
207 /* These structures are initialized from the topology at start up */
210 /* This holds a matrix with all possible hydrogen bonds */
216 /* For parallelization reasons this will have to be a pointer.
217 * Otherwise discrepancies may arise between the periodicity data
218 * seen by different threads. */
222 static void clearPshift(t_pShift *pShift)
227 sfree(pShift->frame);
232 static void calcBoxProjection(matrix B, matrix P)
234 const int vp[] = {XX, YY, ZZ};
239 for (i = 0; i < 3; i++)
242 for (j = 0; j < 3; j++)
245 U[m][n] = i == j ? 1 : 0;
249 for (i = 0; i < 3; i++)
252 mvmul(M, U[m], P[m]);
257 static void calcBoxDistance(matrix P, rvec d, ivec ibd)
259 /* returns integer distance in box coordinates.
260 * P is the projection matrix from cartesian coordinates
261 * obtained with calcBoxProjection(). */
265 /* extend it by 0.5 in all directions since (int) rounds toward 0.*/
266 for (i = 0; i < 3; i++)
268 bd[i] = bd[i] + (bd[i] < 0 ? -0.5 : 0.5);
270 ibd[XX] = (int)bd[XX];
271 ibd[YY] = (int)bd[YY];
272 ibd[ZZ] = (int)bd[ZZ];
275 /* Changed argument 'bMerge' into 'oneHB' below,
276 * since -contact should cause maxhydro to be 1,
278 * - Erik Marklund May 29, 2006
281 static PSTYPE periodicIndex(ivec r, t_gemPeriod *per, gmx_bool daSwap)
283 /* Try to merge hbonds on the fly. That means that if the
284 * acceptor and donor are mergable, then:
285 * 1) store the hb-info so that acceptor id > donor id,
286 * 2) add the periodic shift in pairs, so that [-x,-y,-z] is
287 * stored in per.p2i[] whenever acceptor id < donor id.
288 * Note that [0,0,0] should already be the first element of per.p2i
289 * by the time this function is called. */
291 /* daSwap is TRUE if the donor and acceptor were swapped.
292 * If so, then the negative vector should be used. */
295 if (per->p2i == NULL || per->nper == 0)
297 gmx_fatal(FARGS, "'per' not initialized properly.");
299 for (i = 0; i < per->nper; i++)
301 if (r[XX] == per->p2i[i][XX] &&
302 r[YY] == per->p2i[i][YY] &&
303 r[ZZ] == per->p2i[i][ZZ])
308 /* Not found apparently. Add it to the list! */
309 /* printf("New shift found: %i,%i,%i\n",r[XX],r[YY],r[ZZ]); */
315 fprintf(stderr, "p2i not initialized. This shouldn't happen!\n");
320 srenew(per->p2i, per->nper+2);
322 copy_ivec(r, per->p2i[per->nper]);
325 /* Add the mirror too. It's rather likely that it'll be needed. */
326 per->p2i[per->nper][XX] = -r[XX];
327 per->p2i[per->nper][YY] = -r[YY];
328 per->p2i[per->nper][ZZ] = -r[ZZ];
331 return per->nper - 1 - (daSwap ? 0 : 1);
334 static t_hbdata *mk_hbdata(gmx_bool bHBmap, gmx_bool bDAnr, gmx_bool oneHB, gmx_bool bGem, int gemmode)
339 hb->wordlen = 8*sizeof(unsigned int);
349 hb->maxhydro = MAXHYDRO;
352 hb->per->gemtype = bGem ? gemmode : 0;
357 static void mk_hbmap(t_hbdata *hb)
361 snew(hb->hbmap, hb->d.nrd);
362 for (i = 0; (i < hb->d.nrd); i++)
364 snew(hb->hbmap[i], hb->a.nra);
365 if (hb->hbmap[i] == NULL)
367 gmx_fatal(FARGS, "Could not allocate enough memory for hbmap");
369 for (j = 0; (j > hb->a.nra); j++)
371 hb->hbmap[i][j] = NULL;
376 /* Consider redoing pHist so that is only stores transitions between
377 * periodicities and not the periodicity for all frames. This eats heaps of memory. */
378 static void mk_per(t_hbdata *hb)
383 snew(hb->per->pHist, hb->d.nrd);
384 for (i = 0; i < hb->d.nrd; i++)
386 snew(hb->per->pHist[i], hb->a.nra);
387 if (hb->per->pHist[i] == NULL)
389 gmx_fatal(FARGS, "Could not allocate enough memory for per->pHist");
391 for (j = 0; j < hb->a.nra; j++)
393 clearPshift(&(hb->per->pHist[i][j]));
396 /* add the [0,0,0] shift to element 0 of p2i. */
397 snew(hb->per->p2i, 1);
398 clear_ivec(hb->per->p2i[0]);
404 static void mk_hbEmap (t_hbdata *hb, int n0)
409 snew(hb->hbE.E, hb->d.nrd);
410 for (i = 0; i < hb->d.nrd; i++)
412 snew(hb->hbE.E[i], hb->a.nra);
413 for (j = 0; j < hb->a.nra; j++)
415 snew(hb->hbE.E[i][j], MAXHYDRO);
416 for (k = 0; k < MAXHYDRO; k++)
418 hb->hbE.E[i][j][k] = NULL;
425 static void free_hbEmap (t_hbdata *hb)
428 for (i = 0; i < hb->d.nrd; i++)
430 for (j = 0; j < hb->a.nra; j++)
432 for (k = 0; k < MAXHYDRO; k++)
434 sfree(hb->hbE.E[i][j][k]);
436 sfree(hb->hbE.E[i][j]);
444 static void addFramesNN(t_hbdata *hb, int frame)
447 #define DELTAFRAMES_HBE 10
449 int d, a, h, nframes;
451 if (frame >= hb->hbE.nframes)
453 nframes = hb->hbE.nframes + DELTAFRAMES_HBE;
454 srenew(hb->hbE.Etot, nframes);
456 for (d = 0; d < hb->d.nrd; d++)
458 for (a = 0; a < hb->a.nra; a++)
460 for (h = 0; h < hb->d.nhydro[d]; h++)
462 srenew(hb->hbE.E[d][a][h], nframes);
467 hb->hbE.nframes += DELTAFRAMES_HBE;
471 static t_E calcHbEnergy(int d, int a, int h, rvec x[], t_EEst EEst,
472 matrix box, rvec hbox, t_donors *donors)
477 * alpha - angle between dipoles
478 * x[] - atomic positions
479 * EEst - the type of energy estimate (see enum in hbplugin.h)
480 * box - the box vectors \
481 * hbox - half box lengths _These two are only needed for the pbc correction
486 rvec dipole[2], xmol[3], xmean[2];
492 /* Self-interaction */
499 /* This is a simple binary existence function that sets E=1 whenever
500 * the distance between the oxygens is equal too or less than 0.35 nm.
502 rvec_sub(x[d], x[a], dist);
503 pbc_correct_gem(dist, box, hbox);
504 if (norm(dist) <= 0.35)
515 /* Negative potential energy of a dipole.
516 * E = -cos(alpha) * 1/r^3 */
518 copy_rvec(x[d], xmol[0]); /* donor */
519 copy_rvec(x[donors->hydro[donors->dptr[d]][0]], xmol[1]); /* hydrogen */
520 copy_rvec(x[donors->hydro[donors->dptr[d]][1]], xmol[2]); /* hydrogen */
522 svmul(15.9994*(1/1.008), xmol[0], xmean[0]);
523 rvec_inc(xmean[0], xmol[1]);
524 rvec_inc(xmean[0], xmol[2]);
525 for (i = 0; i < 3; i++)
527 xmean[0][i] /= (15.9994 + 1.008 + 1.008)/1.008;
530 /* Assumes that all acceptors are also donors. */
531 copy_rvec(x[a], xmol[0]); /* acceptor */
532 copy_rvec(x[donors->hydro[donors->dptr[a]][0]], xmol[1]); /* hydrogen */
533 copy_rvec(x[donors->hydro[donors->dptr[a]][1]], xmol[2]); /* hydrogen */
536 svmul(15.9994*(1/1.008), xmol[0], xmean[1]);
537 rvec_inc(xmean[1], xmol[1]);
538 rvec_inc(xmean[1], xmol[2]);
539 for (i = 0; i < 3; i++)
541 xmean[1][i] /= (15.9994 + 1.008 + 1.008)/1.008;
544 rvec_sub(xmean[0], xmean[1], dist);
545 pbc_correct_gem(dist, box, hbox);
548 realE = pow(r, -3.0);
549 E = (t_E)(SCALEFACTOR_E * realE);
553 /* Negative potential energy of a (unpolarizable) dipole.
554 * E = -cos(alpha) * 1/r^3 */
555 clear_rvec(dipole[1]);
556 clear_rvec(dipole[0]);
558 copy_rvec(x[d], xmol[0]); /* donor */
559 copy_rvec(x[donors->hydro[donors->dptr[d]][0]], xmol[1]); /* hydrogen */
560 copy_rvec(x[donors->hydro[donors->dptr[d]][1]], xmol[2]); /* hydrogen */
562 rvec_inc(dipole[0], xmol[1]);
563 rvec_inc(dipole[0], xmol[2]);
564 for (i = 0; i < 3; i++)
568 rvec_dec(dipole[0], xmol[0]);
570 svmul(15.9994*(1/1.008), xmol[0], xmean[0]);
571 rvec_inc(xmean[0], xmol[1]);
572 rvec_inc(xmean[0], xmol[2]);
573 for (i = 0; i < 3; i++)
575 xmean[0][i] /= (15.9994 + 1.008 + 1.008)/1.008;
578 /* Assumes that all acceptors are also donors. */
579 copy_rvec(x[a], xmol[0]); /* acceptor */
580 copy_rvec(x[donors->hydro[donors->dptr[a]][0]], xmol[1]); /* hydrogen */
581 copy_rvec(x[donors->hydro[donors->dptr[a]][2]], xmol[2]); /* hydrogen */
584 rvec_inc(dipole[1], xmol[1]);
585 rvec_inc(dipole[1], xmol[2]);
586 for (i = 0; i < 3; i++)
590 rvec_dec(dipole[1], xmol[0]);
592 svmul(15.9994*(1/1.008), xmol[0], xmean[1]);
593 rvec_inc(xmean[1], xmol[1]);
594 rvec_inc(xmean[1], xmol[2]);
595 for (i = 0; i < 3; i++)
597 xmean[1][i] /= (15.9994 + 1.008 + 1.008)/1.008;
600 rvec_sub(xmean[0], xmean[1], dist);
601 pbc_correct_gem(dist, box, hbox);
604 double cosalpha = cos_angle(dipole[0], dipole[1]);
605 realE = cosalpha * pow(r, -3.0);
606 E = (t_E)(SCALEFACTOR_E * realE);
610 printf("Can't do that type of energy estimate: %i\n.", EEst);
617 static void storeHbEnergy(t_hbdata *hb, int d, int a, int h, t_E E, int frame)
619 /* hb - hbond data structure
623 E - estimate of the energy
624 frame - the current frame.
627 /* Store the estimated energy */
633 hb->hbE.E[d][a][h][frame] = E;
637 hb->hbE.Etot[frame] += E;
640 #endif /* HAVE_NN_LOOPS */
643 /* Finds -v[] in the periodicity index */
644 static int findMirror(PSTYPE p, ivec v[], PSTYPE nper)
648 for (i = 0; i < nper; i++)
650 if (v[i][XX] == -(v[p][XX]) &&
651 v[i][YY] == -(v[p][YY]) &&
652 v[i][ZZ] == -(v[p][ZZ]))
657 printf("Couldn't find mirror of [%i, %i, %i], index \n",
665 static void add_frames(t_hbdata *hb, int nframes)
669 if (nframes >= hb->max_frames)
671 hb->max_frames += 4096;
672 srenew(hb->time, hb->max_frames);
673 srenew(hb->nhb, hb->max_frames);
674 srenew(hb->ndist, hb->max_frames);
675 srenew(hb->n_bound, hb->max_frames);
676 srenew(hb->nhx, hb->max_frames);
679 srenew(hb->danr, hb->max_frames);
682 hb->nframes = nframes;
685 #define OFFSET(frame) (frame / 32)
686 #define MASK(frame) (1 << (frame % 32))
688 static void _set_hb(unsigned int hbexist[], unsigned int frame, gmx_bool bValue)
692 hbexist[OFFSET(frame)] |= MASK(frame);
696 hbexist[OFFSET(frame)] &= ~MASK(frame);
700 static gmx_bool is_hb(unsigned int hbexist[], int frame)
702 return ((hbexist[OFFSET(frame)] & MASK(frame)) != 0) ? 1 : 0;
705 static void set_hb(t_hbdata *hb, int id, int ih, int ia, int frame, int ihb)
707 unsigned int *ghptr = NULL;
711 ghptr = hb->hbmap[id][ia]->h[ih];
713 else if (ihb == hbDist)
715 ghptr = hb->hbmap[id][ia]->g[ih];
719 gmx_fatal(FARGS, "Incomprehensible iValue %d in set_hb", ihb);
722 _set_hb(ghptr, frame-hb->hbmap[id][ia]->n0, TRUE);
725 static void addPshift(t_pShift *pHist, PSTYPE p, int frame)
729 snew(pHist->frame, 1);
732 pHist->frame[0] = frame;
737 if (pHist->p[pHist->len-1] != p)
740 srenew(pHist->frame, pHist->len);
741 srenew(pHist->p, pHist->len);
742 pHist->frame[pHist->len-1] = frame;
743 pHist->p[pHist->len-1] = p;
744 } /* Otherwise, there is no transition. */
748 static PSTYPE getPshift(t_pShift pHist, int frame)
753 || (pHist.len > 0 && pHist.frame[0] > frame))
758 for (i = 0; i < pHist.len; i++)
771 /* It seems that frame is after the last periodic transition. Return the last periodicity. */
772 return pHist.p[pHist.len-1];
775 static void add_ff(t_hbdata *hbd, int id, int h, int ia, int frame, int ihb, PSTYPE p)
778 t_hbond *hb = hbd->hbmap[id][ia];
779 int maxhydro = min(hbd->maxhydro, hbd->d.nhydro[id]);
780 int wlen = hbd->wordlen;
782 gmx_bool bGem = hbd->bGem;
787 hb->maxframes = delta;
788 for (i = 0; (i < maxhydro); i++)
790 snew(hb->h[i], hb->maxframes/wlen);
791 snew(hb->g[i], hb->maxframes/wlen);
796 hb->nframes = frame-hb->n0;
797 /* We need a while loop here because hbonds may be returning
800 while (hb->nframes >= hb->maxframes)
802 n = hb->maxframes + delta;
803 for (i = 0; (i < maxhydro); i++)
805 srenew(hb->h[i], n/wlen);
806 srenew(hb->g[i], n/wlen);
807 for (j = hb->maxframes/wlen; (j < n/wlen); j++)
819 set_hb(hbd, id, h, ia, frame, ihb);
822 if (p >= hbd->per->nper)
824 gmx_fatal(FARGS, "invalid shift: p=%u, nper=%u", p, hbd->per->nper);
828 addPshift(&(hbd->per->pHist[id][ia]), p, frame);
836 static void inc_nhbonds(t_donors *ddd, int d, int h)
839 int dptr = ddd->dptr[d];
841 for (j = 0; (j < ddd->nhydro[dptr]); j++)
843 if (ddd->hydro[dptr][j] == h)
845 ddd->nhbonds[dptr][j]++;
849 if (j == ddd->nhydro[dptr])
851 gmx_fatal(FARGS, "No such hydrogen %d on donor %d\n", h+1, d+1);
855 static int _acceptor_index(t_acceptors *a, int grp, atom_id i,
856 const char *file, int line)
860 if (a->grp[ai] != grp)
864 fprintf(debug, "Acc. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n",
865 ai, a->grp[ai], grp, file, line);
874 #define acceptor_index(a, grp, i) _acceptor_index(a, grp, i, __FILE__, __LINE__)
876 static int _donor_index(t_donors *d, int grp, atom_id i, const char *file, int line)
885 if (d->grp[di] != grp)
889 fprintf(debug, "Don. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n",
890 di, d->grp[di], grp, file, line);
899 #define donor_index(d, grp, i) _donor_index(d, grp, i, __FILE__, __LINE__)
901 static gmx_bool isInterchangable(t_hbdata *hb, int d, int a, int grpa, int grpd)
903 /* g_hbond doesn't allow overlapping groups */
909 donor_index(&hb->d, grpd, a) != NOTSET
910 && acceptor_index(&hb->a, grpa, d) != NOTSET;
914 static void add_hbond(t_hbdata *hb, int d, int a, int h, int grpd, int grpa,
915 int frame, gmx_bool bMerge, int ihb, gmx_bool bContact, PSTYPE p)
918 gmx_bool daSwap = FALSE;
920 if ((id = hb->d.dptr[d]) == NOTSET)
922 gmx_fatal(FARGS, "No donor atom %d", d+1);
924 else if (grpd != hb->d.grp[id])
926 gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
927 grpd, hb->d.grp[id], d+1);
929 if ((ia = hb->a.aptr[a]) == NOTSET)
931 gmx_fatal(FARGS, "No acceptor atom %d", a+1);
933 else if (grpa != hb->a.grp[ia])
935 gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
936 grpa, hb->a.grp[ia], a+1);
942 if (isInterchangable(hb, d, a, grpd, grpa) && d > a)
943 /* Then swap identity so that the id of d is lower then that of a.
945 * This should really be redundant by now, as is_hbond() now ought to return
946 * hbNo in the cases where this conditional is TRUE. */
953 /* Now repeat donor/acc check. */
954 if ((id = hb->d.dptr[d]) == NOTSET)
956 gmx_fatal(FARGS, "No donor atom %d", d+1);
958 else if (grpd != hb->d.grp[id])
960 gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
961 grpd, hb->d.grp[id], d+1);
963 if ((ia = hb->a.aptr[a]) == NOTSET)
965 gmx_fatal(FARGS, "No acceptor atom %d", a+1);
967 else if (grpa != hb->a.grp[ia])
969 gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
970 grpa, hb->a.grp[ia], a+1);
977 /* Loop over hydrogens to find which hydrogen is in this particular HB */
978 if ((ihb == hbHB) && !bMerge && !bContact)
980 for (k = 0; (k < hb->d.nhydro[id]); k++)
982 if (hb->d.hydro[id][k] == h)
987 if (k == hb->d.nhydro[id])
989 gmx_fatal(FARGS, "Donor %d does not have hydrogen %d (a = %d)",
1001 #pragma omp critical
1003 if (hb->hbmap[id][ia] == NULL)
1005 snew(hb->hbmap[id][ia], 1);
1006 snew(hb->hbmap[id][ia]->h, hb->maxhydro);
1007 snew(hb->hbmap[id][ia]->g, hb->maxhydro);
1009 add_ff(hb, id, k, ia, frame, ihb, p);
1013 /* Strange construction with frame >=0 is a relic from old code
1014 * for selected hbond analysis. It may be necessary again if that
1015 * is made to work again.
1019 hh = hb->hbmap[id][ia]->history[k];
1025 hb->hbmap[id][ia]->history[k] = hh | 2;
1036 hb->hbmap[id][ia]->history[k] = hh | 1;
1060 if (bMerge && daSwap)
1062 h = hb->d.hydro[id][0];
1064 /* Increment number if HBonds per H */
1065 if (ihb == hbHB && !bContact)
1067 inc_nhbonds(&(hb->d), d, h);
1071 static char *mkatomname(t_atoms *atoms, int i)
1073 static char buf[32];
1076 rnr = atoms->atom[i].resind;
1077 sprintf(buf, "%4s%d%-4s",
1078 *atoms->resinfo[rnr].name, atoms->resinfo[rnr].nr, *atoms->atomname[i]);
1083 static void gen_datable(atom_id *index, int isize, unsigned char *datable, int natoms)
1085 /* Generates table of all atoms and sets the ingroup bit for atoms in index[] */
1088 for (i = 0; i < isize; i++)
1090 if (index[i] >= natoms)
1092 gmx_fatal(FARGS, "Atom has index %d larger than number of atoms %d.", index[i], natoms);
1094 datable[index[i]] |= INGROUP;
1098 static void clear_datable_grp(unsigned char *datable, int size)
1100 /* Clears group information from the table */
1102 const char mask = !(char)INGROUP;
1105 for (i = 0; i < size; i++)
1112 static void add_acc(t_acceptors *a, int ia, int grp)
1114 if (a->nra >= a->max_nra)
1117 srenew(a->acc, a->max_nra);
1118 srenew(a->grp, a->max_nra);
1120 a->grp[a->nra] = grp;
1121 a->acc[a->nra++] = ia;
1124 static void search_acceptors(t_topology *top, int isize,
1125 atom_id *index, t_acceptors *a, int grp,
1127 gmx_bool bContact, gmx_bool bDoIt, unsigned char *datable)
1133 for (i = 0; (i < isize); i++)
1137 (((*top->atoms.atomname[n])[0] == 'O') ||
1138 (bNitAcc && ((*top->atoms.atomname[n])[0] == 'N')))) &&
1139 ISINGRP(datable[n]))
1141 datable[n] |= ACC; /* set the atom's acceptor flag in datable. */
1146 snew(a->aptr, top->atoms.nr);
1147 for (i = 0; (i < top->atoms.nr); i++)
1149 a->aptr[i] = NOTSET;
1151 for (i = 0; (i < a->nra); i++)
1153 a->aptr[a->acc[i]] = i;
1157 static void add_h2d(int id, int ih, t_donors *ddd)
1161 for (i = 0; (i < ddd->nhydro[id]); i++)
1163 if (ddd->hydro[id][i] == ih)
1165 printf("Hm. This isn't the first time I found this donor (%d,%d)\n",
1170 if (i == ddd->nhydro[id])
1172 if (ddd->nhydro[id] >= MAXHYDRO)
1174 gmx_fatal(FARGS, "Donor %d has more than %d hydrogens!",
1175 ddd->don[id], MAXHYDRO);
1177 ddd->hydro[id][i] = ih;
1182 static void add_dh(t_donors *ddd, int id, int ih, int grp, unsigned char *datable)
1186 if (!datable || ISDON(datable[id]))
1188 if (ddd->dptr[id] == NOTSET) /* New donor */
1200 if (ddd->nrd >= ddd->max_nrd)
1202 ddd->max_nrd += 128;
1203 srenew(ddd->don, ddd->max_nrd);
1204 srenew(ddd->nhydro, ddd->max_nrd);
1205 srenew(ddd->hydro, ddd->max_nrd);
1206 srenew(ddd->nhbonds, ddd->max_nrd);
1207 srenew(ddd->grp, ddd->max_nrd);
1209 ddd->don[ddd->nrd] = id;
1210 ddd->nhydro[ddd->nrd] = 0;
1211 ddd->grp[ddd->nrd] = grp;
1218 add_h2d(i, ih, ddd);
1223 printf("Warning: Atom %d is not in the d/a-table!\n", id);
1227 static void search_donors(t_topology *top, int isize, atom_id *index,
1228 t_donors *ddd, int grp, gmx_bool bContact, gmx_bool bDoIt,
1229 unsigned char *datable)
1232 t_functype func_type;
1233 t_ilist *interaction;
1234 atom_id nr1, nr2, nr3;
1239 snew(ddd->dptr, top->atoms.nr);
1240 for (i = 0; (i < top->atoms.nr); i++)
1242 ddd->dptr[i] = NOTSET;
1250 for (i = 0; (i < isize); i++)
1252 datable[index[i]] |= DON;
1253 add_dh(ddd, index[i], -1, grp, datable);
1259 for (func_type = 0; (func_type < F_NRE); func_type++)
1261 interaction = &(top->idef.il[func_type]);
1262 if (func_type == F_POSRES || func_type == F_FBPOSRES)
1264 /* The ilist looks strange for posre. Bug in grompp?
1265 * We don't need posre interactions for hbonds anyway.*/
1268 for (i = 0; i < interaction->nr;
1269 i += interaction_function[top->idef.functype[interaction->iatoms[i]]].nratoms+1)
1272 if (func_type != top->idef.functype[interaction->iatoms[i]])
1274 fprintf(stderr, "Error in func_type %s",
1275 interaction_function[func_type].longname);
1279 /* check out this functype */
1280 if (func_type == F_SETTLE)
1282 nr1 = interaction->iatoms[i+1];
1283 nr2 = interaction->iatoms[i+2];
1284 nr3 = interaction->iatoms[i+3];
1286 if (ISINGRP(datable[nr1]))
1288 if (ISINGRP(datable[nr2]))
1290 datable[nr1] |= DON;
1291 add_dh(ddd, nr1, nr1+1, grp, datable);
1293 if (ISINGRP(datable[nr3]))
1295 datable[nr1] |= DON;
1296 add_dh(ddd, nr1, nr1+2, grp, datable);
1300 else if (IS_CHEMBOND(func_type))
1302 for (j = 0; j < 2; j++)
1304 nr1 = interaction->iatoms[i+1+j];
1305 nr2 = interaction->iatoms[i+2-j];
1306 if ((*top->atoms.atomname[nr1][0] == 'H') &&
1307 ((*top->atoms.atomname[nr2][0] == 'O') ||
1308 (*top->atoms.atomname[nr2][0] == 'N')) &&
1309 ISINGRP(datable[nr1]) && ISINGRP(datable[nr2]))
1311 datable[nr2] |= DON;
1312 add_dh(ddd, nr2, nr1, grp, datable);
1319 for (func_type = 0; func_type < F_NRE; func_type++)
1321 interaction = &top->idef.il[func_type];
1322 for (i = 0; i < interaction->nr;
1323 i += interaction_function[top->idef.functype[interaction->iatoms[i]]].nratoms+1)
1326 if (func_type != top->idef.functype[interaction->iatoms[i]])
1328 gmx_incons("function type in search_donors");
1331 if (interaction_function[func_type].flags & IF_VSITE)
1333 nr1 = interaction->iatoms[i+1];
1334 if (*top->atoms.atomname[nr1][0] == 'H')
1338 while (!stop && ( *top->atoms.atomname[nr2][0] == 'H'))
1349 if (!stop && ( ( *top->atoms.atomname[nr2][0] == 'O') ||
1350 ( *top->atoms.atomname[nr2][0] == 'N') ) &&
1351 ISINGRP(datable[nr1]) && ISINGRP(datable[nr2]))
1353 datable[nr2] |= DON;
1354 add_dh(ddd, nr2, nr1, grp, datable);
1364 static t_gridcell ***init_grid(gmx_bool bBox, rvec box[], real rcut, ivec ngrid)
1371 for (i = 0; i < DIM; i++)
1373 ngrid[i] = (box[i][i]/(1.2*rcut));
1377 if (!bBox || (ngrid[XX] < 3) || (ngrid[YY] < 3) || (ngrid[ZZ] < 3) )
1379 for (i = 0; i < DIM; i++)
1386 printf("\nWill do grid-seach on %dx%dx%d grid, rcut=%g\n",
1387 ngrid[XX], ngrid[YY], ngrid[ZZ], rcut);
1389 snew(grid, ngrid[ZZ]);
1390 for (z = 0; z < ngrid[ZZ]; z++)
1392 snew((grid)[z], ngrid[YY]);
1393 for (y = 0; y < ngrid[YY]; y++)
1395 snew((grid)[z][y], ngrid[XX]);
1401 static void reset_nhbonds(t_donors *ddd)
1405 for (i = 0; (i < ddd->nrd); i++)
1407 for (j = 0; (j < MAXHH); j++)
1409 ddd->nhbonds[i][j] = 0;
1414 void pbc_correct_gem(rvec dx, matrix box, rvec hbox);
1416 static void build_grid(t_hbdata *hb, rvec x[], rvec xshell,
1417 gmx_bool bBox, matrix box, rvec hbox,
1418 real rcut, real rshell,
1419 ivec ngrid, t_gridcell ***grid)
1421 int i, m, gr, xi, yi, zi, nr;
1424 rvec invdelta, dshell, xtemp = {0, 0, 0};
1426 gmx_bool bDoRshell, bInShell, bAcc;
1431 bDoRshell = (rshell > 0);
1432 rshell2 = sqr(rshell);
1435 #define DBB(x) if (debug && bDebug) fprintf(debug, "build_grid, line %d, %s = %d\n", __LINE__,#x, x)
1437 for (m = 0; m < DIM; m++)
1439 hbox[m] = box[m][m]*0.5;
1442 invdelta[m] = ngrid[m]/box[m][m];
1443 if (1/invdelta[m] < rcut)
1445 gmx_fatal(FARGS, "Your computational box has shrunk too much.\n"
1446 "%s can not handle this situation, sorry.\n",
1459 /* resetting atom counts */
1460 for (gr = 0; (gr < grNR); gr++)
1462 for (zi = 0; zi < ngrid[ZZ]; zi++)
1464 for (yi = 0; yi < ngrid[YY]; yi++)
1466 for (xi = 0; xi < ngrid[XX]; xi++)
1468 grid[zi][yi][xi].d[gr].nr = 0;
1469 grid[zi][yi][xi].a[gr].nr = 0;
1475 /* put atoms in grid cells */
1476 for (bAcc = FALSE; (bAcc <= TRUE); bAcc++)
1489 for (i = 0; (i < nr); i++)
1491 /* check if we are inside the shell */
1492 /* if bDoRshell=FALSE then bInShell=TRUE always */
1497 rvec_sub(x[ad[i]], xshell, dshell);
1500 if (FALSE && !hb->bGem)
1502 for (m = DIM-1; m >= 0 && bInShell; m--)
1504 if (dshell[m] < -hbox[m])
1506 rvec_inc(dshell, box[m]);
1508 else if (dshell[m] >= hbox[m])
1510 dshell[m] -= 2*hbox[m];
1512 /* if we're outside the cube, we're outside the sphere also! */
1513 if ( (dshell[m] > rshell) || (-dshell[m] > rshell) )
1521 gmx_bool bDone = FALSE;
1525 for (m = DIM-1; m >= 0 && bInShell; m--)
1527 if (dshell[m] < -hbox[m])
1530 rvec_inc(dshell, box[m]);
1532 if (dshell[m] >= hbox[m])
1535 dshell[m] -= 2*hbox[m];
1539 for (m = DIM-1; m >= 0 && bInShell; m--)
1541 /* if we're outside the cube, we're outside the sphere also! */
1542 if ( (dshell[m] > rshell) || (-dshell[m] > rshell) )
1549 /* if we're inside the cube, check if we're inside the sphere */
1552 bInShell = norm2(dshell) < rshell2;
1562 copy_rvec(x[ad[i]], xtemp);
1564 pbc_correct_gem(x[ad[i]], box, hbox);
1566 for (m = DIM-1; m >= 0; m--)
1568 if (TRUE || !hb->bGem)
1570 /* put atom in the box */
1571 while (x[ad[i]][m] < 0)
1573 rvec_inc(x[ad[i]], box[m]);
1575 while (x[ad[i]][m] >= box[m][m])
1577 rvec_dec(x[ad[i]], box[m]);
1580 /* determine grid index of atom */
1581 grididx[m] = x[ad[i]][m]*invdelta[m];
1582 grididx[m] = (grididx[m]+ngrid[m]) % ngrid[m];
1586 copy_rvec(xtemp, x[ad[i]]); /* copy back */
1591 range_check(gx, 0, ngrid[XX]);
1592 range_check(gy, 0, ngrid[YY]);
1593 range_check(gz, 0, ngrid[ZZ]);
1597 /* add atom to grid cell */
1600 newgrid = &(grid[gz][gy][gx].a[gr]);
1604 newgrid = &(grid[gz][gy][gx].d[gr]);
1606 if (newgrid->nr >= newgrid->maxnr)
1608 newgrid->maxnr += 10;
1609 DBB(newgrid->maxnr);
1610 srenew(newgrid->atoms, newgrid->maxnr);
1613 newgrid->atoms[newgrid->nr] = ad[i];
1621 static void count_da_grid(ivec ngrid, t_gridcell ***grid, t_icell danr)
1625 for (gr = 0; (gr < grNR); gr++)
1628 for (zi = 0; zi < ngrid[ZZ]; zi++)
1630 for (yi = 0; yi < ngrid[YY]; yi++)
1632 for (xi = 0; xi < ngrid[XX]; xi++)
1634 danr[gr] += grid[zi][yi][xi].d[gr].nr;
1642 * Without a box, the grid is 1x1x1, so all loops are 1 long.
1643 * With a rectangular box (bTric==FALSE) all loops are 3 long.
1644 * With a triclinic box all loops are 3 long, except when a cell is
1645 * located next to one of the box edges which is not parallel to the
1646 * x/y-plane, in that case all cells in a line or layer are searched.
1647 * This could be implemented slightly more efficient, but the code
1648 * would get much more complicated.
1650 static gmx_inline gmx_bool grid_loop_begin(int n, int x, gmx_bool bTric, gmx_bool bEdge)
1652 return ((n == 1) ? x : bTric && bEdge ? 0 : (x-1));
1654 static gmx_inline gmx_bool grid_loop_end(int n, int x, gmx_bool bTric, gmx_bool bEdge)
1656 return ((n == 1) ? x : bTric && bEdge ? (n-1) : (x+1));
1658 static gmx_inline int grid_mod(int j, int n)
1663 static void dump_grid(FILE *fp, ivec ngrid, t_gridcell ***grid)
1665 int gr, x, y, z, sum[grNR];
1667 fprintf(fp, "grid %dx%dx%d\n", ngrid[XX], ngrid[YY], ngrid[ZZ]);
1668 for (gr = 0; gr < grNR; gr++)
1671 fprintf(fp, "GROUP %d (%s)\n", gr, grpnames[gr]);
1672 for (z = 0; z < ngrid[ZZ]; z += 2)
1674 fprintf(fp, "Z=%d,%d\n", z, z+1);
1675 for (y = 0; y < ngrid[YY]; y++)
1677 for (x = 0; x < ngrid[XX]; x++)
1679 fprintf(fp, "%3d", grid[x][y][z].d[gr].nr);
1680 sum[gr] += grid[z][y][x].d[gr].nr;
1681 fprintf(fp, "%3d", grid[x][y][z].a[gr].nr);
1682 sum[gr] += grid[z][y][x].a[gr].nr;
1686 if ( (z+1) < ngrid[ZZ])
1688 for (x = 0; x < ngrid[XX]; x++)
1690 fprintf(fp, "%3d", grid[z+1][y][x].d[gr].nr);
1691 sum[gr] += grid[z+1][y][x].d[gr].nr;
1692 fprintf(fp, "%3d", grid[z+1][y][x].a[gr].nr);
1693 sum[gr] += grid[z+1][y][x].a[gr].nr;
1700 fprintf(fp, "TOTALS:");
1701 for (gr = 0; gr < grNR; gr++)
1703 fprintf(fp, " %d=%d", gr, sum[gr]);
1708 /* New GMX record! 5 * in a row. Congratulations!
1709 * Sorry, only four left.
1711 static void free_grid(ivec ngrid, t_gridcell ****grid)
1714 t_gridcell ***g = *grid;
1716 for (z = 0; z < ngrid[ZZ]; z++)
1718 for (y = 0; y < ngrid[YY]; y++)
1728 void pbc_correct_gem(rvec dx, matrix box, rvec hbox)
1731 gmx_bool bDone = FALSE;
1735 for (m = DIM-1; m >= 0; m--)
1737 if (dx[m] < -hbox[m])
1740 rvec_inc(dx, box[m]);
1742 if (dx[m] >= hbox[m])
1745 rvec_dec(dx, box[m]);
1751 /* Added argument r2cut, changed contact and implemented
1752 * use of second cut-off.
1753 * - Erik Marklund, June 29, 2006
1755 static int is_hbond(t_hbdata *hb, int grpd, int grpa, int d, int a,
1756 real rcut, real r2cut, real ccut,
1757 rvec x[], gmx_bool bBox, matrix box, rvec hbox,
1758 real *d_ha, real *ang, gmx_bool bDA, int *hhh,
1759 gmx_bool bContact, gmx_bool bMerge, PSTYPE *p)
1761 int h, hh, id, ja, ihb;
1762 rvec r_da, r_ha, r_dh, r = {0, 0, 0};
1764 real rc2, r2c2, rda2, rha2, ca;
1765 gmx_bool HAinrange = FALSE; /* If !bDA. Needed for returning hbDist in a correct way. */
1766 gmx_bool daSwap = FALSE;
1773 if (((id = donor_index(&hb->d, grpd, d)) == NOTSET) ||
1774 ((ja = acceptor_index(&hb->a, grpa, a)) == NOTSET))
1782 rvec_sub(x[d], x[a], r_da);
1783 /* Insert projection code here */
1785 if (bMerge && d > a && isInterchangable(hb, d, a, grpd, grpa))
1787 /* Then this hbond/contact will be found again, or it has already been found. */
1792 if (d > a && bMerge && isInterchangable(hb, d, a, grpd, grpa)) /* acceptor is also a donor and vice versa? */
1793 { /* return hbNo; */
1794 daSwap = TRUE; /* If so, then their history should be filed with donor and acceptor swapped. */
1798 copy_rvec(r_da, r); /* Save this for later */
1799 pbc_correct_gem(r_da, box, hbox);
1803 pbc_correct_gem(r_da, box, hbox);
1806 rda2 = iprod(r_da, r_da);
1810 if (daSwap && grpa == grpd)
1818 calcBoxDistance(hb->per->P, r, ri);
1819 *p = periodicIndex(ri, hb->per, daSwap); /* find (or add) periodicity index. */
1823 else if (rda2 < r2c2)
1834 if (bDA && (rda2 > rc2))
1839 for (h = 0; (h < hb->d.nhydro[id]); h++)
1841 hh = hb->d.hydro[id][h];
1845 rvec_sub(x[hh], x[a], r_ha);
1848 pbc_correct_gem(r_ha, box, hbox);
1850 rha2 = iprod(r_ha, r_ha);
1855 calcBoxDistance(hb->per->P, r, ri);
1856 *p = periodicIndex(ri, hb->per, daSwap); /* find periodicity index. */
1859 if (bDA || (!bDA && (rha2 <= rc2)))
1861 rvec_sub(x[d], x[hh], r_dh);
1864 pbc_correct_gem(r_dh, box, hbox);
1871 ca = cos_angle(r_dh, r_da);
1872 /* if angle is smaller, cos is larger */
1876 *d_ha = sqrt(bDA ? rda2 : rha2);
1882 if (bDA || (!bDA && HAinrange))
1892 /* Fixed previously undiscovered bug in the merge
1893 code, where the last frame of each hbond disappears.
1894 - Erik Marklund, June 1, 2006 */
1895 /* Added the following arguments:
1896 * ptmp[] - temporary periodicity hisory
1897 * a1 - identity of first acceptor/donor
1898 * a2 - identity of second acceptor/donor
1899 * - Erik Marklund, FEB 20 2010 */
1901 /* Merging is now done on the fly, so do_merge is most likely obsolete now.
1902 * Will do some more testing before removing the function entirely.
1903 * - Erik Marklund, MAY 10 2010 */
1904 static void do_merge(t_hbdata *hb, int ntmp,
1905 unsigned int htmp[], unsigned int gtmp[], PSTYPE ptmp[],
1906 t_hbond *hb0, t_hbond *hb1, int a1, int a2)
1908 /* Here we need to make sure we're treating periodicity in
1909 * the right way for the geminate recombination kinetics. */
1911 int m, mm, n00, n01, nn0, nnframes;
1915 /* Decide where to start from when merging */
1918 nn0 = min(n00, n01);
1919 nnframes = max(n00 + hb0->nframes, n01 + hb1->nframes) - nn0;
1920 /* Initiate tmp arrays */
1921 for (m = 0; (m < ntmp); m++)
1927 /* Fill tmp arrays with values due to first HB */
1928 /* Once again '<' had to be replaced with '<='
1929 to catch the last frame in which the hbond
1931 - Erik Marklund, June 1, 2006 */
1932 for (m = 0; (m <= hb0->nframes); m++)
1935 htmp[mm] = is_hb(hb0->h[0], m);
1938 pm = getPshift(hb->per->pHist[a1][a2], m+hb0->n0);
1939 if (pm > hb->per->nper)
1941 gmx_fatal(FARGS, "Illegal shift!");
1945 ptmp[mm] = pm; /*hb->per->pHist[a1][a2][m];*/
1949 /* If we're doing geminate recompbination we usually don't need the distances.
1950 * Let's save some memory and time. */
1951 if (TRUE || !hb->bGem || hb->per->gemtype == gemAD)
1953 for (m = 0; (m <= hb0->nframes); m++)
1956 gtmp[mm] = is_hb(hb0->g[0], m);
1960 for (m = 0; (m <= hb1->nframes); m++)
1963 htmp[mm] = htmp[mm] || is_hb(hb1->h[0], m);
1964 gtmp[mm] = gtmp[mm] || is_hb(hb1->g[0], m);
1965 if (hb->bGem /* && ptmp[mm] != 0 */)
1968 /* If this hbond has been seen before with donor and acceptor swapped,
1969 * then we need to find the mirrored (*-1) periodicity vector to truely
1970 * merge the hbond history. */
1971 pm = findMirror(getPshift(hb->per->pHist[a2][a1], m+hb1->n0), hb->per->p2i, hb->per->nper);
1972 /* Store index of mirror */
1973 if (pm > hb->per->nper)
1975 gmx_fatal(FARGS, "Illegal shift!");
1980 /* Reallocate target array */
1981 if (nnframes > hb0->maxframes)
1983 srenew(hb0->h[0], 4+nnframes/hb->wordlen);
1984 srenew(hb0->g[0], 4+nnframes/hb->wordlen);
1986 if (NULL != hb->per->pHist)
1988 clearPshift(&(hb->per->pHist[a1][a2]));
1991 /* Copy temp array to target array */
1992 for (m = 0; (m <= nnframes); m++)
1994 _set_hb(hb0->h[0], m, htmp[m]);
1995 _set_hb(hb0->g[0], m, gtmp[m]);
1998 addPshift(&(hb->per->pHist[a1][a2]), ptmp[m], m+nn0);
2002 /* Set scalar variables */
2004 hb0->maxframes = nnframes;
2007 /* Added argument bContact for nicer output.
2008 * Erik Marklund, June 29, 2006
2010 static void merge_hb(t_hbdata *hb, gmx_bool bTwo, gmx_bool bContact)
2012 int i, inrnew, indnew, j, ii, jj, m, id, ia, grp, ogrp, ntmp;
2013 unsigned int *htmp, *gtmp;
2018 indnew = hb->nrdist;
2020 /* Check whether donors are also acceptors */
2021 printf("Merging hbonds with Acceptor and Donor swapped\n");
2023 ntmp = 2*hb->max_frames;
2027 for (i = 0; (i < hb->d.nrd); i++)
2029 fprintf(stderr, "\r%d/%d", i+1, hb->d.nrd);
2031 ii = hb->a.aptr[id];
2032 for (j = 0; (j < hb->a.nra); j++)
2035 jj = hb->d.dptr[ia];
2036 if ((id != ia) && (ii != NOTSET) && (jj != NOTSET) &&
2037 (!bTwo || (bTwo && (hb->d.grp[i] != hb->a.grp[j]))))
2039 hb0 = hb->hbmap[i][j];
2040 hb1 = hb->hbmap[jj][ii];
2041 if (hb0 && hb1 && ISHB(hb0->history[0]) && ISHB(hb1->history[0]))
2043 do_merge(hb, ntmp, htmp, gtmp, ptmp, hb0, hb1, i, j);
2044 if (ISHB(hb1->history[0]))
2048 else if (ISDIST(hb1->history[0]))
2055 gmx_incons("No contact history");
2059 gmx_incons("Neither hydrogen bond nor distance");
2065 clearPshift(&(hb->per->pHist[jj][ii]));
2069 hb1->history[0] = hbNo;
2074 fprintf(stderr, "\n");
2075 printf("- Reduced number of hbonds from %d to %d\n", hb->nrhb, inrnew);
2076 printf("- Reduced number of distances from %d to %d\n", hb->nrdist, indnew);
2078 hb->nrdist = indnew;
2084 static void do_nhb_dist(FILE *fp, t_hbdata *hb, real t)
2086 int i, j, k, n_bound[MAXHH], nbtot;
2090 /* Set array to 0 */
2091 for (k = 0; (k < MAXHH); k++)
2095 /* Loop over possible donors */
2096 for (i = 0; (i < hb->d.nrd); i++)
2098 for (j = 0; (j < hb->d.nhydro[i]); j++)
2100 n_bound[hb->d.nhbonds[i][j]]++;
2103 fprintf(fp, "%12.5e", t);
2105 for (k = 0; (k < MAXHH); k++)
2107 fprintf(fp, " %8d", n_bound[k]);
2108 nbtot += n_bound[k]*k;
2110 fprintf(fp, " %8d\n", nbtot);
2113 /* Added argument bContact in do_hblife(...). Also
2114 * added support for -contact in function body.
2115 * - Erik Marklund, May 31, 2006 */
2116 /* Changed the contact code slightly.
2117 * - Erik Marklund, June 29, 2006
2119 static void do_hblife(const char *fn, t_hbdata *hb, gmx_bool bMerge, gmx_bool bContact,
2120 const output_env_t oenv)
2123 const char *leg[] = { "p(t)", "t p(t)" };
2125 int i, j, j0, k, m, nh, ihb, ohb, nhydro, ndump = 0;
2126 int nframes = hb->nframes;
2129 double sum, integral;
2132 snew(h, hb->maxhydro);
2133 snew(histo, nframes+1);
2134 /* Total number of hbonds analyzed here */
2135 for (i = 0; (i < hb->d.nrd); i++)
2137 for (k = 0; (k < hb->a.nra); k++)
2139 hbh = hb->hbmap[i][k];
2157 for (m = 0; (m < hb->maxhydro); m++)
2161 h[nhydro++] = bContact ? hbh->g[m] : hbh->h[m];
2165 for (nh = 0; (nh < nhydro); nh++)
2170 /* Changed '<' into '<=' below, just like I
2171 did in the hbm-output-loop in the main code.
2172 - Erik Marklund, May 31, 2006
2174 for (j = 0; (j <= hbh->nframes); j++)
2176 ihb = is_hb(h[nh], j);
2177 if (debug && (ndump < 10))
2179 fprintf(debug, "%5d %5d\n", j, ihb);
2199 fprintf(stderr, "\n");
2202 fp = xvgropen(fn, "Uninterrupted contact lifetime", output_env_get_xvgr_tlabel(oenv), "()", oenv);
2206 fp = xvgropen(fn, "Uninterrupted hydrogen bond lifetime", output_env_get_xvgr_tlabel(oenv), "()",
2210 xvgr_legend(fp, asize(leg), leg, oenv);
2212 while ((j0 > 0) && (histo[j0] == 0))
2217 for (i = 0; (i <= j0); i++)
2221 dt = hb->time[1]-hb->time[0];
2224 for (i = 1; (i <= j0); i++)
2226 t = hb->time[i] - hb->time[0] - 0.5*dt;
2227 x1 = t*histo[i]/sum;
2228 fprintf(fp, "%8.3f %10.3e %10.3e\n", t, histo[i]/sum, x1);
2233 printf("%s lifetime = %.2f ps\n", bContact ? "Contact" : "HB", integral);
2234 printf("Note that the lifetime obtained in this manner is close to useless\n");
2235 printf("Use the -ac option instead and check the Forward lifetime\n");
2236 please_cite(stdout, "Spoel2006b");
2241 /* Changed argument bMerge into oneHB to handle contacts properly.
2242 * - Erik Marklund, June 29, 2006
2244 static void dump_ac(t_hbdata *hb, gmx_bool oneHB, int nDump)
2247 int i, j, k, m, nd, ihb, idist;
2248 int nframes = hb->nframes;
2256 fp = gmx_ffopen("debug-ac.xvg", "w");
2257 for (j = 0; (j < nframes); j++)
2259 fprintf(fp, "%10.3f", hb->time[j]);
2260 for (i = nd = 0; (i < hb->d.nrd) && (nd < nDump); i++)
2262 for (k = 0; (k < hb->a.nra) && (nd < nDump); k++)
2266 hbh = hb->hbmap[i][k];
2271 ihb = is_hb(hbh->h[0], j);
2272 idist = is_hb(hbh->g[0], j);
2278 for (m = 0; (m < hb->maxhydro) && !ihb; m++)
2280 ihb = ihb || ((hbh->h[m]) && is_hb(hbh->h[m], j));
2281 idist = idist || ((hbh->g[m]) && is_hb(hbh->g[m], j));
2283 /* This is not correct! */
2284 /* What isn't correct? -Erik M */
2289 fprintf(fp, " %1d-%1d", ihb, idist);
2299 static real calc_dg(real tau, real temp)
2310 return kbt*log(kbt*tau/PLANCK);
2315 int n0, n1, nparams, ndelta;
2317 real *t, *ct, *nt, *kt, *sigma_ct, *sigma_nt, *sigma_kt;
2320 static real compute_weighted_rates(int n, real t[], real ct[], real nt[],
2321 real kt[], real sigma_ct[], real sigma_nt[],
2322 real sigma_kt[], real *k, real *kp,
2323 real *sigma_k, real *sigma_kp,
2329 real kkk = 0, kkp = 0, kk2 = 0, kp2 = 0, chi2;
2334 for (i = 0; (i < n); i++)
2336 if (t[i] >= fit_start)
2349 tl.sigma_ct = sigma_ct;
2350 tl.sigma_nt = sigma_nt;
2351 tl.sigma_kt = sigma_kt;
2355 chi2 = 0; /*optimize_luzar_parameters(debug, &tl, 1000, 1e-3); */
2357 *kp = tl.kkk[1] = *kp;
2359 for (j = 0; (j < NK); j++)
2361 /* (void) optimize_luzar_parameters(debug, &tl, 1000, 1e-3); */
2364 kk2 += sqr(tl.kkk[0]);
2365 kp2 += sqr(tl.kkk[1]);
2368 *sigma_k = sqrt(kk2/NK - sqr(kkk/NK));
2369 *sigma_kp = sqrt(kp2/NK - sqr(kkp/NK));
2374 static void smooth_tail(int n, real t[], real c[], real sigma_c[], real start,
2375 const output_env_t oenv)
2378 real e_1, fitparm[4];
2382 for (i = 0; (i < n); i++)
2398 do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(), effnEXP2, fitparm, 0);
2401 void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
2402 real sigma_ct[], real sigma_nt[], real sigma_kt[],
2403 real fit_start, real temp, real smooth_tail_start,
2404 const output_env_t oenv)
2407 real k = 1, kp = 1, kow = 1;
2408 real Q = 0, chi22, chi2, dg, dgp, tau_hb, dtau, tau_rlx, e_1, dt, sigma_k, sigma_kp, ddg;
2409 double tmp, sn2 = 0, sc2 = 0, sk2 = 0, scn = 0, sck = 0, snk = 0;
2410 gmx_bool bError = (sigma_ct != NULL) && (sigma_nt != NULL) && (sigma_kt != NULL);
2412 if (smooth_tail_start >= 0)
2414 smooth_tail(n, t, ct, sigma_ct, smooth_tail_start, oenv);
2415 smooth_tail(n, t, nt, sigma_nt, smooth_tail_start, oenv);
2416 smooth_tail(n, t, kt, sigma_kt, smooth_tail_start, oenv);
2418 for (i0 = 0; (i0 < n-2) && ((t[i0]-t[0]) < fit_start); i0++)
2424 for (i = i0; (i < n); i++)
2433 printf("Hydrogen bond thermodynamics at T = %g K\n", temp);
2434 tmp = (sn2*sc2-sqr(scn));
2435 if ((tmp > 0) && (sn2 > 0))
2437 k = (sn2*sck-scn*snk)/tmp;
2438 kp = (k*scn-snk)/sn2;
2442 for (i = i0; (i < n); i++)
2444 chi2 += sqr(k*ct[i]-kp*nt[i]-kt[i]);
2446 chi22 = compute_weighted_rates(n, t, ct, nt, kt, sigma_ct, sigma_nt,
2448 &sigma_k, &sigma_kp, fit_start);
2449 Q = 0; /* quality_of_fit(chi2, 2);*/
2450 ddg = BOLTZ*temp*sigma_k/k;
2451 printf("Fitting paramaters chi^2 = %10g, Quality of fit = %10g\n",
2453 printf("The Rate and Delta G are followed by an error estimate\n");
2454 printf("----------------------------------------------------------\n"
2455 "Type Rate (1/ps) Sigma Time (ps) DG (kJ/mol) Sigma\n");
2456 printf("Forward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
2457 k, sigma_k, 1/k, calc_dg(1/k, temp), ddg);
2458 ddg = BOLTZ*temp*sigma_kp/kp;
2459 printf("Backward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
2460 kp, sigma_kp, 1/kp, calc_dg(1/kp, temp), ddg);
2465 for (i = i0; (i < n); i++)
2467 chi2 += sqr(k*ct[i]-kp*nt[i]-kt[i]);
2469 printf("Fitting parameters chi^2 = %10g\nQ = %10g\n",
2471 printf("--------------------------------------------------\n"
2472 "Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2\n");
2473 printf("Forward %10.3f %8.3f %10.3f %10g\n",
2474 k, 1/k, calc_dg(1/k, temp), chi2);
2475 printf("Backward %10.3f %8.3f %10.3f\n",
2476 kp, 1/kp, calc_dg(1/kp, temp));
2482 printf("One-way %10.3f %s%8.3f %10.3f\n",
2483 kow, bError ? " " : "", 1/kow, calc_dg(1/kow, temp));
2487 printf(" - Numerical problems computing HB thermodynamics:\n"
2488 "sc2 = %g sn2 = %g sk2 = %g sck = %g snk = %g scn = %g\n",
2489 sc2, sn2, sk2, sck, snk, scn);
2491 /* Determine integral of the correlation function */
2492 tau_hb = evaluate_integral(n, t, ct, NULL, (t[n-1]-t[0])/2, &dtau);
2493 printf("Integral %10.3f %s%8.3f %10.3f\n", 1/tau_hb,
2494 bError ? " " : "", tau_hb, calc_dg(tau_hb, temp));
2496 for (i = 0; (i < n-2); i++)
2498 if ((ct[i] > e_1) && (ct[i+1] <= e_1))
2505 /* Determine tau_relax from linear interpolation */
2506 tau_rlx = t[i]-t[0] + (e_1-ct[i])*(t[i+1]-t[i])/(ct[i+1]-ct[i]);
2507 printf("Relaxation %10.3f %8.3f %s%10.3f\n", 1/tau_rlx,
2508 tau_rlx, bError ? " " : "",
2509 calc_dg(tau_rlx, temp));
2514 printf("Correlation functions too short to compute thermodynamics\n");
2518 void compute_derivative(int nn, real x[], real y[], real dydx[])
2522 /* Compute k(t) = dc(t)/dt */
2523 for (j = 1; (j < nn-1); j++)
2525 dydx[j] = (y[j+1]-y[j-1])/(x[j+1]-x[j-1]);
2527 /* Extrapolate endpoints */
2528 dydx[0] = 2*dydx[1] - dydx[2];
2529 dydx[nn-1] = 2*dydx[nn-2] - dydx[nn-3];
2532 static void parallel_print(int *data, int nThreads)
2534 /* This prints the donors on which each tread is currently working. */
2537 fprintf(stderr, "\r");
2538 for (i = 0; i < nThreads; i++)
2540 fprintf(stderr, "%-7i", data[i]);
2544 static void normalizeACF(real *ct, real *gt, int nhb, int len)
2546 real ct_fac, gt_fac = 0;
2549 /* Xu and Berne use the same normalization constant */
2554 gt_fac = 1.0/(real)nhb;
2557 printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
2558 for (i = 0; i < len; i++)
2568 /* Added argument bContact in do_hbac(...). Also
2569 * added support for -contact in the actual code.
2570 * - Erik Marklund, May 31, 2006 */
2571 /* Changed contact code and added argument R2
2572 * - Erik Marklund, June 29, 2006
2574 static void do_hbac(const char *fn, t_hbdata *hb,
2575 int nDump, gmx_bool bMerge, gmx_bool bContact, real fit_start,
2576 real temp, gmx_bool R2, real smooth_tail_start, const output_env_t oenv,
2577 const char *gemType, int nThreads,
2578 const int NN, const gmx_bool bBallistic, const gmx_bool bGemFit)
2581 int i, j, k, m, n, o, nd, ihb, idist, n2, nn, iter, nSets;
2582 const char *legNN[] = {
2586 static char **legGem;
2588 const char *legLuzar[] = {
2589 "Ac\\sfin sys\\v{}\\z{}(t)",
2591 "Cc\\scontact,hb\\v{}\\z{}(t)",
2592 "-dAc\\sfs\\v{}\\z{}/dt"
2594 gmx_bool bNorm = FALSE, bOMP = FALSE;
2597 real *rhbex = NULL, *ht, *gt, *ght, *dght, *kt;
2598 real *ct, *p_ct, tail, tail2, dtail, ct_fac, ght_fac, *cct;
2599 const real tol = 1e-3;
2600 int nframes = hb->nframes, nf;
2601 unsigned int **h = NULL, **g = NULL;
2602 int nh, nhbonds, nhydro, ngh;
2604 PSTYPE p, *pfound = NULL, np;
2606 int *ptimes = NULL, *poff = NULL, anhb, n0, mMax = INT_MIN;
2607 real **rHbExGem = NULL;
2611 double *ctdouble, *timedouble, *fittedct;
2612 double fittolerance = 0.1;
2613 int *dondata = NULL, thisThread;
2616 AC_NONE, AC_NN, AC_GEM, AC_LUZAR
2625 printf("Doing autocorrelation ");
2627 /* Decide what kind of ACF calculations to do. */
2628 if (NN > NN_NONE && NN < NN_NR)
2630 #ifdef HAVE_NN_LOOPS
2632 printf("using the energy estimate.\n");
2635 printf("Can't do the NN-loop. Yet.\n");
2641 printf("according to the reversible geminate recombination model by Omer Markowitch.\n");
2643 nSets = 1 + (bBallistic ? 1 : 0) + (bGemFit ? 1 : 0);
2644 snew(legGem, nSets);
2645 for (i = 0; i < nSets; i++)
2647 snew(legGem[i], 128);
2649 sprintf(legGem[0], "Ac\\s%s\\v{}\\z{}(t)", gemType);
2652 sprintf(legGem[1], "Ac'(t)");
2656 sprintf(legGem[(bBallistic ? 3 : 2)], "Ac\\s%s,fit\\v{}\\z{}(t)", gemType);
2663 printf("according to the theory of Luzar and Chandler.\n");
2667 /* build hbexist matrix in reals for autocorr */
2668 /* Allocate memory for computing ACF (rhbex) and aggregating the ACF (ct) */
2670 while (n2 < nframes)
2677 if (acType != AC_NN || bOMP)
2679 snew(h, hb->maxhydro);
2680 snew(g, hb->maxhydro);
2683 /* Dump hbonds for debugging */
2684 dump_ac(hb, bMerge || bContact, nDump);
2686 /* Total number of hbonds analyzed here */
2691 if (acType != AC_LUZAR && bOMP)
2693 nThreads = min((nThreads <= 0) ? INT_MAX : nThreads, gmx_omp_get_max_threads());
2695 gmx_omp_set_num_threads(nThreads);
2696 snew(dondata, nThreads);
2697 for (i = 0; i < nThreads; i++)
2701 printf("ACF calculations parallelized with OpenMP using %i threads.\n"
2702 "Expect close to linear scaling over this donor-loop.\n", nThreads);
2704 fprintf(stderr, "Donors: [thread no]\n");
2707 for (i = 0; i < nThreads; i++)
2709 snprintf(tmpstr, 7, "[%i]", i);
2710 fprintf(stderr, "%-7s", tmpstr);
2713 fprintf(stderr, "\n");
2717 /* Build the ACF according to acType */
2722 #ifdef HAVE_NN_LOOPS
2723 /* Here we're using the estimated energy for the hydrogen bonds. */
2726 #pragma omp parallel \
2727 private(i, j, k, nh, E, rhbex, thisThread) \
2731 thisThread = gmx_omp_get_thread_num();
2735 memset(rhbex, 0, n2*sizeof(real)); /* Trust no-one, not even malloc()! */
2738 #pragma omp for schedule (dynamic)
2739 for (i = 0; i < hb->d.nrd; i++) /* loop over donors */
2743 #pragma omp critical
2745 dondata[thisThread] = i;
2746 parallel_print(dondata, nThreads);
2751 fprintf(stderr, "\r %i", i);
2754 for (j = 0; j < hb->a.nra; j++) /* loop over acceptors */
2756 for (nh = 0; nh < hb->d.nhydro[i]; nh++) /* loop over donors' hydrogens */
2758 E = hb->hbE.E[i][j][nh];
2761 for (k = 0; k < nframes; k++)
2763 if (E[k] != NONSENSE_E)
2765 rhbex[k] = (real)E[k];
2769 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &(rhbex), hb->time[1]-hb->time[0],
2770 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0, 1);
2771 #pragma omp critical
2773 for (k = 0; (k < nn); k++)
2790 normalizeACF(ct, NULL, 0, nn);
2792 snew(timedouble, nn);
2793 for (j = 0; j < nn; j++)
2795 timedouble[j] = (double)(hb->time[j]);
2796 ctdouble[j] = (double)(ct[j]);
2799 /* Remove ballistic term */
2800 /* Ballistic component removal and fitting to the reversible geminate recombination model
2801 * will be taken out for the time being. First of all, one can remove the ballistic
2802 * component with g_analyze afterwards. Secondly, and more importantly, there are still
2803 * problems with the robustness of the fitting to the model. More work is needed.
2804 * A third reason is that we're currently using gsl for this and wish to reduce dependence
2805 * on external libraries. There are Levenberg-Marquardt and nsimplex solvers that come with
2806 * a BSD-licence that can do the job.
2808 * - Erik Marklund, June 18 2010.
2810 /* if (params->ballistic/params->tDelta >= params->nExpFit*2+1) */
2811 /* takeAwayBallistic(ctdouble, timedouble, nn, params->ballistic, params->nExpFit, params->bDt); */
2813 /* printf("\nNumber of data points is less than the number of parameters to fit\n." */
2814 /* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
2816 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)");
2817 xvgr_legend(fp, asize(legNN), legNN);
2819 for (j = 0; (j < nn); j++)
2821 fprintf(fp, "%10g %10g %10g\n",
2822 hb->time[j]-hb->time[0],
2830 #endif /* HAVE_NN_LOOPS */
2831 break; /* case AC_NN */
2835 memset(ct, 0, 2*n2*sizeof(real));
2837 fprintf(stderr, "Donor:\n");
2840 #define __ACDATA p_ct
2843 #pragma omp parallel \
2844 private(i, k, nh, hbh, pHist, h, g, n0, nf, np, j, m, \
2845 pfound, poff, rHbExGem, p, ihb, mMax, \
2848 { /* ########## THE START OF THE ENORMOUS PARALLELIZED BLOCK! ########## */
2851 thisThread = gmx_omp_get_thread_num();
2852 snew(h, hb->maxhydro);
2853 snew(g, hb->maxhydro);
2860 memset(p_ct, 0, 2*n2*sizeof(real));
2862 /* I'm using a chunk size of 1, since I expect \
2863 * the overhead to be really small compared \
2864 * to the actual calculations \ */
2865 #pragma omp for schedule(dynamic,1) nowait
2866 for (i = 0; i < hb->d.nrd; i++)
2871 #pragma omp critical
2873 dondata[thisThread] = i;
2874 parallel_print(dondata, nThreads);
2879 fprintf(stderr, "\r %i", i);
2881 for (k = 0; k < hb->a.nra; k++)
2883 for (nh = 0; nh < ((bMerge || bContact) ? 1 : hb->d.nhydro[i]); nh++)
2885 hbh = hb->hbmap[i][k];
2888 /* Note that if hb->per->gemtype==gemDD, then distances will be stored in
2889 * hb->hbmap[d][a].h array anyway, because the contact flag will be set.
2890 * hence, it's only with the gemAD mode that hb->hbmap[d][a].g will be used. */
2891 pHist = &(hb->per->pHist[i][k]);
2892 if (ISHB(hbh->history[nh]) && pHist->len != 0)
2897 g[nh] = hb->per->gemtype == gemAD ? hbh->g[nh] : NULL;
2901 /* count the number of periodic shifts encountered and store
2902 * them in separate arrays. */
2904 for (j = 0; j < pHist->len; j++)
2907 for (m = 0; m <= np; m++)
2909 if (m == np) /* p not recognized in list. Add it and set up new array. */
2912 if (np > hb->per->nper)
2914 gmx_fatal(FARGS, "Too many pshifts. Something's utterly wrong here.");
2916 if (m >= mMax) /* Extend the arrays.
2917 * Doing it like this, using mMax to keep track of the sizes,
2918 * eleviates the need for freeing and re-allocating the arrays
2919 * when taking on the next donor-acceptor pair */
2922 srenew(pfound, np); /* The list of found periodic shifts. */
2923 srenew(rHbExGem, np); /* The hb existence functions (-aver_hb). */
2924 snew(rHbExGem[m], 2*n2);
2929 if (rHbExGem != NULL && rHbExGem[m] != NULL)
2931 /* This must be done, as this array was most likey
2932 * used to store stuff in some previous iteration. */
2933 memset(rHbExGem[m], 0, (sizeof(real)) * (2*n2));
2937 fprintf(stderr, "rHbExGem not initialized! m = %i\n", m);
2949 } /* m: Loop over found shifts */
2950 } /* j: Loop over shifts */
2952 /* Now unpack and disentangle the existence funtions. */
2953 for (j = 0; j < nf; j++)
2960 * pfound: list of periodic shifts found for this pair.
2961 * poff: list of frame offsets; that is, the first
2962 * frame a hbond has a particular periodic shift. */
2963 p = getPshift(*pHist, j+n0);
2966 for (m = 0; m < np; m++)
2974 gmx_fatal(FARGS, "Shift not found, but must be there.");
2978 ihb = is_hb(h[nh], j) || ((hb->per->gemtype != gemAD || j == 0) ? FALSE : is_hb(g[nh], j));
2983 poff[m] = j; /* Here's where the first hbond with shift p is,
2984 * relative to the start of h[0].*/
2988 gmx_fatal(FARGS, "j<poff[m]");
2990 rHbExGem[m][j-poff[m]] += 1;
2995 /* Now, build ac. */
2996 for (m = 0; m < np; m++)
2998 if (rHbExGem[m][0] > 0 && n0+poff[m] < nn /* && m==0 */)
3000 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &(rHbExGem[m]), hb->time[1]-hb->time[0],
3001 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0);
3002 for (j = 0; (j < nn); j++)
3004 __ACDATA[j] += rHbExGem[m][j];
3007 } /* Building of ac. */
3010 } /* hydrogen loop */
3011 } /* acceptor loop */
3014 for (m = 0; m <= mMax; m++)
3027 #pragma omp critical
3029 for (i = 0; i < nn; i++)
3037 } /* ########## THE END OF THE ENORMOUS PARALLELIZED BLOCK ########## */
3043 normalizeACF(ct, NULL, 0, nn);
3045 fprintf(stderr, "\n\nACF successfully calculated.\n");
3047 /* Use this part to fit to geminate recombination - JCP 129, 84505 (2008) */
3050 snew(timedouble, nn);
3053 for (j = 0; j < nn; j++)
3055 timedouble[j] = (double)(hb->time[j]);
3056 ctdouble[j] = (double)(ct[j]);
3059 /* Remove ballistic term */
3060 /* Ballistic component removal and fitting to the reversible geminate recombination model
3061 * will be taken out for the time being. First of all, one can remove the ballistic
3062 * component with g_analyze afterwards. Secondly, and more importantly, there are still
3063 * problems with the robustness of the fitting to the model. More work is needed.
3064 * A third reason is that we're currently using gsl for this and wish to reduce dependence
3065 * on external libraries. There are Levenberg-Marquardt and nsimplex solvers that come with
3066 * a BSD-licence that can do the job.
3068 * - Erik Marklund, June 18 2010.
3070 /* if (bBallistic) { */
3071 /* if (params->ballistic/params->tDelta >= params->nExpFit*2+1) */
3072 /* takeAwayBallistic(ctdouble, timedouble, nn, params->ballistic, params->nExpFit, params->bDt); */
3074 /* printf("\nNumber of data points is less than the number of parameters to fit\n." */
3075 /* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
3078 /* fitGemRecomb(ctdouble, timedouble, &fittedct, nn, params); */
3083 fp = xvgropen(fn, "Contact Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3087 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3089 xvgr_legend(fp, asize(legGem), (const char**)legGem, oenv);
3091 for (j = 0; (j < nn); j++)
3093 fprintf(fp, "%10g %10g", hb->time[j]-hb->time[0], ct[j]);
3096 fprintf(fp, " %10g", ctdouble[j]);
3100 fprintf(fp, " %10g", fittedct[j]);
3111 break; /* case AC_GEM */
3124 for (i = 0; (i < hb->d.nrd); i++)
3126 for (k = 0; (k < hb->a.nra); k++)
3129 hbh = hb->hbmap[i][k];
3133 if (bMerge || bContact)
3135 if (ISHB(hbh->history[0]))
3144 for (m = 0; (m < hb->maxhydro); m++)
3146 if (bContact ? ISDIST(hbh->history[m]) : ISHB(hbh->history[m]))
3148 g[nhydro] = hbh->g[m];
3149 h[nhydro] = hbh->h[m];
3156 for (nh = 0; (nh < nhydro); nh++)
3158 int nrint = bContact ? hb->nrdist : hb->nrhb;
3159 if ((((nhbonds+1) % 10) == 0) || (nhbonds+1 == nrint))
3161 fprintf(stderr, "\rACF %d/%d", nhbonds+1, nrint);
3164 for (j = 0; (j < nframes); j++)
3166 /* Changed '<' into '<=' below, just like I did in
3167 the hbm-output-loop in the gmx_hbond() block.
3168 - Erik Marklund, May 31, 2006 */
3171 ihb = is_hb(h[nh], j);
3172 idist = is_hb(g[nh], j);
3179 /* For contacts: if a second cut-off is provided, use it,
3180 * otherwise use g(t) = 1-h(t) */
3181 if (!R2 && bContact)
3187 gt[j] = idist*(1-ihb);
3194 /* The autocorrelation function is normalized after summation only */
3195 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &rhbex, hb->time[1]-hb->time[0],
3196 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0);
3198 /* Cross correlation analysis for thermodynamics */
3199 for (j = nframes; (j < n2); j++)
3205 cross_corr(n2, ht, gt, dght);
3207 for (j = 0; (j < nn); j++)
3216 fprintf(stderr, "\n");
3219 normalizeACF(ct, ght, nhb, nn);
3221 /* Determine tail value for statistics */
3224 for (j = nn/2; (j < nn); j++)
3227 tail2 += ct[j]*ct[j];
3229 tail /= (nn - nn/2);
3230 tail2 /= (nn - nn/2);
3231 dtail = sqrt(tail2-tail*tail);
3233 /* Check whether the ACF is long enough */
3236 printf("\nWARNING: Correlation function is probably not long enough\n"
3237 "because the standard deviation in the tail of C(t) > %g\n"
3238 "Tail value (average C(t) over second half of acf): %g +/- %g\n",
3241 for (j = 0; (j < nn); j++)
3244 ct[j] = (cct[j]-tail)/(1-tail);
3246 /* Compute negative derivative k(t) = -dc(t)/dt */
3247 compute_derivative(nn, hb->time, ct, kt);
3248 for (j = 0; (j < nn); j++)
3256 fp = xvgropen(fn, "Contact Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3260 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3262 xvgr_legend(fp, asize(legLuzar), legLuzar, oenv);
3265 for (j = 0; (j < nn); j++)
3267 fprintf(fp, "%10g %10g %10g %10g %10g\n",
3268 hb->time[j]-hb->time[0], ct[j], cct[j], ght[j], kt[j]);
3272 analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
3273 fit_start, temp, smooth_tail_start, oenv);
3275 do_view(oenv, fn, NULL);
3287 break; /* case AC_LUZAR */
3290 gmx_fatal(FARGS, "Unrecognized type of ACF-calulation. acType = %i.", acType);
3291 } /* switch (acType) */
3294 static void init_hbframe(t_hbdata *hb, int nframes, real t)
3298 hb->time[nframes] = t;
3299 hb->nhb[nframes] = 0;
3300 hb->ndist[nframes] = 0;
3301 for (i = 0; (i < max_hx); i++)
3303 hb->nhx[nframes][i] = 0;
3305 /* Loop invalidated */
3306 if (hb->bHBmap && 0)
3308 for (i = 0; (i < hb->d.nrd); i++)
3310 for (j = 0; (j < hb->a.nra); j++)
3312 for (m = 0; (m < hb->maxhydro); m++)
3314 if (hb->hbmap[i][j] && hb->hbmap[i][j]->h[m])
3316 set_hb(hb, i, m, j, nframes, HB_NO);
3322 /*set_hb(hb->hbmap[i][j]->h[m],nframes-hb->hbmap[i][j]->n0,HB_NO);*/
3325 static void analyse_donor_props(const char *fn, t_hbdata *hb, int nframes, real t,
3326 const output_env_t oenv)
3328 static FILE *fp = NULL;
3329 const char *leg[] = { "Nbound", "Nfree" };
3330 int i, j, k, nbound, nb, nhtot;
3338 fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
3339 xvgr_legend(fp, asize(leg), leg, oenv);
3343 for (i = 0; (i < hb->d.nrd); i++)
3345 for (k = 0; (k < hb->d.nhydro[i]); k++)
3349 for (j = 0; (j < hb->a.nra) && (nb == 0); j++)
3351 if (hb->hbmap[i][j] && hb->hbmap[i][j]->h[k] &&
3352 is_hb(hb->hbmap[i][j]->h[k], nframes))
3360 fprintf(fp, "%10.3e %6d %6d\n", t, nbound, nhtot-nbound);
3363 static void dump_hbmap(t_hbdata *hb,
3364 int nfile, t_filenm fnm[], gmx_bool bTwo,
3365 gmx_bool bContact, int isize[], int *index[], char *grpnames[],
3369 int ddd, hhh, aaa, i, j, k, m, grp;
3370 char ds[32], hs[32], as[32];
3373 fp = opt2FILE("-hbn", nfile, fnm, "w");
3374 if (opt2bSet("-g", nfile, fnm))
3376 fplog = gmx_ffopen(opt2fn("-g", nfile, fnm), "w");
3377 fprintf(fplog, "# %10s %12s %12s\n", "Donor", "Hydrogen", "Acceptor");
3383 for (grp = gr0; grp <= (bTwo ? gr1 : gr0); grp++)
3385 fprintf(fp, "[ %s ]", grpnames[grp]);
3386 for (i = 0; i < isize[grp]; i++)
3388 fprintf(fp, (i%15) ? " " : "\n");
3389 fprintf(fp, " %4u", index[grp][i]+1);
3393 Added -contact support below.
3394 - Erik Marklund, May 29, 2006
3398 fprintf(fp, "[ donors_hydrogens_%s ]\n", grpnames[grp]);
3399 for (i = 0; (i < hb->d.nrd); i++)
3401 if (hb->d.grp[i] == grp)
3403 for (j = 0; (j < hb->d.nhydro[i]); j++)
3405 fprintf(fp, " %4u %4u", hb->d.don[i]+1,
3406 hb->d.hydro[i][j]+1);
3412 fprintf(fp, "[ acceptors_%s ]", grpnames[grp]);
3413 for (i = 0; (i < hb->a.nra); i++)
3415 if (hb->a.grp[i] == grp)
3417 fprintf(fp, (i%15 && !first) ? " " : "\n");
3418 fprintf(fp, " %4u", hb->a.acc[i]+1);
3427 fprintf(fp, bContact ? "[ contacts_%s-%s ]\n" :
3428 "[ hbonds_%s-%s ]\n", grpnames[0], grpnames[1]);
3432 fprintf(fp, bContact ? "[ contacts_%s ]" : "[ hbonds_%s ]\n", grpnames[0]);
3435 for (i = 0; (i < hb->d.nrd); i++)
3438 for (k = 0; (k < hb->a.nra); k++)
3441 for (m = 0; (m < hb->d.nhydro[i]); m++)
3443 if (hb->hbmap[i][k] && ISHB(hb->hbmap[i][k]->history[m]))
3445 sprintf(ds, "%s", mkatomname(atoms, ddd));
3446 sprintf(as, "%s", mkatomname(atoms, aaa));
3449 fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
3452 fprintf(fplog, "%12s %12s\n", ds, as);
3457 hhh = hb->d.hydro[i][m];
3458 sprintf(hs, "%s", mkatomname(atoms, hhh));
3459 fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
3462 fprintf(fplog, "%12s %12s %12s\n", ds, hs, as);
3476 /* sync_hbdata() updates the parallel t_hbdata p_hb using hb as template.
3477 * It mimics add_frames() and init_frame() to some extent. */
3478 static void sync_hbdata(t_hbdata *p_hb, int nframes)
3481 if (nframes >= p_hb->max_frames)
3483 p_hb->max_frames += 4096;
3484 srenew(p_hb->nhb, p_hb->max_frames);
3485 srenew(p_hb->ndist, p_hb->max_frames);
3486 srenew(p_hb->n_bound, p_hb->max_frames);
3487 srenew(p_hb->nhx, p_hb->max_frames);
3490 srenew(p_hb->danr, p_hb->max_frames);
3492 memset(&(p_hb->nhb[nframes]), 0, sizeof(int) * (p_hb->max_frames-nframes));
3493 memset(&(p_hb->ndist[nframes]), 0, sizeof(int) * (p_hb->max_frames-nframes));
3494 p_hb->nhb[nframes] = 0;
3495 p_hb->ndist[nframes] = 0;
3498 p_hb->nframes = nframes;
3501 /* p_hb->nhx[nframes][i] */
3503 memset(&(p_hb->nhx[nframes]), 0, sizeof(int)*max_hx); /* zero the helix count for this frame */
3505 /* hb->per will remain constant througout the frame loop,
3506 * even though the data its members point to will change,
3507 * hence no need for re-syncing. */
3510 int gmx_hbond(int argc, char *argv[])
3512 const char *desc[] = {
3513 "[THISMODULE] computes and analyzes hydrogen bonds. Hydrogen bonds are",
3514 "determined based on cutoffs for the angle Hydrogen - Donor - Acceptor",
3515 "(zero is extended) and the distance Donor - Acceptor",
3516 "(or Hydrogen - Acceptor using [TT]-noda[tt]).",
3517 "OH and NH groups are regarded as donors, O is an acceptor always,",
3518 "N is an acceptor by default, but this can be switched using",
3519 "[TT]-nitacc[tt]. Dummy hydrogen atoms are assumed to be connected",
3520 "to the first preceding non-hydrogen atom.[PAR]",
3522 "You need to specify two groups for analysis, which must be either",
3523 "identical or non-overlapping. All hydrogen bonds between the two",
3524 "groups are analyzed.[PAR]",
3526 "If you set [TT]-shell[tt], you will be asked for an additional index group",
3527 "which should contain exactly one atom. In this case, only hydrogen",
3528 "bonds between atoms within the shell distance from the one atom are",
3531 "With option -ac, rate constants for hydrogen bonding can be derived with the model of Luzar and Chandler",
3532 "(Nature 394, 1996; J. Chem. Phys. 113:23, 2000) or that of Markovitz and Agmon (J. Chem. Phys 129, 2008).",
3533 "If contact kinetics are analyzed by using the -contact option, then",
3534 "n(t) can be defined as either all pairs that are not within contact distance r at time t",
3535 "(corresponding to leaving the -r2 option at the default value 0) or all pairs that",
3536 "are within distance r2 (corresponding to setting a second cut-off value with option -r2).",
3537 "See mentioned literature for more details and definitions."
3540 /* "It is also possible to analyse specific hydrogen bonds with",
3541 "[TT]-sel[tt]. This index file must contain a group of atom triplets",
3542 "Donor Hydrogen Acceptor, in the following way:[PAR]",
3550 "Note that the triplets need not be on separate lines.",
3551 "Each atom triplet specifies a hydrogen bond to be analyzed,",
3552 "note also that no check is made for the types of atoms.[PAR]",
3554 "[BB]Output:[bb][BR]",
3555 "[TT]-num[tt]: number of hydrogen bonds as a function of time.[BR]",
3556 "[TT]-ac[tt]: average over all autocorrelations of the existence",
3557 "functions (either 0 or 1) of all hydrogen bonds.[BR]",
3558 "[TT]-dist[tt]: distance distribution of all hydrogen bonds.[BR]",
3559 "[TT]-ang[tt]: angle distribution of all hydrogen bonds.[BR]",
3560 "[TT]-hx[tt]: the number of n-n+i hydrogen bonds as a function of time",
3561 "where n and n+i stand for residue numbers and i ranges from 0 to 6.",
3562 "This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated",
3563 "with helices in proteins.[BR]",
3564 "[TT]-hbn[tt]: all selected groups, donors, hydrogens and acceptors",
3565 "for selected groups, all hydrogen bonded atoms from all groups and",
3566 "all solvent atoms involved in insertion.[BR]",
3567 "[TT]-hbm[tt]: existence matrix for all hydrogen bonds over all",
3568 "frames, this also contains information on solvent insertion",
3569 "into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
3571 "[TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
3572 "each timeframe. This is especially useful when using [TT]-shell[tt].[BR]",
3573 "[TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
3574 "compare results to Raman Spectroscopy.",
3576 "Note: options [TT]-ac[tt], [TT]-life[tt], [TT]-hbn[tt] and [TT]-hbm[tt]",
3577 "require an amount of memory proportional to the total numbers of donors",
3578 "times the total number of acceptors in the selected group(s)."
3581 static real acut = 30, abin = 1, rcut = 0.35, r2cut = 0, rbin = 0.005, rshell = -1;
3582 static real maxnhb = 0, fit_start = 1, fit_end = 60, temp = 298.15, smooth_tail_start = -1, D = -1;
3583 static gmx_bool bNitAcc = TRUE, bDA = TRUE, bMerge = TRUE;
3584 static int nDump = 0, nFitPoints = 100;
3585 static int nThreads = 0, nBalExp = 4;
3587 static gmx_bool bContact = FALSE, bBallistic = FALSE, bGemFit = FALSE;
3588 static real logAfterTime = 10, gemBallistic = 0.2; /* ps */
3589 static const char *NNtype[] = {NULL, "none", "binary", "oneOverR3", "dipole", NULL};
3593 { "-a", FALSE, etREAL, {&acut},
3594 "Cutoff angle (degrees, Hydrogen - Donor - Acceptor)" },
3595 { "-r", FALSE, etREAL, {&rcut},
3596 "Cutoff radius (nm, X - Acceptor, see next option)" },
3597 { "-da", FALSE, etBOOL, {&bDA},
3598 "Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)" },
3599 { "-r2", FALSE, etREAL, {&r2cut},
3600 "Second cutoff radius. Mainly useful with [TT]-contact[tt] and [TT]-ac[tt]"},
3601 { "-abin", FALSE, etREAL, {&abin},
3602 "Binwidth angle distribution (degrees)" },
3603 { "-rbin", FALSE, etREAL, {&rbin},
3604 "Binwidth distance distribution (nm)" },
3605 { "-nitacc", FALSE, etBOOL, {&bNitAcc},
3606 "Regard nitrogen atoms as acceptors" },
3607 { "-contact", FALSE, etBOOL, {&bContact},
3608 "Do not look for hydrogen bonds, but merely for contacts within the cut-off distance" },
3609 { "-shell", FALSE, etREAL, {&rshell},
3610 "when > 0, only calculate hydrogen bonds within # nm shell around "
3612 { "-fitstart", FALSE, etREAL, {&fit_start},
3613 "Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With [TT]-gemfit[tt] we suggest [TT]-fitstart 0[tt]" },
3614 { "-fitend", FALSE, etREAL, {&fit_end},
3615 "Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with [TT]-gemfit[tt])" },
3616 { "-temp", FALSE, etREAL, {&temp},
3617 "Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming" },
3618 { "-smooth", FALSE, etREAL, {&smooth_tail_start},
3619 "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
3620 { "-dump", FALSE, etINT, {&nDump},
3621 "Dump the first N hydrogen bond ACFs in a single [TT].xvg[tt] file for debugging" },
3622 { "-max_hb", FALSE, etREAL, {&maxnhb},
3623 "Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly" },
3624 { "-merge", FALSE, etBOOL, {&bMerge},
3625 "H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF." },
3626 { "-geminate", FALSE, etENUM, {gemType},
3627 "HIDDENUse reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details."},
3628 { "-diff", FALSE, etREAL, {&D},
3629 "HIDDENDffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd."},
3631 { "-nthreads", FALSE, etINT, {&nThreads},
3632 "Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of cores (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3)"},
3635 const char *bugs[] = {
3636 "The option [TT]-sel[tt] that used to work on selected hbonds is out of order, and therefore not available for the time being."
3639 { efTRX, "-f", NULL, ffREAD },
3640 { efTPR, NULL, NULL, ffREAD },
3641 { efNDX, NULL, NULL, ffOPTRD },
3642 /* { efNDX, "-sel", "select", ffOPTRD },*/
3643 { efXVG, "-num", "hbnum", ffWRITE },
3644 { efLOG, "-g", "hbond", ffOPTWR },
3645 { efXVG, "-ac", "hbac", ffOPTWR },
3646 { efXVG, "-dist", "hbdist", ffOPTWR },
3647 { efXVG, "-ang", "hbang", ffOPTWR },
3648 { efXVG, "-hx", "hbhelix", ffOPTWR },
3649 { efNDX, "-hbn", "hbond", ffOPTWR },
3650 { efXPM, "-hbm", "hbmap", ffOPTWR },
3651 { efXVG, "-don", "donor", ffOPTWR },
3652 { efXVG, "-dan", "danum", ffOPTWR },
3653 { efXVG, "-life", "hblife", ffOPTWR },
3654 { efXVG, "-nhbdist", "nhbdist", ffOPTWR }
3657 #define NFILE asize(fnm)
3659 char hbmap [HB_NR] = { ' ', 'o', '-', '*' };
3660 const char *hbdesc[HB_NR] = { "None", "Present", "Inserted", "Present & Inserted" };
3661 t_rgb hbrgb [HB_NR] = { {1, 1, 1}, {1, 0, 0}, {0, 0, 1}, {1, 0, 1} };
3663 t_trxstatus *status;
3668 int npargs, natoms, nframes = 0, shatom;
3674 real t, ccut, dist = 0.0, ang = 0.0;
3675 double max_nhb, aver_nhb, aver_dist;
3676 int h = 0, i = 0, j, k = 0, l, start, end, id, ja, ogrp, nsel;
3678 int xj, yj, zj, aj, xjj, yjj, zjj;
3679 int xk, yk, zk, ak, xkk, ykk, zkk;
3680 gmx_bool bSelected, bHBmap, bStop, bTwo, was, bBox, bTric;
3681 int *adist, *rdist, *aptr, *rprt;
3682 int grp, nabin, nrbin, bin, resdist, ihb;
3684 t_hbdata *hb, *hbptr;
3685 FILE *fp, *fpins = NULL, *fpnhb = NULL;
3687 t_ncell *icell, *jcell, *kcell;
3689 unsigned char *datable;
3694 int ii, jj, hh, actual_nThreads;
3696 gmx_bool bGem, bNN, bParallel;
3697 t_gemParams *params = NULL;
3698 gmx_bool bEdge_yjj, bEdge_xjj, bOMP;
3700 t_hbdata **p_hb = NULL; /* one per thread, then merge after the frame loop */
3701 int **p_adist = NULL, **p_rdist = NULL; /* a histogram for each thread. */
3710 ppa = add_acf_pargs(&npargs, pa);
3712 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
3713 ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
3718 /* NN-loop? If so, what estimator to use ?*/
3720 /* Outcommented for now DvdS 2010-07-13
3721 while (NN < NN_NR && gmx_strcasecmp(NNtype[0], NNtype[NN])!=0)
3724 gmx_fatal(FARGS, "Invalid NN-loop type.");
3727 for (i = 2; bNN == FALSE && i < NN_NR; i++)
3729 bNN = bNN || NN == i;
3732 if (NN > NN_NONE && bMerge)
3737 /* geminate recombination? If so, which flavor? */
3739 while (gemmode < gemNR && gmx_strcasecmp(gemType[0], gemType[gemmode]) != 0)
3743 if (gemmode == gemNR)
3745 gmx_fatal(FARGS, "Invalid recombination type.");
3749 for (i = 2; bGem == FALSE && i < gemNR; i++)
3751 bGem = bGem || gemmode == i;
3756 printf("Geminate recombination: %s\n", gemType[gemmode]);
3759 if (gemmode != gemDD)
3761 printf("Turning off -contact option...\n");
3767 if (gemmode == gemDD)
3769 printf("Turning on -contact option...\n");
3775 if (gemmode == gemAA)
3777 printf("Turning off -merge option...\n");
3783 if (gemmode != gemAA)
3785 printf("Turning on -merge option...\n");
3793 ccut = cos(acut*DEG2RAD);
3799 gmx_fatal(FARGS, "Can not analyze selected contacts.");
3803 gmx_fatal(FARGS, "Can not analyze contact between H and A: turn off -noda");
3807 /* Initiate main data structure! */
3808 bHBmap = (opt2bSet("-ac", NFILE, fnm) ||
3809 opt2bSet("-life", NFILE, fnm) ||
3810 opt2bSet("-hbn", NFILE, fnm) ||
3811 opt2bSet("-hbm", NFILE, fnm) ||
3814 if (opt2bSet("-nhbdist", NFILE, fnm))
3816 const char *leg[MAXHH+1] = { "0 HBs", "1 HB", "2 HBs", "3 HBs", "Total" };
3817 fpnhb = xvgropen(opt2fn("-nhbdist", NFILE, fnm),
3818 "Number of donor-H with N HBs", output_env_get_xvgr_tlabel(oenv), "N", oenv);
3819 xvgr_legend(fpnhb, asize(leg), leg, oenv);
3822 hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
3825 read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
3827 snew(grpnames, grNR);
3830 /* Make Donor-Acceptor table */
3831 snew(datable, top.atoms.nr);
3832 gen_datable(index[0], isize[0], datable, top.atoms.nr);
3836 /* analyze selected hydrogen bonds */
3837 printf("Select group with selected atoms:\n");
3838 get_index(&(top.atoms), opt2fn("-sel", NFILE, fnm),
3839 1, &nsel, index, grpnames);
3842 gmx_fatal(FARGS, "Number of atoms in group '%s' not a multiple of 3\n"
3843 "and therefore cannot contain triplets of "
3844 "Donor-Hydrogen-Acceptor", grpnames[0]);
3848 for (i = 0; (i < nsel); i += 3)
3850 int dd = index[0][i];
3851 int aa = index[0][i+2];
3852 /* int */ hh = index[0][i+1];
3853 add_dh (&hb->d, dd, hh, i, datable);
3854 add_acc(&hb->a, aa, i);
3855 /* Should this be here ? */
3856 snew(hb->d.dptr, top.atoms.nr);
3857 snew(hb->a.aptr, top.atoms.nr);
3858 add_hbond(hb, dd, aa, hh, gr0, gr0, 0, bMerge, 0, bContact, peri);
3860 printf("Analyzing %d selected hydrogen bonds from '%s'\n",
3861 isize[0], grpnames[0]);
3865 /* analyze all hydrogen bonds: get group(s) */
3866 printf("Specify 2 groups to analyze:\n");
3867 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
3868 2, isize, index, grpnames);
3870 /* check if we have two identical or two non-overlapping groups */
3871 bTwo = isize[0] != isize[1];
3872 for (i = 0; (i < isize[0]) && !bTwo; i++)
3874 bTwo = index[0][i] != index[1][i];
3878 printf("Checking for overlap in atoms between %s and %s\n",
3879 grpnames[0], grpnames[1]);
3880 for (i = 0; i < isize[1]; i++)
3882 if (ISINGRP(datable[index[1][i]]))
3884 gmx_fatal(FARGS, "Partial overlap between groups '%s' and '%s'",
3885 grpnames[0], grpnames[1]);
3889 printf("Checking for overlap in atoms between %s and %s\n",
3890 grpnames[0],grpnames[1]);
3891 for (i=0; i<isize[0]; i++)
3892 for (j=0; j<isize[1]; j++)
3893 if (index[0][i] == index[1][j])
3894 gmx_fatal(FARGS,"Partial overlap between groups '%s' and '%s'",
3895 grpnames[0],grpnames[1]);
3900 printf("Calculating %s "
3901 "between %s (%d atoms) and %s (%d atoms)\n",
3902 bContact ? "contacts" : "hydrogen bonds",
3903 grpnames[0], isize[0], grpnames[1], isize[1]);
3907 fprintf(stderr, "Calculating %s in %s (%d atoms)\n",
3908 bContact ? "contacts" : "hydrogen bonds", grpnames[0], isize[0]);
3913 /* search donors and acceptors in groups */
3914 snew(datable, top.atoms.nr);
3915 for (i = 0; (i < grNR); i++)
3917 if ( ((i == gr0) && !bSelected ) ||
3918 ((i == gr1) && bTwo ))
3920 gen_datable(index[i], isize[i], datable, top.atoms.nr);
3923 search_acceptors(&top, isize[i], index[i], &hb->a, i,
3924 bNitAcc, TRUE, (bTwo && (i == gr0)) || !bTwo, datable);
3925 search_donors (&top, isize[i], index[i], &hb->d, i,
3926 TRUE, (bTwo && (i == gr1)) || !bTwo, datable);
3930 search_acceptors(&top, isize[i], index[i], &hb->a, i, bNitAcc, FALSE, TRUE, datable);
3931 search_donors (&top, isize[i], index[i], &hb->d, i, FALSE, TRUE, datable);
3935 clear_datable_grp(datable, top.atoms.nr);
3940 printf("Found %d donors and %d acceptors\n", hb->d.nrd, hb->a.nra);
3942 snew(donors[gr0D], dons[gr0D].nrd);*/
3946 printf("Making hbmap structure...");
3947 /* Generate hbond data structure */
3952 #ifdef HAVE_NN_LOOPS
3961 printf("Making per structure...");
3962 /* Generate hbond data structure */
3969 if (hb->d.nrd + hb->a.nra == 0)
3971 printf("No Donors or Acceptors found\n");
3978 printf("No Donors found\n");
3983 printf("No Acceptors found\n");
3989 gmx_fatal(FARGS, "Nothing to be done");
3998 /* get index group with atom for shell */
4001 printf("Select atom for shell (1 atom):\n");
4002 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
4003 1, &shisz, &shidx, &shgrpnm);
4006 printf("group contains %d atoms, should be 1 (one)\n", shisz);
4011 printf("Will calculate hydrogen bonds within a shell "
4012 "of %g nm around atom %i\n", rshell, shatom+1);
4015 /* Analyze trajectory */
4016 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
4017 if (natoms > top.atoms.nr)
4019 gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
4020 top.atoms.nr, natoms);
4023 bBox = ir.ePBC != epbcNONE;
4024 grid = init_grid(bBox, box, (rcut > r2cut) ? rcut : r2cut, ngrid);
4027 snew(adist, nabin+1);
4028 snew(rdist, nrbin+1);
4032 gmx_fatal(FARGS, "Can't do geminate recombination without periodic box.");
4038 #define __ADIST adist
4039 #define __RDIST rdist
4041 #else /* GMX_OPENMP ================================================== \
4042 * Set up the OpenMP stuff, |
4043 * like the number of threads and such |
4044 * Also start the parallel loop. |
4046 #define __ADIST p_adist[threadNr]
4047 #define __RDIST p_rdist[threadNr]
4048 #define __HBDATA p_hb[threadNr]
4052 bParallel = !bSelected;
4056 actual_nThreads = min((nThreads <= 0) ? INT_MAX : nThreads, gmx_omp_get_max_threads());
4058 gmx_omp_set_num_threads(actual_nThreads);
4059 printf("Frame loop parallelized with OpenMP using %i threads.\n", actual_nThreads);
4064 actual_nThreads = 1;
4067 snew(p_hb, actual_nThreads);
4068 snew(p_adist, actual_nThreads);
4069 snew(p_rdist, actual_nThreads);
4070 for (i = 0; i < actual_nThreads; i++)
4073 snew(p_adist[i], nabin+1);
4074 snew(p_rdist[i], nrbin+1);
4076 p_hb[i]->max_frames = 0;
4077 p_hb[i]->nhb = NULL;
4078 p_hb[i]->ndist = NULL;
4079 p_hb[i]->n_bound = NULL;
4080 p_hb[i]->time = NULL;
4081 p_hb[i]->nhx = NULL;
4083 p_hb[i]->bHBmap = hb->bHBmap;
4084 p_hb[i]->bDAnr = hb->bDAnr;
4085 p_hb[i]->bGem = hb->bGem;
4086 p_hb[i]->wordlen = hb->wordlen;
4087 p_hb[i]->nframes = hb->nframes;
4088 p_hb[i]->maxhydro = hb->maxhydro;
4089 p_hb[i]->danr = hb->danr;
4092 p_hb[i]->hbmap = hb->hbmap;
4093 p_hb[i]->time = hb->time; /* This may need re-syncing at every frame. */
4094 p_hb[i]->per = hb->per;
4096 #ifdef HAVE_NN_LOOPS
4097 p_hb[i]->hbE = hb->hbE;
4101 p_hb[i]->nrdist = 0;
4105 /* Make a thread pool here,
4106 * instead of forking anew at every frame. */
4108 #pragma omp parallel \
4110 private(j, h, ii, jj, hh, E, \
4111 xi, yi, zi, xj, yj, zj, threadNr, \
4112 dist, ang, peri, icell, jcell, \
4113 grp, ogrp, ai, aj, xjj, yjj, zjj, \
4114 xk, yk, zk, ihb, id, resdist, \
4115 xkk, ykk, zkk, kcell, ak, k, bTric, \
4116 bEdge_xjj, bEdge_yjj) \
4118 { /* Start of parallel region */
4119 threadNr = gmx_omp_get_thread_num();
4124 bTric = bBox && TRICLINIC(box);
4128 sync_hbdata(p_hb[threadNr], nframes);
4132 build_grid(hb, x, x[shatom], bBox, box, hbox, (rcut > r2cut) ? rcut : r2cut,
4133 rshell, ngrid, grid);
4134 reset_nhbonds(&(hb->d));
4136 if (debug && bDebug)
4138 dump_grid(debug, ngrid, grid);
4141 add_frames(hb, nframes);
4142 init_hbframe(hb, nframes, output_env_conv_time(oenv, t));
4146 count_da_grid(ngrid, grid, hb->danr[nframes]);
4152 p_hb[threadNr]->time = hb->time; /* This pointer may have changed. */
4157 #ifdef HAVE_NN_LOOPS /* Unlock this feature when testing */
4158 /* Loop over all atom pairs and estimate interaction energy */
4162 addFramesNN(hb, nframes);
4166 #pragma omp for schedule(dynamic)
4167 for (i = 0; i < hb->d.nrd; i++)
4169 for (j = 0; j < hb->a.nra; j++)
4172 h < (bContact ? 1 : hb->d.nhydro[i]);
4175 if (i == hb->d.nrd || j == hb->a.nra)
4177 gmx_fatal(FARGS, "out of bounds");
4180 /* Get the real atom ids */
4183 hh = hb->d.hydro[i][h];
4185 /* Estimate the energy from the geometry */
4186 E = calcHbEnergy(ii, jj, hh, x, NN, box, hbox, &(hb->d));
4187 /* Store the energy */
4188 storeHbEnergy(hb, i, j, h, E, nframes);
4192 #endif /* HAVE_NN_LOOPS */
4201 /* Do not parallelize this just yet. */
4203 for (ii = 0; (ii < nsel); ii++)
4205 int dd = index[0][i];
4206 int aa = index[0][i+2];
4207 /* int */ hh = index[0][i+1];
4208 ihb = is_hbond(hb, ii, ii, dd, aa, rcut, r2cut, ccut, x, bBox, box,
4209 hbox, &dist, &ang, bDA, &h, bContact, bMerge, &peri);
4213 /* add to index if not already there */
4215 add_hbond(hb, dd, aa, hh, ii, ii, nframes, bMerge, ihb, bContact, peri);
4219 } /* if (bSelected) */
4227 calcBoxProjection(box, hb->per->P);
4230 /* loop over all gridcells (xi,yi,zi) */
4231 /* Removed confusing macro, DvdS 27/12/98 */
4234 /* The outer grid loop will have to do for now. */
4235 #pragma omp for schedule(dynamic)
4236 for (xi = 0; xi < ngrid[XX]; xi++)
4238 for (yi = 0; (yi < ngrid[YY]); yi++)
4240 for (zi = 0; (zi < ngrid[ZZ]); zi++)
4243 /* loop over donor groups gr0 (always) and gr1 (if necessary) */
4244 for (grp = gr0; (grp <= (bTwo ? gr1 : gr0)); grp++)
4246 icell = &(grid[zi][yi][xi].d[grp]);
4257 /* loop over all hydrogen atoms from group (grp)
4258 * in this gridcell (icell)
4260 for (ai = 0; (ai < icell->nr); ai++)
4262 i = icell->atoms[ai];
4264 /* loop over all adjacent gridcells (xj,yj,zj) */
4265 for (zjj = grid_loop_begin(ngrid[ZZ], zi, bTric, FALSE);
4266 zjj <= grid_loop_end(ngrid[ZZ], zi, bTric, FALSE);
4269 zj = grid_mod(zjj, ngrid[ZZ]);
4270 bEdge_yjj = (zj == 0) || (zj == ngrid[ZZ] - 1);
4271 for (yjj = grid_loop_begin(ngrid[YY], yi, bTric, bEdge_yjj);
4272 yjj <= grid_loop_end(ngrid[YY], yi, bTric, bEdge_yjj);
4275 yj = grid_mod(yjj, ngrid[YY]);
4277 (yj == 0) || (yj == ngrid[YY] - 1) ||
4278 (zj == 0) || (zj == ngrid[ZZ] - 1);
4279 for (xjj = grid_loop_begin(ngrid[XX], xi, bTric, bEdge_xjj);
4280 xjj <= grid_loop_end(ngrid[XX], xi, bTric, bEdge_xjj);
4283 xj = grid_mod(xjj, ngrid[XX]);
4284 jcell = &(grid[zj][yj][xj].a[ogrp]);
4285 /* loop over acceptor atoms from other group (ogrp)
4286 * in this adjacent gridcell (jcell)
4288 for (aj = 0; (aj < jcell->nr); aj++)
4290 j = jcell->atoms[aj];
4292 /* check if this once was a h-bond */
4294 ihb = is_hbond(__HBDATA, grp, ogrp, i, j, rcut, r2cut, ccut, x, bBox, box,
4295 hbox, &dist, &ang, bDA, &h, bContact, bMerge, &peri);
4299 /* add to index if not already there */
4301 add_hbond(__HBDATA, i, j, h, grp, ogrp, nframes, bMerge, ihb, bContact, peri);
4303 /* make angle and distance distributions */
4304 if (ihb == hbHB && !bContact)
4308 gmx_fatal(FARGS, "distance is higher than what is allowed for an hbond: %f", dist);
4311 __ADIST[(int)( ang/abin)]++;
4312 __RDIST[(int)(dist/rbin)]++;
4316 if ((id = donor_index(&hb->d, grp, i)) == NOTSET)
4318 gmx_fatal(FARGS, "Invalid donor %d", i);
4320 if ((ia = acceptor_index(&hb->a, ogrp, j)) == NOTSET)
4322 gmx_fatal(FARGS, "Invalid acceptor %d", j);
4324 resdist = abs(top.atoms.atom[i].resind-
4325 top.atoms.atom[j].resind);
4326 if (resdist >= max_hx)
4330 __HBDATA->nhx[nframes][resdist]++;
4341 } /* for xi,yi,zi */
4344 } /* if (bSelected) {...} else */
4347 /* Better wait for all threads to finnish using x[] before updating it. */
4350 #pragma omp critical
4352 /* Sum up histograms and counts from p_hb[] into hb */
4355 hb->nhb[k] += p_hb[threadNr]->nhb[k];
4356 hb->ndist[k] += p_hb[threadNr]->ndist[k];
4357 for (j = 0; j < max_hx; j++)
4359 hb->nhx[k][j] += p_hb[threadNr]->nhx[k][j];
4364 /* Here are a handful of single constructs
4365 * to share the workload a bit. The most
4366 * important one is of course the last one,
4367 * where there's a potential bottleneck in form
4374 analyse_donor_props(opt2fn_null("-don", NFILE, fnm), hb, k, t, oenv);
4382 do_nhb_dist(fpnhb, hb, t);
4385 } /* if (bNN) {...} else + */
4389 trrStatus = (read_next_x(oenv, status, &t, x, box));
4399 #pragma omp critical
4401 hb->nrhb += p_hb[threadNr]->nrhb;
4402 hb->nrdist += p_hb[threadNr]->nrdist;
4404 /* Free parallel datastructures */
4405 sfree(p_hb[threadNr]->nhb);
4406 sfree(p_hb[threadNr]->ndist);
4407 sfree(p_hb[threadNr]->nhx);
4410 for (i = 0; i < nabin; i++)
4412 for (j = 0; j < actual_nThreads; j++)
4415 adist[i] += p_adist[j][i];
4419 for (i = 0; i <= nrbin; i++)
4421 for (j = 0; j < actual_nThreads; j++)
4423 rdist[i] += p_rdist[j][i];
4427 sfree(p_adist[threadNr]);
4428 sfree(p_rdist[threadNr]);
4430 } /* End of parallel region */
4437 if (nframes < 2 && (opt2bSet("-ac", NFILE, fnm) || opt2bSet("-life", NFILE, fnm)))
4439 gmx_fatal(FARGS, "Cannot calculate autocorrelation of life times with less than two frames");
4442 free_grid(ngrid, &grid);
4450 /* Compute maximum possible number of different hbonds */
4457 max_nhb = 0.5*(hb->d.nrd*hb->a.nra);
4459 /* Added support for -contact below.
4460 * - Erik Marklund, May 29-31, 2006 */
4461 /* Changed contact code.
4462 * - Erik Marklund, June 29, 2006 */
4467 printf("No %s found!!\n", bContact ? "contacts" : "hydrogen bonds");
4471 printf("Found %d different %s in trajectory\n"
4472 "Found %d different atom-pairs within %s distance\n",
4473 hb->nrhb, bContact ? "contacts" : "hydrogen bonds",
4474 hb->nrdist, (r2cut > 0) ? "second cut-off" : "hydrogen bonding");
4476 /*Control the pHist.*/
4480 merge_hb(hb, bTwo, bContact);
4483 if (opt2bSet("-hbn", NFILE, fnm))
4485 dump_hbmap(hb, NFILE, fnm, bTwo, bContact, isize, index, grpnames, &top.atoms);
4488 /* Moved the call to merge_hb() to a line BEFORE dump_hbmap
4489 * to make the -hbn and -hmb output match eachother.
4490 * - Erik Marklund, May 30, 2006 */
4493 /* Print out number of hbonds and distances */
4496 fp = xvgropen(opt2fn("-num", NFILE, fnm), bContact ? "Contacts" :
4497 "Hydrogen Bonds", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
4499 snew(leg[0], STRLEN);
4500 snew(leg[1], STRLEN);
4501 sprintf(leg[0], "%s", bContact ? "Contacts" : "Hydrogen bonds");
4502 sprintf(leg[1], "Pairs within %g nm", (r2cut > 0) ? r2cut : rcut);
4503 xvgr_legend(fp, 2, (const char**)leg, oenv);
4507 for (i = 0; (i < nframes); i++)
4509 fprintf(fp, "%10g %10d %10d\n", hb->time[i], hb->nhb[i], hb->ndist[i]);
4510 aver_nhb += hb->nhb[i];
4511 aver_dist += hb->ndist[i];
4514 aver_nhb /= nframes;
4515 aver_dist /= nframes;
4516 /* Print HB distance distribution */
4517 if (opt2bSet("-dist", NFILE, fnm))
4522 for (i = 0; i < nrbin; i++)
4527 fp = xvgropen(opt2fn("-dist", NFILE, fnm),
4528 "Hydrogen Bond Distribution",
4530 "Donor - Acceptor Distance (nm)" :
4531 "Hydrogen - Acceptor Distance (nm)", "", oenv);
4532 for (i = 0; i < nrbin; i++)
4534 fprintf(fp, "%10g %10g\n", (i+0.5)*rbin, rdist[i]/(rbin*(real)sum));
4539 /* Print HB angle distribution */
4540 if (opt2bSet("-ang", NFILE, fnm))
4545 for (i = 0; i < nabin; i++)
4550 fp = xvgropen(opt2fn("-ang", NFILE, fnm),
4551 "Hydrogen Bond Distribution",
4552 "Hydrogen - Donor - Acceptor Angle (\\SO\\N)", "", oenv);
4553 for (i = 0; i < nabin; i++)
4555 fprintf(fp, "%10g %10g\n", (i+0.5)*abin, adist[i]/(abin*(real)sum));
4560 /* Print HB in alpha-helix */
4561 if (opt2bSet("-hx", NFILE, fnm))
4563 fp = xvgropen(opt2fn("-hx", NFILE, fnm),
4564 "Hydrogen Bonds", output_env_get_xvgr_tlabel(oenv), "Count", oenv);
4565 xvgr_legend(fp, NRHXTYPES, hxtypenames, oenv);
4566 for (i = 0; i < nframes; i++)
4568 fprintf(fp, "%10g", hb->time[i]);
4569 for (j = 0; j < max_hx; j++)
4571 fprintf(fp, " %6d", hb->nhx[i][j]);
4579 printf("Average number of %s per timeframe %.3f out of %g possible\n",
4580 bContact ? "contacts" : "hbonds",
4581 bContact ? aver_dist : aver_nhb, max_nhb);
4584 /* Do Autocorrelation etc. */
4588 Added support for -contact in ac and hbm calculations below.
4589 - Erik Marklund, May 29, 2006
4593 if (opt2bSet("-ac", NFILE, fnm) || opt2bSet("-life", NFILE, fnm))
4595 please_cite(stdout, "Spoel2006b");
4597 if (opt2bSet("-ac", NFILE, fnm))
4599 char *gemstring = NULL;
4603 params = init_gemParams(rcut, D, hb->time, hb->nframes/2, nFitPoints, fit_start, fit_end,
4604 gemBallistic, nBalExp);
4607 gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
4610 gemstring = gmx_strdup(gemType[hb->per->gemtype]);
4611 do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
4612 bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
4613 gemstring, nThreads, NN, bBallistic, bGemFit);
4615 if (opt2bSet("-life", NFILE, fnm))
4617 do_hblife(opt2fn("-life", NFILE, fnm), hb, bMerge, bContact, oenv);
4619 if (opt2bSet("-hbm", NFILE, fnm))
4622 int id, ia, hh, x, y;
4623 mat.flags = mat.y0 = 0;
4625 if ((nframes > 0) && (hb->nrhb > 0))
4630 snew(mat.matrix, mat.nx);
4631 for (x = 0; (x < mat.nx); x++)
4633 snew(mat.matrix[x], mat.ny);
4636 for (id = 0; (id < hb->d.nrd); id++)
4638 for (ia = 0; (ia < hb->a.nra); ia++)
4640 for (hh = 0; (hh < hb->maxhydro); hh++)
4642 if (hb->hbmap[id][ia])
4644 if (ISHB(hb->hbmap[id][ia]->history[hh]))
4646 /* Changed '<' into '<=' in the for-statement below.
4647 * It fixed the previously undiscovered bug that caused
4648 * the last occurance of an hbond/contact to not be
4649 * set in mat.matrix. Have a look at any old -hbm-output
4650 * and you will notice that the last column is allways empty.
4651 * - Erik Marklund May 30, 2006
4653 for (x = 0; (x <= hb->hbmap[id][ia]->nframes); x++)
4655 int nn0 = hb->hbmap[id][ia]->n0;
4656 range_check(y, 0, mat.ny);
4657 mat.matrix[x+nn0][y] = is_hb(hb->hbmap[id][ia]->h[hh], x);
4665 mat.axis_x = hb->time;
4666 snew(mat.axis_y, mat.ny);
4667 for (j = 0; j < mat.ny; j++)
4671 sprintf(mat.title, bContact ? "Contact Existence Map" :
4672 "Hydrogen Bond Existence Map");
4673 sprintf(mat.legend, bContact ? "Contacts" : "Hydrogen Bonds");
4674 sprintf(mat.label_x, "%s", output_env_get_xvgr_tlabel(oenv));
4675 sprintf(mat.label_y, bContact ? "Contact Index" : "Hydrogen Bond Index");
4676 mat.bDiscrete = TRUE;
4678 snew(mat.map, mat.nmap);
4679 for (i = 0; i < mat.nmap; i++)
4681 mat.map[i].code.c1 = hbmap[i];
4682 mat.map[i].desc = hbdesc[i];
4683 mat.map[i].rgb = hbrgb[i];
4685 fp = opt2FILE("-hbm", NFILE, fnm, "w");
4686 write_xpm_m(fp, mat);
4688 for (x = 0; x < mat.nx; x++)
4690 sfree(mat.matrix[x]);
4698 fprintf(stderr, "No hydrogen bonds/contacts found. No hydrogen bond map will be printed.\n");
4705 fprintf(stderr, "There were %i periodic shifts\n", hb->per->nper);
4706 fprintf(stderr, "Freeing pHist for all donors...\n");
4707 for (i = 0; i < hb->d.nrd; i++)
4709 fprintf(stderr, "\r%i", i);
4710 if (hb->per->pHist[i] != NULL)
4712 for (j = 0; j < hb->a.nra; j++)
4714 clearPshift(&(hb->per->pHist[i][j]));
4716 sfree(hb->per->pHist[i]);
4719 sfree(hb->per->pHist);
4720 sfree(hb->per->p2i);
4722 fprintf(stderr, "...done.\n");
4725 #ifdef HAVE_NN_LOOPS
4738 #define USE_THIS_GROUP(j) ( (j == gr0) || (bTwo && (j == gr1)) )
4740 fp = xvgropen(opt2fn("-dan", NFILE, fnm),
4741 "Donors and Acceptors", output_env_get_xvgr_tlabel(oenv), "Count", oenv);
4742 nleg = (bTwo ? 2 : 1)*2;
4743 snew(legnames, nleg);
4745 for (j = 0; j < grNR; j++)
4747 if (USE_THIS_GROUP(j) )
4749 sprintf(buf, "Donors %s", grpnames[j]);
4750 legnames[i++] = gmx_strdup(buf);
4751 sprintf(buf, "Acceptors %s", grpnames[j]);
4752 legnames[i++] = gmx_strdup(buf);
4757 gmx_incons("number of legend entries");
4759 xvgr_legend(fp, nleg, (const char**)legnames, oenv);
4760 for (i = 0; i < nframes; i++)
4762 fprintf(fp, "%10g", hb->time[i]);
4763 for (j = 0; (j < grNR); j++)
4765 if (USE_THIS_GROUP(j) )
4767 fprintf(fp, " %6d", hb->danr[i][j]);