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40 /*#define HAVE_NN_LOOPS*/
42 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/math/units.h"
47 #include "gromacs/utility/fatalerror.h"
48 #include "gromacs/topology/index.h"
49 #include "gromacs/utility/smalloc.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/fileio/xvgr.h"
54 #include "gromacs/utility/cstringutil.h"
55 #include "gromacs/pbcutil/pbc.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/fileio/matio.h"
62 #include "gromacs/fileio/tpxio.h"
63 #include "gromacs/fileio/trxio.h"
64 #include "gromacs/utility/gmxomp.h"
66 typedef short int t_E;
69 typedef int t_hx[max_hx];
70 #define NRHXTYPES max_hx
71 const char *hxtypenames[NRHXTYPES] =
72 {"n-n", "n-n+1", "n-n+2", "n-n+3", "n-n+4", "n-n+5", "n-n>6"};
76 #define MASTER_THREAD_ONLY(threadNr) ((threadNr) == 0)
78 #define MASTER_THREAD_ONLY(threadNr) ((threadNr) == (threadNr))
81 /* -----------------------------------------*/
87 hbNo, hbDist, hbHB, hbNR, hbR2
90 noDA, ACC, DON, DA, INGROUP
93 NN_NULL, NN_NONE, NN_BINARY, NN_1_over_r3, NN_dipole, NN_NR
96 static const char *grpnames[grNR] = {"0", "1", "I" };
98 static gmx_bool bDebug = FALSE;
103 #define HB_YESINS HB_YES|HB_INS
107 #define ISHB(h) (((h) & 2) == 2)
108 #define ISDIST(h) (((h) & 1) == 1)
109 #define ISDIST2(h) (((h) & 4) == 4)
110 #define ISACC(h) (((h) & 1) == 1)
111 #define ISDON(h) (((h) & 2) == 2)
112 #define ISINGRP(h) (((h) & 4) == 4)
125 typedef int t_icell[grNR];
126 typedef atom_id h_id[MAXHYDRO];
129 int history[MAXHYDRO];
130 /* Has this hbond existed ever? If so as hbDist or hbHB or both.
131 * Result is stored as a bitmap (1 = hbDist) || (2 = hbHB)
133 /* Bitmask array which tells whether a hbond is present
134 * at a given time. Either of these may be NULL
136 int n0; /* First frame a HB was found */
137 int nframes, maxframes; /* Amount of frames in this hbond */
140 /* See Xu and Berne, JPCB 105 (2001), p. 11929. We define the
141 * function g(t) = [1-h(t)] H(t) where H(t) is one when the donor-
142 * acceptor distance is less than the user-specified distance (typically
149 atom_id *acc; /* Atom numbers of the acceptors */
150 int *grp; /* Group index */
151 int *aptr; /* Map atom number to acceptor index */
156 int *don; /* Atom numbers of the donors */
157 int *grp; /* Group index */
158 int *dptr; /* Map atom number to donor index */
159 int *nhydro; /* Number of hydrogens for each donor */
160 h_id *hydro; /* The atom numbers of the hydrogens */
161 h_id *nhbonds; /* The number of HBs per H at current */
164 /* Tune this to match memory requirements. It should be a signed integer type, e.g. signed char.*/
168 int len; /* The length of frame and p. */
169 int *frame; /* The frames at which transitio*/
174 /* Periodicity history. Used for the reversible geminate recombination. */
175 t_pShift **pHist; /* The periodicity of every hbond in t_hbdata->hbmap:
176 * pHist[d][a]. We can safely assume that the same
177 * periodic shift holds for all hydrogens of a da-pair.
179 * Nowadays it only stores TRANSITIONS, and not the shift at every frame.
180 * That saves a LOT of memory, an hopefully kills a mysterious bug where
181 * pHist gets contaminated. */
183 PSTYPE nper; /* The length of p2i */
184 ivec *p2i; /* Maps integer to periodic shift for a pair.*/
185 matrix P; /* Projection matrix to find the box shifts. */
186 int gemtype; /* enumerated type */
191 int *Etot; /* Total energy for each frame */
192 t_E ****E; /* Energy estimate for [d][a][h][frame-n0] */
196 gmx_bool bHBmap, bDAnr, bGem;
198 /* The following arrays are nframes long */
199 int nframes, max_frames, maxhydro;
205 /* These structures are initialized from the topology at start up */
208 /* This holds a matrix with all possible hydrogen bonds */
214 /* For parallelization reasons this will have to be a pointer.
215 * Otherwise discrepancies may arise between the periodicity data
216 * seen by different threads. */
220 static void clearPshift(t_pShift *pShift)
225 sfree(pShift->frame);
230 static void calcBoxProjection(matrix B, matrix P)
232 const int vp[] = {XX, YY, ZZ};
237 for (i = 0; i < 3; i++)
240 for (j = 0; j < 3; j++)
243 U[m][n] = i == j ? 1 : 0;
247 for (i = 0; i < 3; i++)
250 mvmul(M, U[m], P[m]);
255 static void calcBoxDistance(matrix P, rvec d, ivec ibd)
257 /* returns integer distance in box coordinates.
258 * P is the projection matrix from cartesian coordinates
259 * obtained with calcBoxProjection(). */
263 /* extend it by 0.5 in all directions since (int) rounds toward 0.*/
264 for (i = 0; i < 3; i++)
266 bd[i] = bd[i] + (bd[i] < 0 ? -0.5 : 0.5);
268 ibd[XX] = (int)bd[XX];
269 ibd[YY] = (int)bd[YY];
270 ibd[ZZ] = (int)bd[ZZ];
273 /* Changed argument 'bMerge' into 'oneHB' below,
274 * since -contact should cause maxhydro to be 1,
276 * - Erik Marklund May 29, 2006
279 static PSTYPE periodicIndex(ivec r, t_gemPeriod *per, gmx_bool daSwap)
281 /* Try to merge hbonds on the fly. That means that if the
282 * acceptor and donor are mergable, then:
283 * 1) store the hb-info so that acceptor id > donor id,
284 * 2) add the periodic shift in pairs, so that [-x,-y,-z] is
285 * stored in per.p2i[] whenever acceptor id < donor id.
286 * Note that [0,0,0] should already be the first element of per.p2i
287 * by the time this function is called. */
289 /* daSwap is TRUE if the donor and acceptor were swapped.
290 * If so, then the negative vector should be used. */
293 if (per->p2i == NULL || per->nper == 0)
295 gmx_fatal(FARGS, "'per' not initialized properly.");
297 for (i = 0; i < per->nper; i++)
299 if (r[XX] == per->p2i[i][XX] &&
300 r[YY] == per->p2i[i][YY] &&
301 r[ZZ] == per->p2i[i][ZZ])
306 /* Not found apparently. Add it to the list! */
307 /* printf("New shift found: %i,%i,%i\n",r[XX],r[YY],r[ZZ]); */
313 fprintf(stderr, "p2i not initialized. This shouldn't happen!\n");
318 srenew(per->p2i, per->nper+2);
320 copy_ivec(r, per->p2i[per->nper]);
323 /* Add the mirror too. It's rather likely that it'll be needed. */
324 per->p2i[per->nper][XX] = -r[XX];
325 per->p2i[per->nper][YY] = -r[YY];
326 per->p2i[per->nper][ZZ] = -r[ZZ];
329 return per->nper - 1 - (daSwap ? 0 : 1);
332 static t_hbdata *mk_hbdata(gmx_bool bHBmap, gmx_bool bDAnr, gmx_bool oneHB, gmx_bool bGem, int gemmode)
337 hb->wordlen = 8*sizeof(unsigned int);
347 hb->maxhydro = MAXHYDRO;
350 hb->per->gemtype = bGem ? gemmode : 0;
355 static void mk_hbmap(t_hbdata *hb)
359 snew(hb->hbmap, hb->d.nrd);
360 for (i = 0; (i < hb->d.nrd); i++)
362 snew(hb->hbmap[i], hb->a.nra);
363 if (hb->hbmap[i] == NULL)
365 gmx_fatal(FARGS, "Could not allocate enough memory for hbmap");
367 for (j = 0; (j > hb->a.nra); j++)
369 hb->hbmap[i][j] = NULL;
374 /* Consider redoing pHist so that is only stores transitions between
375 * periodicities and not the periodicity for all frames. This eats heaps of memory. */
376 static void mk_per(t_hbdata *hb)
381 snew(hb->per->pHist, hb->d.nrd);
382 for (i = 0; i < hb->d.nrd; i++)
384 snew(hb->per->pHist[i], hb->a.nra);
385 if (hb->per->pHist[i] == NULL)
387 gmx_fatal(FARGS, "Could not allocate enough memory for per->pHist");
389 for (j = 0; j < hb->a.nra; j++)
391 clearPshift(&(hb->per->pHist[i][j]));
394 /* add the [0,0,0] shift to element 0 of p2i. */
395 snew(hb->per->p2i, 1);
396 clear_ivec(hb->per->p2i[0]);
402 static void mk_hbEmap (t_hbdata *hb, int n0)
407 snew(hb->hbE.E, hb->d.nrd);
408 for (i = 0; i < hb->d.nrd; i++)
410 snew(hb->hbE.E[i], hb->a.nra);
411 for (j = 0; j < hb->a.nra; j++)
413 snew(hb->hbE.E[i][j], MAXHYDRO);
414 for (k = 0; k < MAXHYDRO; k++)
416 hb->hbE.E[i][j][k] = NULL;
423 static void free_hbEmap (t_hbdata *hb)
426 for (i = 0; i < hb->d.nrd; i++)
428 for (j = 0; j < hb->a.nra; j++)
430 for (k = 0; k < MAXHYDRO; k++)
432 sfree(hb->hbE.E[i][j][k]);
434 sfree(hb->hbE.E[i][j]);
442 static void addFramesNN(t_hbdata *hb, int frame)
445 #define DELTAFRAMES_HBE 10
447 int d, a, h, nframes;
449 if (frame >= hb->hbE.nframes)
451 nframes = hb->hbE.nframes + DELTAFRAMES_HBE;
452 srenew(hb->hbE.Etot, nframes);
454 for (d = 0; d < hb->d.nrd; d++)
456 for (a = 0; a < hb->a.nra; a++)
458 for (h = 0; h < hb->d.nhydro[d]; h++)
460 srenew(hb->hbE.E[d][a][h], nframes);
465 hb->hbE.nframes += DELTAFRAMES_HBE;
469 static t_E calcHbEnergy(int d, int a, int h, rvec x[], t_EEst EEst,
470 matrix box, rvec hbox, t_donors *donors)
475 * alpha - angle between dipoles
476 * x[] - atomic positions
477 * EEst - the type of energy estimate (see enum in hbplugin.h)
478 * box - the box vectors \
479 * hbox - half box lengths _These two are only needed for the pbc correction
484 rvec dipole[2], xmol[3], xmean[2];
490 /* Self-interaction */
497 /* This is a simple binary existence function that sets E=1 whenever
498 * the distance between the oxygens is equal too or less than 0.35 nm.
500 rvec_sub(x[d], x[a], dist);
501 pbc_correct_gem(dist, box, hbox);
502 if (norm(dist) <= 0.35)
513 /* Negative potential energy of a dipole.
514 * E = -cos(alpha) * 1/r^3 */
516 copy_rvec(x[d], xmol[0]); /* donor */
517 copy_rvec(x[donors->hydro[donors->dptr[d]][0]], xmol[1]); /* hydrogen */
518 copy_rvec(x[donors->hydro[donors->dptr[d]][1]], xmol[2]); /* hydrogen */
520 svmul(15.9994*(1/1.008), xmol[0], xmean[0]);
521 rvec_inc(xmean[0], xmol[1]);
522 rvec_inc(xmean[0], xmol[2]);
523 for (i = 0; i < 3; i++)
525 xmean[0][i] /= (15.9994 + 1.008 + 1.008)/1.008;
528 /* Assumes that all acceptors are also donors. */
529 copy_rvec(x[a], xmol[0]); /* acceptor */
530 copy_rvec(x[donors->hydro[donors->dptr[a]][0]], xmol[1]); /* hydrogen */
531 copy_rvec(x[donors->hydro[donors->dptr[a]][1]], xmol[2]); /* hydrogen */
534 svmul(15.9994*(1/1.008), xmol[0], xmean[1]);
535 rvec_inc(xmean[1], xmol[1]);
536 rvec_inc(xmean[1], xmol[2]);
537 for (i = 0; i < 3; i++)
539 xmean[1][i] /= (15.9994 + 1.008 + 1.008)/1.008;
542 rvec_sub(xmean[0], xmean[1], dist);
543 pbc_correct_gem(dist, box, hbox);
546 realE = pow(r, -3.0);
547 E = (t_E)(SCALEFACTOR_E * realE);
551 /* Negative potential energy of a (unpolarizable) dipole.
552 * E = -cos(alpha) * 1/r^3 */
553 clear_rvec(dipole[1]);
554 clear_rvec(dipole[0]);
556 copy_rvec(x[d], xmol[0]); /* donor */
557 copy_rvec(x[donors->hydro[donors->dptr[d]][0]], xmol[1]); /* hydrogen */
558 copy_rvec(x[donors->hydro[donors->dptr[d]][1]], xmol[2]); /* hydrogen */
560 rvec_inc(dipole[0], xmol[1]);
561 rvec_inc(dipole[0], xmol[2]);
562 for (i = 0; i < 3; i++)
566 rvec_dec(dipole[0], xmol[0]);
568 svmul(15.9994*(1/1.008), xmol[0], xmean[0]);
569 rvec_inc(xmean[0], xmol[1]);
570 rvec_inc(xmean[0], xmol[2]);
571 for (i = 0; i < 3; i++)
573 xmean[0][i] /= (15.9994 + 1.008 + 1.008)/1.008;
576 /* Assumes that all acceptors are also donors. */
577 copy_rvec(x[a], xmol[0]); /* acceptor */
578 copy_rvec(x[donors->hydro[donors->dptr[a]][0]], xmol[1]); /* hydrogen */
579 copy_rvec(x[donors->hydro[donors->dptr[a]][2]], xmol[2]); /* hydrogen */
582 rvec_inc(dipole[1], xmol[1]);
583 rvec_inc(dipole[1], xmol[2]);
584 for (i = 0; i < 3; i++)
588 rvec_dec(dipole[1], xmol[0]);
590 svmul(15.9994*(1/1.008), xmol[0], xmean[1]);
591 rvec_inc(xmean[1], xmol[1]);
592 rvec_inc(xmean[1], xmol[2]);
593 for (i = 0; i < 3; i++)
595 xmean[1][i] /= (15.9994 + 1.008 + 1.008)/1.008;
598 rvec_sub(xmean[0], xmean[1], dist);
599 pbc_correct_gem(dist, box, hbox);
602 double cosalpha = cos_angle(dipole[0], dipole[1]);
603 realE = cosalpha * pow(r, -3.0);
604 E = (t_E)(SCALEFACTOR_E * realE);
608 printf("Can't do that type of energy estimate: %i\n.", EEst);
615 static void storeHbEnergy(t_hbdata *hb, int d, int a, int h, t_E E, int frame)
617 /* hb - hbond data structure
621 E - estimate of the energy
622 frame - the current frame.
625 /* Store the estimated energy */
631 hb->hbE.E[d][a][h][frame] = E;
635 hb->hbE.Etot[frame] += E;
638 #endif /* HAVE_NN_LOOPS */
641 /* Finds -v[] in the periodicity index */
642 static int findMirror(PSTYPE p, ivec v[], PSTYPE nper)
646 for (i = 0; i < nper; i++)
648 if (v[i][XX] == -(v[p][XX]) &&
649 v[i][YY] == -(v[p][YY]) &&
650 v[i][ZZ] == -(v[p][ZZ]))
655 printf("Couldn't find mirror of [%i, %i, %i], index \n",
663 static void add_frames(t_hbdata *hb, int nframes)
667 if (nframes >= hb->max_frames)
669 hb->max_frames += 4096;
670 srenew(hb->time, hb->max_frames);
671 srenew(hb->nhb, hb->max_frames);
672 srenew(hb->ndist, hb->max_frames);
673 srenew(hb->n_bound, hb->max_frames);
674 srenew(hb->nhx, hb->max_frames);
677 srenew(hb->danr, hb->max_frames);
680 hb->nframes = nframes;
683 #define OFFSET(frame) (frame / 32)
684 #define MASK(frame) (1 << (frame % 32))
686 static void _set_hb(unsigned int hbexist[], unsigned int frame, gmx_bool bValue)
690 hbexist[OFFSET(frame)] |= MASK(frame);
694 hbexist[OFFSET(frame)] &= ~MASK(frame);
698 static gmx_bool is_hb(unsigned int hbexist[], int frame)
700 return ((hbexist[OFFSET(frame)] & MASK(frame)) != 0) ? 1 : 0;
703 static void set_hb(t_hbdata *hb, int id, int ih, int ia, int frame, int ihb)
705 unsigned int *ghptr = NULL;
709 ghptr = hb->hbmap[id][ia]->h[ih];
711 else if (ihb == hbDist)
713 ghptr = hb->hbmap[id][ia]->g[ih];
717 gmx_fatal(FARGS, "Incomprehensible iValue %d in set_hb", ihb);
720 _set_hb(ghptr, frame-hb->hbmap[id][ia]->n0, TRUE);
723 static void addPshift(t_pShift *pHist, PSTYPE p, int frame)
727 snew(pHist->frame, 1);
730 pHist->frame[0] = frame;
735 if (pHist->p[pHist->len-1] != p)
738 srenew(pHist->frame, pHist->len);
739 srenew(pHist->p, pHist->len);
740 pHist->frame[pHist->len-1] = frame;
741 pHist->p[pHist->len-1] = p;
742 } /* Otherwise, there is no transition. */
746 static PSTYPE getPshift(t_pShift pHist, int frame)
751 || (pHist.len > 0 && pHist.frame[0] > frame))
756 for (i = 0; i < pHist.len; i++)
769 /* It seems that frame is after the last periodic transition. Return the last periodicity. */
770 return pHist.p[pHist.len-1];
773 static void add_ff(t_hbdata *hbd, int id, int h, int ia, int frame, int ihb, PSTYPE p)
776 t_hbond *hb = hbd->hbmap[id][ia];
777 int maxhydro = min(hbd->maxhydro, hbd->d.nhydro[id]);
778 int wlen = hbd->wordlen;
780 gmx_bool bGem = hbd->bGem;
785 hb->maxframes = delta;
786 for (i = 0; (i < maxhydro); i++)
788 snew(hb->h[i], hb->maxframes/wlen);
789 snew(hb->g[i], hb->maxframes/wlen);
794 hb->nframes = frame-hb->n0;
795 /* We need a while loop here because hbonds may be returning
798 while (hb->nframes >= hb->maxframes)
800 n = hb->maxframes + delta;
801 for (i = 0; (i < maxhydro); i++)
803 srenew(hb->h[i], n/wlen);
804 srenew(hb->g[i], n/wlen);
805 for (j = hb->maxframes/wlen; (j < n/wlen); j++)
817 set_hb(hbd, id, h, ia, frame, ihb);
820 if (p >= hbd->per->nper)
822 gmx_fatal(FARGS, "invalid shift: p=%u, nper=%u", p, hbd->per->nper);
826 addPshift(&(hbd->per->pHist[id][ia]), p, frame);
834 static void inc_nhbonds(t_donors *ddd, int d, int h)
837 int dptr = ddd->dptr[d];
839 for (j = 0; (j < ddd->nhydro[dptr]); j++)
841 if (ddd->hydro[dptr][j] == h)
843 ddd->nhbonds[dptr][j]++;
847 if (j == ddd->nhydro[dptr])
849 gmx_fatal(FARGS, "No such hydrogen %d on donor %d\n", h+1, d+1);
853 static int _acceptor_index(t_acceptors *a, int grp, atom_id i,
854 const char *file, int line)
858 if (a->grp[ai] != grp)
862 fprintf(debug, "Acc. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n",
863 ai, a->grp[ai], grp, file, line);
872 #define acceptor_index(a, grp, i) _acceptor_index(a, grp, i, __FILE__, __LINE__)
874 static int _donor_index(t_donors *d, int grp, atom_id i, const char *file, int line)
883 if (d->grp[di] != grp)
887 fprintf(debug, "Don. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n",
888 di, d->grp[di], grp, file, line);
897 #define donor_index(d, grp, i) _donor_index(d, grp, i, __FILE__, __LINE__)
899 static gmx_bool isInterchangable(t_hbdata *hb, int d, int a, int grpa, int grpd)
901 /* g_hbond doesn't allow overlapping groups */
907 donor_index(&hb->d, grpd, a) != NOTSET
908 && acceptor_index(&hb->a, grpa, d) != NOTSET;
912 static void add_hbond(t_hbdata *hb, int d, int a, int h, int grpd, int grpa,
913 int frame, gmx_bool bMerge, int ihb, gmx_bool bContact, PSTYPE p)
916 gmx_bool daSwap = FALSE;
918 if ((id = hb->d.dptr[d]) == NOTSET)
920 gmx_fatal(FARGS, "No donor atom %d", d+1);
922 else if (grpd != hb->d.grp[id])
924 gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
925 grpd, hb->d.grp[id], d+1);
927 if ((ia = hb->a.aptr[a]) == NOTSET)
929 gmx_fatal(FARGS, "No acceptor atom %d", a+1);
931 else if (grpa != hb->a.grp[ia])
933 gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
934 grpa, hb->a.grp[ia], a+1);
940 if (isInterchangable(hb, d, a, grpd, grpa) && d > a)
941 /* Then swap identity so that the id of d is lower then that of a.
943 * This should really be redundant by now, as is_hbond() now ought to return
944 * hbNo in the cases where this conditional is TRUE. */
951 /* Now repeat donor/acc check. */
952 if ((id = hb->d.dptr[d]) == NOTSET)
954 gmx_fatal(FARGS, "No donor atom %d", d+1);
956 else if (grpd != hb->d.grp[id])
958 gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
959 grpd, hb->d.grp[id], d+1);
961 if ((ia = hb->a.aptr[a]) == NOTSET)
963 gmx_fatal(FARGS, "No acceptor atom %d", a+1);
965 else if (grpa != hb->a.grp[ia])
967 gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
968 grpa, hb->a.grp[ia], a+1);
975 /* Loop over hydrogens to find which hydrogen is in this particular HB */
976 if ((ihb == hbHB) && !bMerge && !bContact)
978 for (k = 0; (k < hb->d.nhydro[id]); k++)
980 if (hb->d.hydro[id][k] == h)
985 if (k == hb->d.nhydro[id])
987 gmx_fatal(FARGS, "Donor %d does not have hydrogen %d (a = %d)",
1001 if (hb->hbmap[id][ia] == NULL)
1003 snew(hb->hbmap[id][ia], 1);
1004 snew(hb->hbmap[id][ia]->h, hb->maxhydro);
1005 snew(hb->hbmap[id][ia]->g, hb->maxhydro);
1007 add_ff(hb, id, k, ia, frame, ihb, p);
1011 /* Strange construction with frame >=0 is a relic from old code
1012 * for selected hbond analysis. It may be necessary again if that
1013 * is made to work again.
1017 hh = hb->hbmap[id][ia]->history[k];
1023 hb->hbmap[id][ia]->history[k] = hh | 2;
1034 hb->hbmap[id][ia]->history[k] = hh | 1;
1058 if (bMerge && daSwap)
1060 h = hb->d.hydro[id][0];
1062 /* Increment number if HBonds per H */
1063 if (ihb == hbHB && !bContact)
1065 inc_nhbonds(&(hb->d), d, h);
1069 static char *mkatomname(t_atoms *atoms, int i)
1071 static char buf[32];
1074 rnr = atoms->atom[i].resind;
1075 sprintf(buf, "%4s%d%-4s",
1076 *atoms->resinfo[rnr].name, atoms->resinfo[rnr].nr, *atoms->atomname[i]);
1081 static void gen_datable(atom_id *index, int isize, unsigned char *datable, int natoms)
1083 /* Generates table of all atoms and sets the ingroup bit for atoms in index[] */
1086 for (i = 0; i < isize; i++)
1088 if (index[i] >= natoms)
1090 gmx_fatal(FARGS, "Atom has index %d larger than number of atoms %d.", index[i], natoms);
1092 datable[index[i]] |= INGROUP;
1096 static void clear_datable_grp(unsigned char *datable, int size)
1098 /* Clears group information from the table */
1100 const char mask = !(char)INGROUP;
1103 for (i = 0; i < size; i++)
1110 static void add_acc(t_acceptors *a, int ia, int grp)
1112 if (a->nra >= a->max_nra)
1115 srenew(a->acc, a->max_nra);
1116 srenew(a->grp, a->max_nra);
1118 a->grp[a->nra] = grp;
1119 a->acc[a->nra++] = ia;
1122 static void search_acceptors(t_topology *top, int isize,
1123 atom_id *index, t_acceptors *a, int grp,
1125 gmx_bool bContact, gmx_bool bDoIt, unsigned char *datable)
1131 for (i = 0; (i < isize); i++)
1135 (((*top->atoms.atomname[n])[0] == 'O') ||
1136 (bNitAcc && ((*top->atoms.atomname[n])[0] == 'N')))) &&
1137 ISINGRP(datable[n]))
1139 datable[n] |= ACC; /* set the atom's acceptor flag in datable. */
1144 snew(a->aptr, top->atoms.nr);
1145 for (i = 0; (i < top->atoms.nr); i++)
1147 a->aptr[i] = NOTSET;
1149 for (i = 0; (i < a->nra); i++)
1151 a->aptr[a->acc[i]] = i;
1155 static void add_h2d(int id, int ih, t_donors *ddd)
1159 for (i = 0; (i < ddd->nhydro[id]); i++)
1161 if (ddd->hydro[id][i] == ih)
1163 printf("Hm. This isn't the first time I found this donor (%d,%d)\n",
1168 if (i == ddd->nhydro[id])
1170 if (ddd->nhydro[id] >= MAXHYDRO)
1172 gmx_fatal(FARGS, "Donor %d has more than %d hydrogens!",
1173 ddd->don[id], MAXHYDRO);
1175 ddd->hydro[id][i] = ih;
1180 static void add_dh(t_donors *ddd, int id, int ih, int grp, unsigned char *datable)
1184 if (!datable || ISDON(datable[id]))
1186 if (ddd->dptr[id] == NOTSET) /* New donor */
1198 if (ddd->nrd >= ddd->max_nrd)
1200 ddd->max_nrd += 128;
1201 srenew(ddd->don, ddd->max_nrd);
1202 srenew(ddd->nhydro, ddd->max_nrd);
1203 srenew(ddd->hydro, ddd->max_nrd);
1204 srenew(ddd->nhbonds, ddd->max_nrd);
1205 srenew(ddd->grp, ddd->max_nrd);
1207 ddd->don[ddd->nrd] = id;
1208 ddd->nhydro[ddd->nrd] = 0;
1209 ddd->grp[ddd->nrd] = grp;
1216 add_h2d(i, ih, ddd);
1221 printf("Warning: Atom %d is not in the d/a-table!\n", id);
1225 static void search_donors(t_topology *top, int isize, atom_id *index,
1226 t_donors *ddd, int grp, gmx_bool bContact, gmx_bool bDoIt,
1227 unsigned char *datable)
1230 t_functype func_type;
1231 t_ilist *interaction;
1232 atom_id nr1, nr2, nr3;
1237 snew(ddd->dptr, top->atoms.nr);
1238 for (i = 0; (i < top->atoms.nr); i++)
1240 ddd->dptr[i] = NOTSET;
1248 for (i = 0; (i < isize); i++)
1250 datable[index[i]] |= DON;
1251 add_dh(ddd, index[i], -1, grp, datable);
1257 for (func_type = 0; (func_type < F_NRE); func_type++)
1259 interaction = &(top->idef.il[func_type]);
1260 if (func_type == F_POSRES || func_type == F_FBPOSRES)
1262 /* The ilist looks strange for posre. Bug in grompp?
1263 * We don't need posre interactions for hbonds anyway.*/
1266 for (i = 0; i < interaction->nr;
1267 i += interaction_function[top->idef.functype[interaction->iatoms[i]]].nratoms+1)
1270 if (func_type != top->idef.functype[interaction->iatoms[i]])
1272 fprintf(stderr, "Error in func_type %s",
1273 interaction_function[func_type].longname);
1277 /* check out this functype */
1278 if (func_type == F_SETTLE)
1280 nr1 = interaction->iatoms[i+1];
1281 nr2 = interaction->iatoms[i+2];
1282 nr3 = interaction->iatoms[i+3];
1284 if (ISINGRP(datable[nr1]))
1286 if (ISINGRP(datable[nr2]))
1288 datable[nr1] |= DON;
1289 add_dh(ddd, nr1, nr1+1, grp, datable);
1291 if (ISINGRP(datable[nr3]))
1293 datable[nr1] |= DON;
1294 add_dh(ddd, nr1, nr1+2, grp, datable);
1298 else if (IS_CHEMBOND(func_type))
1300 for (j = 0; j < 2; j++)
1302 nr1 = interaction->iatoms[i+1+j];
1303 nr2 = interaction->iatoms[i+2-j];
1304 if ((*top->atoms.atomname[nr1][0] == 'H') &&
1305 ((*top->atoms.atomname[nr2][0] == 'O') ||
1306 (*top->atoms.atomname[nr2][0] == 'N')) &&
1307 ISINGRP(datable[nr1]) && ISINGRP(datable[nr2]))
1309 datable[nr2] |= DON;
1310 add_dh(ddd, nr2, nr1, grp, datable);
1317 for (func_type = 0; func_type < F_NRE; func_type++)
1319 interaction = &top->idef.il[func_type];
1320 for (i = 0; i < interaction->nr;
1321 i += interaction_function[top->idef.functype[interaction->iatoms[i]]].nratoms+1)
1324 if (func_type != top->idef.functype[interaction->iatoms[i]])
1326 gmx_incons("function type in search_donors");
1329 if (interaction_function[func_type].flags & IF_VSITE)
1331 nr1 = interaction->iatoms[i+1];
1332 if (*top->atoms.atomname[nr1][0] == 'H')
1336 while (!stop && ( *top->atoms.atomname[nr2][0] == 'H'))
1347 if (!stop && ( ( *top->atoms.atomname[nr2][0] == 'O') ||
1348 ( *top->atoms.atomname[nr2][0] == 'N') ) &&
1349 ISINGRP(datable[nr1]) && ISINGRP(datable[nr2]))
1351 datable[nr2] |= DON;
1352 add_dh(ddd, nr2, nr1, grp, datable);
1362 static t_gridcell ***init_grid(gmx_bool bBox, rvec box[], real rcut, ivec ngrid)
1369 for (i = 0; i < DIM; i++)
1371 ngrid[i] = (box[i][i]/(1.2*rcut));
1375 if (!bBox || (ngrid[XX] < 3) || (ngrid[YY] < 3) || (ngrid[ZZ] < 3) )
1377 for (i = 0; i < DIM; i++)
1384 printf("\nWill do grid-seach on %dx%dx%d grid, rcut=%g\n",
1385 ngrid[XX], ngrid[YY], ngrid[ZZ], rcut);
1387 snew(grid, ngrid[ZZ]);
1388 for (z = 0; z < ngrid[ZZ]; z++)
1390 snew((grid)[z], ngrid[YY]);
1391 for (y = 0; y < ngrid[YY]; y++)
1393 snew((grid)[z][y], ngrid[XX]);
1399 static void reset_nhbonds(t_donors *ddd)
1403 for (i = 0; (i < ddd->nrd); i++)
1405 for (j = 0; (j < MAXHH); j++)
1407 ddd->nhbonds[i][j] = 0;
1412 void pbc_correct_gem(rvec dx, matrix box, rvec hbox);
1414 static void build_grid(t_hbdata *hb, rvec x[], rvec xshell,
1415 gmx_bool bBox, matrix box, rvec hbox,
1416 real rcut, real rshell,
1417 ivec ngrid, t_gridcell ***grid)
1419 int i, m, gr, xi, yi, zi, nr;
1422 rvec invdelta, dshell, xtemp = {0, 0, 0};
1424 gmx_bool bDoRshell, bInShell, bAcc;
1429 bDoRshell = (rshell > 0);
1430 rshell2 = sqr(rshell);
1433 #define DBB(x) if (debug && bDebug) fprintf(debug, "build_grid, line %d, %s = %d\n", __LINE__,#x, x)
1435 for (m = 0; m < DIM; m++)
1437 hbox[m] = box[m][m]*0.5;
1440 invdelta[m] = ngrid[m]/box[m][m];
1441 if (1/invdelta[m] < rcut)
1443 gmx_fatal(FARGS, "Your computational box has shrunk too much.\n"
1444 "%s can not handle this situation, sorry.\n",
1457 /* resetting atom counts */
1458 for (gr = 0; (gr < grNR); gr++)
1460 for (zi = 0; zi < ngrid[ZZ]; zi++)
1462 for (yi = 0; yi < ngrid[YY]; yi++)
1464 for (xi = 0; xi < ngrid[XX]; xi++)
1466 grid[zi][yi][xi].d[gr].nr = 0;
1467 grid[zi][yi][xi].a[gr].nr = 0;
1473 /* put atoms in grid cells */
1474 for (bAcc = FALSE; (bAcc <= TRUE); bAcc++)
1487 for (i = 0; (i < nr); i++)
1489 /* check if we are inside the shell */
1490 /* if bDoRshell=FALSE then bInShell=TRUE always */
1495 rvec_sub(x[ad[i]], xshell, dshell);
1498 if (FALSE && !hb->bGem)
1500 for (m = DIM-1; m >= 0 && bInShell; m--)
1502 if (dshell[m] < -hbox[m])
1504 rvec_inc(dshell, box[m]);
1506 else if (dshell[m] >= hbox[m])
1508 dshell[m] -= 2*hbox[m];
1510 /* if we're outside the cube, we're outside the sphere also! */
1511 if ( (dshell[m] > rshell) || (-dshell[m] > rshell) )
1519 gmx_bool bDone = FALSE;
1523 for (m = DIM-1; m >= 0 && bInShell; m--)
1525 if (dshell[m] < -hbox[m])
1528 rvec_inc(dshell, box[m]);
1530 if (dshell[m] >= hbox[m])
1533 dshell[m] -= 2*hbox[m];
1537 for (m = DIM-1; m >= 0 && bInShell; m--)
1539 /* if we're outside the cube, we're outside the sphere also! */
1540 if ( (dshell[m] > rshell) || (-dshell[m] > rshell) )
1547 /* if we're inside the cube, check if we're inside the sphere */
1550 bInShell = norm2(dshell) < rshell2;
1560 copy_rvec(x[ad[i]], xtemp);
1562 pbc_correct_gem(x[ad[i]], box, hbox);
1564 for (m = DIM-1; m >= 0; m--)
1566 if (TRUE || !hb->bGem)
1568 /* put atom in the box */
1569 while (x[ad[i]][m] < 0)
1571 rvec_inc(x[ad[i]], box[m]);
1573 while (x[ad[i]][m] >= box[m][m])
1575 rvec_dec(x[ad[i]], box[m]);
1578 /* determine grid index of atom */
1579 grididx[m] = x[ad[i]][m]*invdelta[m];
1580 grididx[m] = (grididx[m]+ngrid[m]) % ngrid[m];
1584 copy_rvec(xtemp, x[ad[i]]); /* copy back */
1589 range_check(gx, 0, ngrid[XX]);
1590 range_check(gy, 0, ngrid[YY]);
1591 range_check(gz, 0, ngrid[ZZ]);
1595 /* add atom to grid cell */
1598 newgrid = &(grid[gz][gy][gx].a[gr]);
1602 newgrid = &(grid[gz][gy][gx].d[gr]);
1604 if (newgrid->nr >= newgrid->maxnr)
1606 newgrid->maxnr += 10;
1607 DBB(newgrid->maxnr);
1608 srenew(newgrid->atoms, newgrid->maxnr);
1611 newgrid->atoms[newgrid->nr] = ad[i];
1619 static void count_da_grid(ivec ngrid, t_gridcell ***grid, t_icell danr)
1623 for (gr = 0; (gr < grNR); gr++)
1626 for (zi = 0; zi < ngrid[ZZ]; zi++)
1628 for (yi = 0; yi < ngrid[YY]; yi++)
1630 for (xi = 0; xi < ngrid[XX]; xi++)
1632 danr[gr] += grid[zi][yi][xi].d[gr].nr;
1640 * Without a box, the grid is 1x1x1, so all loops are 1 long.
1641 * With a rectangular box (bTric==FALSE) all loops are 3 long.
1642 * With a triclinic box all loops are 3 long, except when a cell is
1643 * located next to one of the box edges which is not parallel to the
1644 * x/y-plane, in that case all cells in a line or layer are searched.
1645 * This could be implemented slightly more efficient, but the code
1646 * would get much more complicated.
1648 static gmx_inline gmx_bool grid_loop_begin(int n, int x, gmx_bool bTric, gmx_bool bEdge)
1650 return ((n == 1) ? x : bTric && bEdge ? 0 : (x-1));
1652 static gmx_inline gmx_bool grid_loop_end(int n, int x, gmx_bool bTric, gmx_bool bEdge)
1654 return ((n == 1) ? x : bTric && bEdge ? (n-1) : (x+1));
1656 static gmx_inline int grid_mod(int j, int n)
1661 static void dump_grid(FILE *fp, ivec ngrid, t_gridcell ***grid)
1663 int gr, x, y, z, sum[grNR];
1665 fprintf(fp, "grid %dx%dx%d\n", ngrid[XX], ngrid[YY], ngrid[ZZ]);
1666 for (gr = 0; gr < grNR; gr++)
1669 fprintf(fp, "GROUP %d (%s)\n", gr, grpnames[gr]);
1670 for (z = 0; z < ngrid[ZZ]; z += 2)
1672 fprintf(fp, "Z=%d,%d\n", z, z+1);
1673 for (y = 0; y < ngrid[YY]; y++)
1675 for (x = 0; x < ngrid[XX]; x++)
1677 fprintf(fp, "%3d", grid[x][y][z].d[gr].nr);
1678 sum[gr] += grid[z][y][x].d[gr].nr;
1679 fprintf(fp, "%3d", grid[x][y][z].a[gr].nr);
1680 sum[gr] += grid[z][y][x].a[gr].nr;
1684 if ( (z+1) < ngrid[ZZ])
1686 for (x = 0; x < ngrid[XX]; x++)
1688 fprintf(fp, "%3d", grid[z+1][y][x].d[gr].nr);
1689 sum[gr] += grid[z+1][y][x].d[gr].nr;
1690 fprintf(fp, "%3d", grid[z+1][y][x].a[gr].nr);
1691 sum[gr] += grid[z+1][y][x].a[gr].nr;
1698 fprintf(fp, "TOTALS:");
1699 for (gr = 0; gr < grNR; gr++)
1701 fprintf(fp, " %d=%d", gr, sum[gr]);
1706 /* New GMX record! 5 * in a row. Congratulations!
1707 * Sorry, only four left.
1709 static void free_grid(ivec ngrid, t_gridcell ****grid)
1712 t_gridcell ***g = *grid;
1714 for (z = 0; z < ngrid[ZZ]; z++)
1716 for (y = 0; y < ngrid[YY]; y++)
1726 void pbc_correct_gem(rvec dx, matrix box, rvec hbox)
1729 gmx_bool bDone = FALSE;
1733 for (m = DIM-1; m >= 0; m--)
1735 if (dx[m] < -hbox[m])
1738 rvec_inc(dx, box[m]);
1740 if (dx[m] >= hbox[m])
1743 rvec_dec(dx, box[m]);
1749 /* Added argument r2cut, changed contact and implemented
1750 * use of second cut-off.
1751 * - Erik Marklund, June 29, 2006
1753 static int is_hbond(t_hbdata *hb, int grpd, int grpa, int d, int a,
1754 real rcut, real r2cut, real ccut,
1755 rvec x[], gmx_bool bBox, matrix box, rvec hbox,
1756 real *d_ha, real *ang, gmx_bool bDA, int *hhh,
1757 gmx_bool bContact, gmx_bool bMerge, PSTYPE *p)
1759 int h, hh, id, ja, ihb;
1760 rvec r_da, r_ha, r_dh, r = {0, 0, 0};
1762 real rc2, r2c2, rda2, rha2, ca;
1763 gmx_bool HAinrange = FALSE; /* If !bDA. Needed for returning hbDist in a correct way. */
1764 gmx_bool daSwap = FALSE;
1771 if (((id = donor_index(&hb->d, grpd, d)) == NOTSET) ||
1772 ((ja = acceptor_index(&hb->a, grpa, a)) == NOTSET))
1780 rvec_sub(x[d], x[a], r_da);
1781 /* Insert projection code here */
1783 if (bMerge && d > a && isInterchangable(hb, d, a, grpd, grpa))
1785 /* Then this hbond/contact will be found again, or it has already been found. */
1790 if (d > a && bMerge && isInterchangable(hb, d, a, grpd, grpa)) /* acceptor is also a donor and vice versa? */
1791 { /* return hbNo; */
1792 daSwap = TRUE; /* If so, then their history should be filed with donor and acceptor swapped. */
1796 copy_rvec(r_da, r); /* Save this for later */
1797 pbc_correct_gem(r_da, box, hbox);
1801 pbc_correct_gem(r_da, box, hbox);
1804 rda2 = iprod(r_da, r_da);
1808 if (daSwap && grpa == grpd)
1816 calcBoxDistance(hb->per->P, r, ri);
1817 *p = periodicIndex(ri, hb->per, daSwap); /* find (or add) periodicity index. */
1821 else if (rda2 < r2c2)
1832 if (bDA && (rda2 > rc2))
1837 for (h = 0; (h < hb->d.nhydro[id]); h++)
1839 hh = hb->d.hydro[id][h];
1843 rvec_sub(x[hh], x[a], r_ha);
1846 pbc_correct_gem(r_ha, box, hbox);
1848 rha2 = iprod(r_ha, r_ha);
1853 calcBoxDistance(hb->per->P, r, ri);
1854 *p = periodicIndex(ri, hb->per, daSwap); /* find periodicity index. */
1857 if (bDA || (!bDA && (rha2 <= rc2)))
1859 rvec_sub(x[d], x[hh], r_dh);
1862 pbc_correct_gem(r_dh, box, hbox);
1869 ca = cos_angle(r_dh, r_da);
1870 /* if angle is smaller, cos is larger */
1874 *d_ha = sqrt(bDA ? rda2 : rha2);
1880 if (bDA || (!bDA && HAinrange))
1890 /* Fixed previously undiscovered bug in the merge
1891 code, where the last frame of each hbond disappears.
1892 - Erik Marklund, June 1, 2006 */
1893 /* Added the following arguments:
1894 * ptmp[] - temporary periodicity hisory
1895 * a1 - identity of first acceptor/donor
1896 * a2 - identity of second acceptor/donor
1897 * - Erik Marklund, FEB 20 2010 */
1899 /* Merging is now done on the fly, so do_merge is most likely obsolete now.
1900 * Will do some more testing before removing the function entirely.
1901 * - Erik Marklund, MAY 10 2010 */
1902 static void do_merge(t_hbdata *hb, int ntmp,
1903 unsigned int htmp[], unsigned int gtmp[], PSTYPE ptmp[],
1904 t_hbond *hb0, t_hbond *hb1, int a1, int a2)
1906 /* Here we need to make sure we're treating periodicity in
1907 * the right way for the geminate recombination kinetics. */
1909 int m, mm, n00, n01, nn0, nnframes;
1913 /* Decide where to start from when merging */
1916 nn0 = min(n00, n01);
1917 nnframes = max(n00 + hb0->nframes, n01 + hb1->nframes) - nn0;
1918 /* Initiate tmp arrays */
1919 for (m = 0; (m < ntmp); m++)
1925 /* Fill tmp arrays with values due to first HB */
1926 /* Once again '<' had to be replaced with '<='
1927 to catch the last frame in which the hbond
1929 - Erik Marklund, June 1, 2006 */
1930 for (m = 0; (m <= hb0->nframes); m++)
1933 htmp[mm] = is_hb(hb0->h[0], m);
1936 pm = getPshift(hb->per->pHist[a1][a2], m+hb0->n0);
1937 if (pm > hb->per->nper)
1939 gmx_fatal(FARGS, "Illegal shift!");
1943 ptmp[mm] = pm; /*hb->per->pHist[a1][a2][m];*/
1947 /* If we're doing geminate recompbination we usually don't need the distances.
1948 * Let's save some memory and time. */
1949 if (TRUE || !hb->bGem || hb->per->gemtype == gemAD)
1951 for (m = 0; (m <= hb0->nframes); m++)
1954 gtmp[mm] = is_hb(hb0->g[0], m);
1958 for (m = 0; (m <= hb1->nframes); m++)
1961 htmp[mm] = htmp[mm] || is_hb(hb1->h[0], m);
1962 gtmp[mm] = gtmp[mm] || is_hb(hb1->g[0], m);
1963 if (hb->bGem /* && ptmp[mm] != 0 */)
1966 /* If this hbond has been seen before with donor and acceptor swapped,
1967 * then we need to find the mirrored (*-1) periodicity vector to truely
1968 * merge the hbond history. */
1969 pm = findMirror(getPshift(hb->per->pHist[a2][a1], m+hb1->n0), hb->per->p2i, hb->per->nper);
1970 /* Store index of mirror */
1971 if (pm > hb->per->nper)
1973 gmx_fatal(FARGS, "Illegal shift!");
1978 /* Reallocate target array */
1979 if (nnframes > hb0->maxframes)
1981 srenew(hb0->h[0], 4+nnframes/hb->wordlen);
1982 srenew(hb0->g[0], 4+nnframes/hb->wordlen);
1984 if (NULL != hb->per->pHist)
1986 clearPshift(&(hb->per->pHist[a1][a2]));
1989 /* Copy temp array to target array */
1990 for (m = 0; (m <= nnframes); m++)
1992 _set_hb(hb0->h[0], m, htmp[m]);
1993 _set_hb(hb0->g[0], m, gtmp[m]);
1996 addPshift(&(hb->per->pHist[a1][a2]), ptmp[m], m+nn0);
2000 /* Set scalar variables */
2002 hb0->maxframes = nnframes;
2005 /* Added argument bContact for nicer output.
2006 * Erik Marklund, June 29, 2006
2008 static void merge_hb(t_hbdata *hb, gmx_bool bTwo, gmx_bool bContact)
2010 int i, inrnew, indnew, j, ii, jj, m, id, ia, grp, ogrp, ntmp;
2011 unsigned int *htmp, *gtmp;
2016 indnew = hb->nrdist;
2018 /* Check whether donors are also acceptors */
2019 printf("Merging hbonds with Acceptor and Donor swapped\n");
2021 ntmp = 2*hb->max_frames;
2025 for (i = 0; (i < hb->d.nrd); i++)
2027 fprintf(stderr, "\r%d/%d", i+1, hb->d.nrd);
2029 ii = hb->a.aptr[id];
2030 for (j = 0; (j < hb->a.nra); j++)
2033 jj = hb->d.dptr[ia];
2034 if ((id != ia) && (ii != NOTSET) && (jj != NOTSET) &&
2035 (!bTwo || (bTwo && (hb->d.grp[i] != hb->a.grp[j]))))
2037 hb0 = hb->hbmap[i][j];
2038 hb1 = hb->hbmap[jj][ii];
2039 if (hb0 && hb1 && ISHB(hb0->history[0]) && ISHB(hb1->history[0]))
2041 do_merge(hb, ntmp, htmp, gtmp, ptmp, hb0, hb1, i, j);
2042 if (ISHB(hb1->history[0]))
2046 else if (ISDIST(hb1->history[0]))
2053 gmx_incons("No contact history");
2057 gmx_incons("Neither hydrogen bond nor distance");
2063 clearPshift(&(hb->per->pHist[jj][ii]));
2067 hb1->history[0] = hbNo;
2072 fprintf(stderr, "\n");
2073 printf("- Reduced number of hbonds from %d to %d\n", hb->nrhb, inrnew);
2074 printf("- Reduced number of distances from %d to %d\n", hb->nrdist, indnew);
2076 hb->nrdist = indnew;
2082 static void do_nhb_dist(FILE *fp, t_hbdata *hb, real t)
2084 int i, j, k, n_bound[MAXHH], nbtot;
2088 /* Set array to 0 */
2089 for (k = 0; (k < MAXHH); k++)
2093 /* Loop over possible donors */
2094 for (i = 0; (i < hb->d.nrd); i++)
2096 for (j = 0; (j < hb->d.nhydro[i]); j++)
2098 n_bound[hb->d.nhbonds[i][j]]++;
2101 fprintf(fp, "%12.5e", t);
2103 for (k = 0; (k < MAXHH); k++)
2105 fprintf(fp, " %8d", n_bound[k]);
2106 nbtot += n_bound[k]*k;
2108 fprintf(fp, " %8d\n", nbtot);
2111 /* Added argument bContact in do_hblife(...). Also
2112 * added support for -contact in function body.
2113 * - Erik Marklund, May 31, 2006 */
2114 /* Changed the contact code slightly.
2115 * - Erik Marklund, June 29, 2006
2117 static void do_hblife(const char *fn, t_hbdata *hb, gmx_bool bMerge, gmx_bool bContact,
2118 const output_env_t oenv)
2121 const char *leg[] = { "p(t)", "t p(t)" };
2123 int i, j, j0, k, m, nh, ihb, ohb, nhydro, ndump = 0;
2124 int nframes = hb->nframes;
2127 double sum, integral;
2130 snew(h, hb->maxhydro);
2131 snew(histo, nframes+1);
2132 /* Total number of hbonds analyzed here */
2133 for (i = 0; (i < hb->d.nrd); i++)
2135 for (k = 0; (k < hb->a.nra); k++)
2137 hbh = hb->hbmap[i][k];
2155 for (m = 0; (m < hb->maxhydro); m++)
2159 h[nhydro++] = bContact ? hbh->g[m] : hbh->h[m];
2163 for (nh = 0; (nh < nhydro); nh++)
2168 /* Changed '<' into '<=' below, just like I
2169 did in the hbm-output-loop in the main code.
2170 - Erik Marklund, May 31, 2006
2172 for (j = 0; (j <= hbh->nframes); j++)
2174 ihb = is_hb(h[nh], j);
2175 if (debug && (ndump < 10))
2177 fprintf(debug, "%5d %5d\n", j, ihb);
2197 fprintf(stderr, "\n");
2200 fp = xvgropen(fn, "Uninterrupted contact lifetime", output_env_get_xvgr_tlabel(oenv), "()", oenv);
2204 fp = xvgropen(fn, "Uninterrupted hydrogen bond lifetime", output_env_get_xvgr_tlabel(oenv), "()",
2208 xvgr_legend(fp, asize(leg), leg, oenv);
2210 while ((j0 > 0) && (histo[j0] == 0))
2215 for (i = 0; (i <= j0); i++)
2219 dt = hb->time[1]-hb->time[0];
2222 for (i = 1; (i <= j0); i++)
2224 t = hb->time[i] - hb->time[0] - 0.5*dt;
2225 x1 = t*histo[i]/sum;
2226 fprintf(fp, "%8.3f %10.3e %10.3e\n", t, histo[i]/sum, x1);
2231 printf("%s lifetime = %.2f ps\n", bContact ? "Contact" : "HB", integral);
2232 printf("Note that the lifetime obtained in this manner is close to useless\n");
2233 printf("Use the -ac option instead and check the Forward lifetime\n");
2234 please_cite(stdout, "Spoel2006b");
2239 /* Changed argument bMerge into oneHB to handle contacts properly.
2240 * - Erik Marklund, June 29, 2006
2242 static void dump_ac(t_hbdata *hb, gmx_bool oneHB, int nDump)
2245 int i, j, k, m, nd, ihb, idist;
2246 int nframes = hb->nframes;
2254 fp = gmx_ffopen("debug-ac.xvg", "w");
2255 for (j = 0; (j < nframes); j++)
2257 fprintf(fp, "%10.3f", hb->time[j]);
2258 for (i = nd = 0; (i < hb->d.nrd) && (nd < nDump); i++)
2260 for (k = 0; (k < hb->a.nra) && (nd < nDump); k++)
2264 hbh = hb->hbmap[i][k];
2269 ihb = is_hb(hbh->h[0], j);
2270 idist = is_hb(hbh->g[0], j);
2276 for (m = 0; (m < hb->maxhydro) && !ihb; m++)
2278 ihb = ihb || ((hbh->h[m]) && is_hb(hbh->h[m], j));
2279 idist = idist || ((hbh->g[m]) && is_hb(hbh->g[m], j));
2281 /* This is not correct! */
2282 /* What isn't correct? -Erik M */
2287 fprintf(fp, " %1d-%1d", ihb, idist);
2297 static real calc_dg(real tau, real temp)
2308 return kbt*log(kbt*tau/PLANCK);
2313 int n0, n1, nparams, ndelta;
2315 real *t, *ct, *nt, *kt, *sigma_ct, *sigma_nt, *sigma_kt;
2318 static real compute_weighted_rates(int n, real t[], real ct[], real nt[],
2319 real kt[], real sigma_ct[], real sigma_nt[],
2320 real sigma_kt[], real *k, real *kp,
2321 real *sigma_k, real *sigma_kp,
2327 real kkk = 0, kkp = 0, kk2 = 0, kp2 = 0, chi2;
2332 for (i = 0; (i < n); i++)
2334 if (t[i] >= fit_start)
2347 tl.sigma_ct = sigma_ct;
2348 tl.sigma_nt = sigma_nt;
2349 tl.sigma_kt = sigma_kt;
2353 chi2 = 0; /*optimize_luzar_parameters(debug, &tl, 1000, 1e-3); */
2355 *kp = tl.kkk[1] = *kp;
2357 for (j = 0; (j < NK); j++)
2359 /* (void) optimize_luzar_parameters(debug, &tl, 1000, 1e-3); */
2362 kk2 += sqr(tl.kkk[0]);
2363 kp2 += sqr(tl.kkk[1]);
2366 *sigma_k = sqrt(kk2/NK - sqr(kkk/NK));
2367 *sigma_kp = sqrt(kp2/NK - sqr(kkp/NK));
2372 static void smooth_tail(int n, real t[], real c[], real sigma_c[], real start,
2373 const output_env_t oenv)
2376 real e_1, fitparm[4];
2380 for (i = 0; (i < n); i++)
2396 do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(), effnEXP2, fitparm, 0);
2399 void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
2400 real sigma_ct[], real sigma_nt[], real sigma_kt[],
2401 real fit_start, real temp, real smooth_tail_start,
2402 const output_env_t oenv)
2405 real k = 1, kp = 1, kow = 1;
2406 real Q = 0, chi22, chi2, dg, dgp, tau_hb, dtau, tau_rlx, e_1, dt, sigma_k, sigma_kp, ddg;
2407 double tmp, sn2 = 0, sc2 = 0, sk2 = 0, scn = 0, sck = 0, snk = 0;
2408 gmx_bool bError = (sigma_ct != NULL) && (sigma_nt != NULL) && (sigma_kt != NULL);
2410 if (smooth_tail_start >= 0)
2412 smooth_tail(n, t, ct, sigma_ct, smooth_tail_start, oenv);
2413 smooth_tail(n, t, nt, sigma_nt, smooth_tail_start, oenv);
2414 smooth_tail(n, t, kt, sigma_kt, smooth_tail_start, oenv);
2416 for (i0 = 0; (i0 < n-2) && ((t[i0]-t[0]) < fit_start); i0++)
2422 for (i = i0; (i < n); i++)
2431 printf("Hydrogen bond thermodynamics at T = %g K\n", temp);
2432 tmp = (sn2*sc2-sqr(scn));
2433 if ((tmp > 0) && (sn2 > 0))
2435 k = (sn2*sck-scn*snk)/tmp;
2436 kp = (k*scn-snk)/sn2;
2440 for (i = i0; (i < n); i++)
2442 chi2 += sqr(k*ct[i]-kp*nt[i]-kt[i]);
2444 chi22 = compute_weighted_rates(n, t, ct, nt, kt, sigma_ct, sigma_nt,
2446 &sigma_k, &sigma_kp, fit_start);
2447 Q = 0; /* quality_of_fit(chi2, 2);*/
2448 ddg = BOLTZ*temp*sigma_k/k;
2449 printf("Fitting paramaters chi^2 = %10g, Quality of fit = %10g\n",
2451 printf("The Rate and Delta G are followed by an error estimate\n");
2452 printf("----------------------------------------------------------\n"
2453 "Type Rate (1/ps) Sigma Time (ps) DG (kJ/mol) Sigma\n");
2454 printf("Forward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
2455 k, sigma_k, 1/k, calc_dg(1/k, temp), ddg);
2456 ddg = BOLTZ*temp*sigma_kp/kp;
2457 printf("Backward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
2458 kp, sigma_kp, 1/kp, calc_dg(1/kp, temp), ddg);
2463 for (i = i0; (i < n); i++)
2465 chi2 += sqr(k*ct[i]-kp*nt[i]-kt[i]);
2467 printf("Fitting parameters chi^2 = %10g\nQ = %10g\n",
2469 printf("--------------------------------------------------\n"
2470 "Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2\n");
2471 printf("Forward %10.3f %8.3f %10.3f %10g\n",
2472 k, 1/k, calc_dg(1/k, temp), chi2);
2473 printf("Backward %10.3f %8.3f %10.3f\n",
2474 kp, 1/kp, calc_dg(1/kp, temp));
2480 printf("One-way %10.3f %s%8.3f %10.3f\n",
2481 kow, bError ? " " : "", 1/kow, calc_dg(1/kow, temp));
2485 printf(" - Numerical problems computing HB thermodynamics:\n"
2486 "sc2 = %g sn2 = %g sk2 = %g sck = %g snk = %g scn = %g\n",
2487 sc2, sn2, sk2, sck, snk, scn);
2489 /* Determine integral of the correlation function */
2490 tau_hb = evaluate_integral(n, t, ct, NULL, (t[n-1]-t[0])/2, &dtau);
2491 printf("Integral %10.3f %s%8.3f %10.3f\n", 1/tau_hb,
2492 bError ? " " : "", tau_hb, calc_dg(tau_hb, temp));
2494 for (i = 0; (i < n-2); i++)
2496 if ((ct[i] > e_1) && (ct[i+1] <= e_1))
2503 /* Determine tau_relax from linear interpolation */
2504 tau_rlx = t[i]-t[0] + (e_1-ct[i])*(t[i+1]-t[i])/(ct[i+1]-ct[i]);
2505 printf("Relaxation %10.3f %8.3f %s%10.3f\n", 1/tau_rlx,
2506 tau_rlx, bError ? " " : "",
2507 calc_dg(tau_rlx, temp));
2512 printf("Correlation functions too short to compute thermodynamics\n");
2516 void compute_derivative(int nn, real x[], real y[], real dydx[])
2520 /* Compute k(t) = dc(t)/dt */
2521 for (j = 1; (j < nn-1); j++)
2523 dydx[j] = (y[j+1]-y[j-1])/(x[j+1]-x[j-1]);
2525 /* Extrapolate endpoints */
2526 dydx[0] = 2*dydx[1] - dydx[2];
2527 dydx[nn-1] = 2*dydx[nn-2] - dydx[nn-3];
2530 static void parallel_print(int *data, int nThreads)
2532 /* This prints the donors on which each tread is currently working. */
2535 fprintf(stderr, "\r");
2536 for (i = 0; i < nThreads; i++)
2538 fprintf(stderr, "%-7i", data[i]);
2542 static void normalizeACF(real *ct, real *gt, int nhb, int len)
2544 real ct_fac, gt_fac = 0;
2547 /* Xu and Berne use the same normalization constant */
2552 gt_fac = 1.0/(real)nhb;
2555 printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
2556 for (i = 0; i < len; i++)
2566 /* Added argument bContact in do_hbac(...). Also
2567 * added support for -contact in the actual code.
2568 * - Erik Marklund, May 31, 2006 */
2569 /* Changed contact code and added argument R2
2570 * - Erik Marklund, June 29, 2006
2572 static void do_hbac(const char *fn, t_hbdata *hb,
2573 int nDump, gmx_bool bMerge, gmx_bool bContact, real fit_start,
2574 real temp, gmx_bool R2, real smooth_tail_start, const output_env_t oenv,
2575 const char *gemType, int nThreads,
2576 const int NN, const gmx_bool bBallistic, const gmx_bool bGemFit)
2579 int i, j, k, m, n, o, nd, ihb, idist, n2, nn, iter, nSets;
2580 const char *legNN[] = {
2584 static char **legGem;
2586 const char *legLuzar[] = {
2587 "Ac\\sfin sys\\v{}\\z{}(t)",
2589 "Cc\\scontact,hb\\v{}\\z{}(t)",
2590 "-dAc\\sfs\\v{}\\z{}/dt"
2592 gmx_bool bNorm = FALSE, bOMP = FALSE;
2595 real *rhbex = NULL, *ht, *gt, *ght, *dght, *kt;
2596 real *ct, *p_ct, tail, tail2, dtail, ct_fac, ght_fac, *cct;
2597 const real tol = 1e-3;
2598 int nframes = hb->nframes, nf;
2599 unsigned int **h = NULL, **g = NULL;
2600 int nh, nhbonds, nhydro, ngh;
2602 PSTYPE p, *pfound = NULL, np;
2604 int *ptimes = NULL, *poff = NULL, anhb, n0, mMax = INT_MIN;
2605 real **rHbExGem = NULL;
2609 double *ctdouble, *timedouble, *fittedct;
2610 double fittolerance = 0.1;
2611 int *dondata = NULL, thisThread;
2614 AC_NONE, AC_NN, AC_GEM, AC_LUZAR
2623 printf("Doing autocorrelation ");
2625 /* Decide what kind of ACF calculations to do. */
2626 if (NN > NN_NONE && NN < NN_NR)
2628 #ifdef HAVE_NN_LOOPS
2630 printf("using the energy estimate.\n");
2633 printf("Can't do the NN-loop. Yet.\n");
2639 printf("according to the reversible geminate recombination model by Omer Markowitch.\n");
2641 nSets = 1 + (bBallistic ? 1 : 0) + (bGemFit ? 1 : 0);
2642 snew(legGem, nSets);
2643 for (i = 0; i < nSets; i++)
2645 snew(legGem[i], 128);
2647 sprintf(legGem[0], "Ac\\s%s\\v{}\\z{}(t)", gemType);
2650 sprintf(legGem[1], "Ac'(t)");
2654 sprintf(legGem[(bBallistic ? 3 : 2)], "Ac\\s%s,fit\\v{}\\z{}(t)", gemType);
2661 printf("according to the theory of Luzar and Chandler.\n");
2665 /* build hbexist matrix in reals for autocorr */
2666 /* Allocate memory for computing ACF (rhbex) and aggregating the ACF (ct) */
2668 while (n2 < nframes)
2675 if (acType != AC_NN || bOMP)
2677 snew(h, hb->maxhydro);
2678 snew(g, hb->maxhydro);
2681 /* Dump hbonds for debugging */
2682 dump_ac(hb, bMerge || bContact, nDump);
2684 /* Total number of hbonds analyzed here */
2689 if (acType != AC_LUZAR && bOMP)
2691 nThreads = min((nThreads <= 0) ? INT_MAX : nThreads, gmx_omp_get_max_threads());
2693 gmx_omp_set_num_threads(nThreads);
2694 snew(dondata, nThreads);
2695 for (i = 0; i < nThreads; i++)
2699 printf("ACF calculations parallelized with OpenMP using %i threads.\n"
2700 "Expect close to linear scaling over this donor-loop.\n", nThreads);
2702 fprintf(stderr, "Donors: [thread no]\n");
2705 for (i = 0; i < nThreads; i++)
2707 snprintf(tmpstr, 7, "[%i]", i);
2708 fprintf(stderr, "%-7s", tmpstr);
2711 fprintf(stderr, "\n");
2715 /* Build the ACF according to acType */
2720 #ifdef HAVE_NN_LOOPS
2721 /* Here we're using the estimated energy for the hydrogen bonds. */
2724 #pragma omp parallel \
2725 private(i, j, k, nh, E, rhbex, thisThread) \
2729 thisThread = gmx_omp_get_thread_num();
2733 memset(rhbex, 0, n2*sizeof(real)); /* Trust no-one, not even malloc()! */
2736 #pragma omp for schedule (dynamic)
2737 for (i = 0; i < hb->d.nrd; i++) /* loop over donors */
2741 #pragma omp critical
2743 dondata[thisThread] = i;
2744 parallel_print(dondata, nThreads);
2749 fprintf(stderr, "\r %i", i);
2752 for (j = 0; j < hb->a.nra; j++) /* loop over acceptors */
2754 for (nh = 0; nh < hb->d.nhydro[i]; nh++) /* loop over donors' hydrogens */
2756 E = hb->hbE.E[i][j][nh];
2759 for (k = 0; k < nframes; k++)
2761 if (E[k] != NONSENSE_E)
2763 rhbex[k] = (real)E[k];
2767 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &(rhbex), hb->time[1]-hb->time[0],
2768 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0, 1);
2769 #pragma omp critical
2771 for (k = 0; (k < nn); k++)
2788 normalizeACF(ct, NULL, 0, nn);
2790 snew(timedouble, nn);
2791 for (j = 0; j < nn; j++)
2793 timedouble[j] = (double)(hb->time[j]);
2794 ctdouble[j] = (double)(ct[j]);
2797 /* Remove ballistic term */
2798 /* Ballistic component removal and fitting to the reversible geminate recombination model
2799 * will be taken out for the time being. First of all, one can remove the ballistic
2800 * component with g_analyze afterwards. Secondly, and more importantly, there are still
2801 * problems with the robustness of the fitting to the model. More work is needed.
2802 * A third reason is that we're currently using gsl for this and wish to reduce dependence
2803 * on external libraries. There are Levenberg-Marquardt and nsimplex solvers that come with
2804 * a BSD-licence that can do the job.
2806 * - Erik Marklund, June 18 2010.
2808 /* if (params->ballistic/params->tDelta >= params->nExpFit*2+1) */
2809 /* takeAwayBallistic(ctdouble, timedouble, nn, params->ballistic, params->nExpFit, params->bDt); */
2811 /* printf("\nNumber of data points is less than the number of parameters to fit\n." */
2812 /* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
2814 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)");
2815 xvgr_legend(fp, asize(legNN), legNN);
2817 for (j = 0; (j < nn); j++)
2819 fprintf(fp, "%10g %10g %10g\n",
2820 hb->time[j]-hb->time[0],
2828 #endif /* HAVE_NN_LOOPS */
2829 break; /* case AC_NN */
2833 memset(ct, 0, 2*n2*sizeof(real));
2835 fprintf(stderr, "Donor:\n");
2838 #define __ACDATA p_ct
2841 #pragma omp parallel \
2842 private(i, k, nh, hbh, pHist, h, g, n0, nf, np, j, m, \
2843 pfound, poff, rHbExGem, p, ihb, mMax, \
2846 { /* ########## THE START OF THE ENORMOUS PARALLELIZED BLOCK! ########## */
2849 thisThread = gmx_omp_get_thread_num();
2850 snew(h, hb->maxhydro);
2851 snew(g, hb->maxhydro);
2858 memset(p_ct, 0, 2*n2*sizeof(real));
2860 /* I'm using a chunk size of 1, since I expect \
2861 * the overhead to be really small compared \
2862 * to the actual calculations \ */
2863 #pragma omp for schedule(dynamic,1) nowait
2864 for (i = 0; i < hb->d.nrd; i++)
2869 #pragma omp critical
2871 dondata[thisThread] = i;
2872 parallel_print(dondata, nThreads);
2877 fprintf(stderr, "\r %i", i);
2879 for (k = 0; k < hb->a.nra; k++)
2881 for (nh = 0; nh < ((bMerge || bContact) ? 1 : hb->d.nhydro[i]); nh++)
2883 hbh = hb->hbmap[i][k];
2886 /* Note that if hb->per->gemtype==gemDD, then distances will be stored in
2887 * hb->hbmap[d][a].h array anyway, because the contact flag will be set.
2888 * hence, it's only with the gemAD mode that hb->hbmap[d][a].g will be used. */
2889 pHist = &(hb->per->pHist[i][k]);
2890 if (ISHB(hbh->history[nh]) && pHist->len != 0)
2895 g[nh] = hb->per->gemtype == gemAD ? hbh->g[nh] : NULL;
2899 /* count the number of periodic shifts encountered and store
2900 * them in separate arrays. */
2902 for (j = 0; j < pHist->len; j++)
2905 for (m = 0; m <= np; m++)
2907 if (m == np) /* p not recognized in list. Add it and set up new array. */
2910 if (np > hb->per->nper)
2912 gmx_fatal(FARGS, "Too many pshifts. Something's utterly wrong here.");
2914 if (m >= mMax) /* Extend the arrays.
2915 * Doing it like this, using mMax to keep track of the sizes,
2916 * eleviates the need for freeing and re-allocating the arrays
2917 * when taking on the next donor-acceptor pair */
2920 srenew(pfound, np); /* The list of found periodic shifts. */
2921 srenew(rHbExGem, np); /* The hb existence functions (-aver_hb). */
2922 snew(rHbExGem[m], 2*n2);
2927 if (rHbExGem != NULL && rHbExGem[m] != NULL)
2929 /* This must be done, as this array was most likey
2930 * used to store stuff in some previous iteration. */
2931 memset(rHbExGem[m], 0, (sizeof(real)) * (2*n2));
2935 fprintf(stderr, "rHbExGem not initialized! m = %i\n", m);
2947 } /* m: Loop over found shifts */
2948 } /* j: Loop over shifts */
2950 /* Now unpack and disentangle the existence funtions. */
2951 for (j = 0; j < nf; j++)
2958 * pfound: list of periodic shifts found for this pair.
2959 * poff: list of frame offsets; that is, the first
2960 * frame a hbond has a particular periodic shift. */
2961 p = getPshift(*pHist, j+n0);
2964 for (m = 0; m < np; m++)
2972 gmx_fatal(FARGS, "Shift not found, but must be there.");
2976 ihb = is_hb(h[nh], j) || ((hb->per->gemtype != gemAD || j == 0) ? FALSE : is_hb(g[nh], j));
2981 poff[m] = j; /* Here's where the first hbond with shift p is,
2982 * relative to the start of h[0].*/
2986 gmx_fatal(FARGS, "j<poff[m]");
2988 rHbExGem[m][j-poff[m]] += 1;
2993 /* Now, build ac. */
2994 for (m = 0; m < np; m++)
2996 if (rHbExGem[m][0] > 0 && n0+poff[m] < nn /* && m==0 */)
2998 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &(rHbExGem[m]), hb->time[1]-hb->time[0],
2999 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0);
3000 for (j = 0; (j < nn); j++)
3002 __ACDATA[j] += rHbExGem[m][j];
3005 } /* Building of ac. */
3008 } /* hydrogen loop */
3009 } /* acceptor loop */
3012 for (m = 0; m <= mMax; m++)
3025 #pragma omp critical
3027 for (i = 0; i < nn; i++)
3035 } /* ########## THE END OF THE ENORMOUS PARALLELIZED BLOCK ########## */
3041 normalizeACF(ct, NULL, 0, nn);
3043 fprintf(stderr, "\n\nACF successfully calculated.\n");
3045 /* Use this part to fit to geminate recombination - JCP 129, 84505 (2008) */
3048 snew(timedouble, nn);
3051 for (j = 0; j < nn; j++)
3053 timedouble[j] = (double)(hb->time[j]);
3054 ctdouble[j] = (double)(ct[j]);
3057 /* Remove ballistic term */
3058 /* Ballistic component removal and fitting to the reversible geminate recombination model
3059 * will be taken out for the time being. First of all, one can remove the ballistic
3060 * component with g_analyze afterwards. Secondly, and more importantly, there are still
3061 * problems with the robustness of the fitting to the model. More work is needed.
3062 * A third reason is that we're currently using gsl for this and wish to reduce dependence
3063 * on external libraries. There are Levenberg-Marquardt and nsimplex solvers that come with
3064 * a BSD-licence that can do the job.
3066 * - Erik Marklund, June 18 2010.
3068 /* if (bBallistic) { */
3069 /* if (params->ballistic/params->tDelta >= params->nExpFit*2+1) */
3070 /* takeAwayBallistic(ctdouble, timedouble, nn, params->ballistic, params->nExpFit, params->bDt); */
3072 /* printf("\nNumber of data points is less than the number of parameters to fit\n." */
3073 /* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
3076 /* fitGemRecomb(ctdouble, timedouble, &fittedct, nn, params); */
3081 fp = xvgropen(fn, "Contact Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3085 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3087 xvgr_legend(fp, asize(legGem), (const char**)legGem, oenv);
3089 for (j = 0; (j < nn); j++)
3091 fprintf(fp, "%10g %10g", hb->time[j]-hb->time[0], ct[j]);
3094 fprintf(fp, " %10g", ctdouble[j]);
3098 fprintf(fp, " %10g", fittedct[j]);
3109 break; /* case AC_GEM */
3122 for (i = 0; (i < hb->d.nrd); i++)
3124 for (k = 0; (k < hb->a.nra); k++)
3127 hbh = hb->hbmap[i][k];
3131 if (bMerge || bContact)
3133 if (ISHB(hbh->history[0]))
3142 for (m = 0; (m < hb->maxhydro); m++)
3144 if (bContact ? ISDIST(hbh->history[m]) : ISHB(hbh->history[m]))
3146 g[nhydro] = hbh->g[m];
3147 h[nhydro] = hbh->h[m];
3154 for (nh = 0; (nh < nhydro); nh++)
3156 int nrint = bContact ? hb->nrdist : hb->nrhb;
3157 if ((((nhbonds+1) % 10) == 0) || (nhbonds+1 == nrint))
3159 fprintf(stderr, "\rACF %d/%d", nhbonds+1, nrint);
3162 for (j = 0; (j < nframes); j++)
3164 /* Changed '<' into '<=' below, just like I did in
3165 the hbm-output-loop in the gmx_hbond() block.
3166 - Erik Marklund, May 31, 2006 */
3169 ihb = is_hb(h[nh], j);
3170 idist = is_hb(g[nh], j);
3177 /* For contacts: if a second cut-off is provided, use it,
3178 * otherwise use g(t) = 1-h(t) */
3179 if (!R2 && bContact)
3185 gt[j] = idist*(1-ihb);
3192 /* The autocorrelation function is normalized after summation only */
3193 low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &rhbex, hb->time[1]-hb->time[0],
3194 eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0);
3196 /* Cross correlation analysis for thermodynamics */
3197 for (j = nframes; (j < n2); j++)
3203 cross_corr(n2, ht, gt, dght);
3205 for (j = 0; (j < nn); j++)
3214 fprintf(stderr, "\n");
3217 normalizeACF(ct, ght, nhb, nn);
3219 /* Determine tail value for statistics */
3222 for (j = nn/2; (j < nn); j++)
3225 tail2 += ct[j]*ct[j];
3227 tail /= (nn - nn/2);
3228 tail2 /= (nn - nn/2);
3229 dtail = sqrt(tail2-tail*tail);
3231 /* Check whether the ACF is long enough */
3234 printf("\nWARNING: Correlation function is probably not long enough\n"
3235 "because the standard deviation in the tail of C(t) > %g\n"
3236 "Tail value (average C(t) over second half of acf): %g +/- %g\n",
3239 for (j = 0; (j < nn); j++)
3242 ct[j] = (cct[j]-tail)/(1-tail);
3244 /* Compute negative derivative k(t) = -dc(t)/dt */
3245 compute_derivative(nn, hb->time, ct, kt);
3246 for (j = 0; (j < nn); j++)
3254 fp = xvgropen(fn, "Contact Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3258 fp = xvgropen(fn, "Hydrogen Bond Autocorrelation", output_env_get_xvgr_tlabel(oenv), "C(t)", oenv);
3260 xvgr_legend(fp, asize(legLuzar), legLuzar, oenv);
3263 for (j = 0; (j < nn); j++)
3265 fprintf(fp, "%10g %10g %10g %10g %10g\n",
3266 hb->time[j]-hb->time[0], ct[j], cct[j], ght[j], kt[j]);
3270 analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
3271 fit_start, temp, smooth_tail_start, oenv);
3273 do_view(oenv, fn, NULL);
3285 break; /* case AC_LUZAR */
3288 gmx_fatal(FARGS, "Unrecognized type of ACF-calulation. acType = %i.", acType);
3289 } /* switch (acType) */
3292 static void init_hbframe(t_hbdata *hb, int nframes, real t)
3296 hb->time[nframes] = t;
3297 hb->nhb[nframes] = 0;
3298 hb->ndist[nframes] = 0;
3299 for (i = 0; (i < max_hx); i++)
3301 hb->nhx[nframes][i] = 0;
3303 /* Loop invalidated */
3304 if (hb->bHBmap && 0)
3306 for (i = 0; (i < hb->d.nrd); i++)
3308 for (j = 0; (j < hb->a.nra); j++)
3310 for (m = 0; (m < hb->maxhydro); m++)
3312 if (hb->hbmap[i][j] && hb->hbmap[i][j]->h[m])
3314 set_hb(hb, i, m, j, nframes, HB_NO);
3320 /*set_hb(hb->hbmap[i][j]->h[m],nframes-hb->hbmap[i][j]->n0,HB_NO);*/
3323 static void analyse_donor_props(const char *fn, t_hbdata *hb, int nframes, real t,
3324 const output_env_t oenv)
3326 static FILE *fp = NULL;
3327 const char *leg[] = { "Nbound", "Nfree" };
3328 int i, j, k, nbound, nb, nhtot;
3336 fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
3337 xvgr_legend(fp, asize(leg), leg, oenv);
3341 for (i = 0; (i < hb->d.nrd); i++)
3343 for (k = 0; (k < hb->d.nhydro[i]); k++)
3347 for (j = 0; (j < hb->a.nra) && (nb == 0); j++)
3349 if (hb->hbmap[i][j] && hb->hbmap[i][j]->h[k] &&
3350 is_hb(hb->hbmap[i][j]->h[k], nframes))
3358 fprintf(fp, "%10.3e %6d %6d\n", t, nbound, nhtot-nbound);
3361 static void dump_hbmap(t_hbdata *hb,
3362 int nfile, t_filenm fnm[], gmx_bool bTwo,
3363 gmx_bool bContact, int isize[], int *index[], char *grpnames[],
3367 int ddd, hhh, aaa, i, j, k, m, grp;
3368 char ds[32], hs[32], as[32];
3371 fp = opt2FILE("-hbn", nfile, fnm, "w");
3372 if (opt2bSet("-g", nfile, fnm))
3374 fplog = gmx_ffopen(opt2fn("-g", nfile, fnm), "w");
3375 fprintf(fplog, "# %10s %12s %12s\n", "Donor", "Hydrogen", "Acceptor");
3381 for (grp = gr0; grp <= (bTwo ? gr1 : gr0); grp++)
3383 fprintf(fp, "[ %s ]", grpnames[grp]);
3384 for (i = 0; i < isize[grp]; i++)
3386 fprintf(fp, (i%15) ? " " : "\n");
3387 fprintf(fp, " %4u", index[grp][i]+1);
3391 Added -contact support below.
3392 - Erik Marklund, May 29, 2006
3396 fprintf(fp, "[ donors_hydrogens_%s ]\n", grpnames[grp]);
3397 for (i = 0; (i < hb->d.nrd); i++)
3399 if (hb->d.grp[i] == grp)
3401 for (j = 0; (j < hb->d.nhydro[i]); j++)
3403 fprintf(fp, " %4u %4u", hb->d.don[i]+1,
3404 hb->d.hydro[i][j]+1);
3410 fprintf(fp, "[ acceptors_%s ]", grpnames[grp]);
3411 for (i = 0; (i < hb->a.nra); i++)
3413 if (hb->a.grp[i] == grp)
3415 fprintf(fp, (i%15 && !first) ? " " : "\n");
3416 fprintf(fp, " %4u", hb->a.acc[i]+1);
3425 fprintf(fp, bContact ? "[ contacts_%s-%s ]\n" :
3426 "[ hbonds_%s-%s ]\n", grpnames[0], grpnames[1]);
3430 fprintf(fp, bContact ? "[ contacts_%s ]" : "[ hbonds_%s ]\n", grpnames[0]);
3433 for (i = 0; (i < hb->d.nrd); i++)
3436 for (k = 0; (k < hb->a.nra); k++)
3439 for (m = 0; (m < hb->d.nhydro[i]); m++)
3441 if (hb->hbmap[i][k] && ISHB(hb->hbmap[i][k]->history[m]))
3443 sprintf(ds, "%s", mkatomname(atoms, ddd));
3444 sprintf(as, "%s", mkatomname(atoms, aaa));
3447 fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
3450 fprintf(fplog, "%12s %12s\n", ds, as);
3455 hhh = hb->d.hydro[i][m];
3456 sprintf(hs, "%s", mkatomname(atoms, hhh));
3457 fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
3460 fprintf(fplog, "%12s %12s %12s\n", ds, hs, as);
3474 /* sync_hbdata() updates the parallel t_hbdata p_hb using hb as template.
3475 * It mimics add_frames() and init_frame() to some extent. */
3476 static void sync_hbdata(t_hbdata *p_hb, int nframes)
3479 if (nframes >= p_hb->max_frames)
3481 p_hb->max_frames += 4096;
3482 srenew(p_hb->nhb, p_hb->max_frames);
3483 srenew(p_hb->ndist, p_hb->max_frames);
3484 srenew(p_hb->n_bound, p_hb->max_frames);
3485 srenew(p_hb->nhx, p_hb->max_frames);
3488 srenew(p_hb->danr, p_hb->max_frames);
3490 memset(&(p_hb->nhb[nframes]), 0, sizeof(int) * (p_hb->max_frames-nframes));
3491 memset(&(p_hb->ndist[nframes]), 0, sizeof(int) * (p_hb->max_frames-nframes));
3492 p_hb->nhb[nframes] = 0;
3493 p_hb->ndist[nframes] = 0;
3496 p_hb->nframes = nframes;
3499 /* p_hb->nhx[nframes][i] */
3501 memset(&(p_hb->nhx[nframes]), 0, sizeof(int)*max_hx); /* zero the helix count for this frame */
3503 /* hb->per will remain constant througout the frame loop,
3504 * even though the data its members point to will change,
3505 * hence no need for re-syncing. */
3508 int gmx_hbond(int argc, char *argv[])
3510 const char *desc[] = {
3511 "[THISMODULE] computes and analyzes hydrogen bonds. Hydrogen bonds are",
3512 "determined based on cutoffs for the angle Hydrogen - Donor - Acceptor",
3513 "(zero is extended) and the distance Donor - Acceptor",
3514 "(or Hydrogen - Acceptor using [TT]-noda[tt]).",
3515 "OH and NH groups are regarded as donors, O is an acceptor always,",
3516 "N is an acceptor by default, but this can be switched using",
3517 "[TT]-nitacc[tt]. Dummy hydrogen atoms are assumed to be connected",
3518 "to the first preceding non-hydrogen atom.[PAR]",
3520 "You need to specify two groups for analysis, which must be either",
3521 "identical or non-overlapping. All hydrogen bonds between the two",
3522 "groups are analyzed.[PAR]",
3524 "If you set [TT]-shell[tt], you will be asked for an additional index group",
3525 "which should contain exactly one atom. In this case, only hydrogen",
3526 "bonds between atoms within the shell distance from the one atom are",
3529 "With option -ac, rate constants for hydrogen bonding can be derived with the model of Luzar and Chandler",
3530 "(Nature 394, 1996; J. Chem. Phys. 113:23, 2000) or that of Markovitz and Agmon (J. Chem. Phys 129, 2008).",
3531 "If contact kinetics are analyzed by using the -contact option, then",
3532 "n(t) can be defined as either all pairs that are not within contact distance r at time t",
3533 "(corresponding to leaving the -r2 option at the default value 0) or all pairs that",
3534 "are within distance r2 (corresponding to setting a second cut-off value with option -r2).",
3535 "See mentioned literature for more details and definitions."
3538 /* "It is also possible to analyse specific hydrogen bonds with",
3539 "[TT]-sel[tt]. This index file must contain a group of atom triplets",
3540 "Donor Hydrogen Acceptor, in the following way:[PAR]",
3548 "Note that the triplets need not be on separate lines.",
3549 "Each atom triplet specifies a hydrogen bond to be analyzed,",
3550 "note also that no check is made for the types of atoms.[PAR]",
3552 "[BB]Output:[bb][BR]",
3553 "[TT]-num[tt]: number of hydrogen bonds as a function of time.[BR]",
3554 "[TT]-ac[tt]: average over all autocorrelations of the existence",
3555 "functions (either 0 or 1) of all hydrogen bonds.[BR]",
3556 "[TT]-dist[tt]: distance distribution of all hydrogen bonds.[BR]",
3557 "[TT]-ang[tt]: angle distribution of all hydrogen bonds.[BR]",
3558 "[TT]-hx[tt]: the number of n-n+i hydrogen bonds as a function of time",
3559 "where n and n+i stand for residue numbers and i ranges from 0 to 6.",
3560 "This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated",
3561 "with helices in proteins.[BR]",
3562 "[TT]-hbn[tt]: all selected groups, donors, hydrogens and acceptors",
3563 "for selected groups, all hydrogen bonded atoms from all groups and",
3564 "all solvent atoms involved in insertion.[BR]",
3565 "[TT]-hbm[tt]: existence matrix for all hydrogen bonds over all",
3566 "frames, this also contains information on solvent insertion",
3567 "into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
3569 "[TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
3570 "each timeframe. This is especially useful when using [TT]-shell[tt].[BR]",
3571 "[TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
3572 "compare results to Raman Spectroscopy.",
3574 "Note: options [TT]-ac[tt], [TT]-life[tt], [TT]-hbn[tt] and [TT]-hbm[tt]",
3575 "require an amount of memory proportional to the total numbers of donors",
3576 "times the total number of acceptors in the selected group(s)."
3579 static real acut = 30, abin = 1, rcut = 0.35, r2cut = 0, rbin = 0.005, rshell = -1;
3580 static real maxnhb = 0, fit_start = 1, fit_end = 60, temp = 298.15, smooth_tail_start = -1, D = -1;
3581 static gmx_bool bNitAcc = TRUE, bDA = TRUE, bMerge = TRUE;
3582 static int nDump = 0, nFitPoints = 100;
3583 static int nThreads = 0, nBalExp = 4;
3585 static gmx_bool bContact = FALSE, bBallistic = FALSE, bGemFit = FALSE;
3586 static real logAfterTime = 10, gemBallistic = 0.2; /* ps */
3587 static const char *NNtype[] = {NULL, "none", "binary", "oneOverR3", "dipole", NULL};
3591 { "-a", FALSE, etREAL, {&acut},
3592 "Cutoff angle (degrees, Hydrogen - Donor - Acceptor)" },
3593 { "-r", FALSE, etREAL, {&rcut},
3594 "Cutoff radius (nm, X - Acceptor, see next option)" },
3595 { "-da", FALSE, etBOOL, {&bDA},
3596 "Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)" },
3597 { "-r2", FALSE, etREAL, {&r2cut},
3598 "Second cutoff radius. Mainly useful with [TT]-contact[tt] and [TT]-ac[tt]"},
3599 { "-abin", FALSE, etREAL, {&abin},
3600 "Binwidth angle distribution (degrees)" },
3601 { "-rbin", FALSE, etREAL, {&rbin},
3602 "Binwidth distance distribution (nm)" },
3603 { "-nitacc", FALSE, etBOOL, {&bNitAcc},
3604 "Regard nitrogen atoms as acceptors" },
3605 { "-contact", FALSE, etBOOL, {&bContact},
3606 "Do not look for hydrogen bonds, but merely for contacts within the cut-off distance" },
3607 { "-shell", FALSE, etREAL, {&rshell},
3608 "when > 0, only calculate hydrogen bonds within # nm shell around "
3610 { "-fitstart", FALSE, etREAL, {&fit_start},
3611 "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]" },
3612 { "-fitend", FALSE, etREAL, {&fit_end},
3613 "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])" },
3614 { "-temp", FALSE, etREAL, {&temp},
3615 "Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming" },
3616 { "-smooth", FALSE, etREAL, {&smooth_tail_start},
3617 "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
3618 { "-dump", FALSE, etINT, {&nDump},
3619 "Dump the first N hydrogen bond ACFs in a single [TT].xvg[tt] file for debugging" },
3620 { "-max_hb", FALSE, etREAL, {&maxnhb},
3621 "Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly" },
3622 { "-merge", FALSE, etBOOL, {&bMerge},
3623 "H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF." },
3624 { "-geminate", FALSE, etENUM, {gemType},
3625 "HIDDENUse reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details."},
3626 { "-diff", FALSE, etREAL, {&D},
3627 "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."},
3629 { "-nthreads", FALSE, etINT, {&nThreads},
3630 "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)"},
3633 const char *bugs[] = {
3634 "The option [TT]-sel[tt] that used to work on selected hbonds is out of order, and therefore not available for the time being."
3637 { efTRX, "-f", NULL, ffREAD },
3638 { efTPX, NULL, NULL, ffREAD },
3639 { efNDX, NULL, NULL, ffOPTRD },
3640 /* { efNDX, "-sel", "select", ffOPTRD },*/
3641 { efXVG, "-num", "hbnum", ffWRITE },
3642 { efLOG, "-g", "hbond", ffOPTWR },
3643 { efXVG, "-ac", "hbac", ffOPTWR },
3644 { efXVG, "-dist", "hbdist", ffOPTWR },
3645 { efXVG, "-ang", "hbang", ffOPTWR },
3646 { efXVG, "-hx", "hbhelix", ffOPTWR },
3647 { efNDX, "-hbn", "hbond", ffOPTWR },
3648 { efXPM, "-hbm", "hbmap", ffOPTWR },
3649 { efXVG, "-don", "donor", ffOPTWR },
3650 { efXVG, "-dan", "danum", ffOPTWR },
3651 { efXVG, "-life", "hblife", ffOPTWR },
3652 { efXVG, "-nhbdist", "nhbdist", ffOPTWR }
3655 #define NFILE asize(fnm)
3657 char hbmap [HB_NR] = { ' ', 'o', '-', '*' };
3658 const char *hbdesc[HB_NR] = { "None", "Present", "Inserted", "Present & Inserted" };
3659 t_rgb hbrgb [HB_NR] = { {1, 1, 1}, {1, 0, 0}, {0, 0, 1}, {1, 0, 1} };
3661 t_trxstatus *status;
3666 int npargs, natoms, nframes = 0, shatom;
3672 real t, ccut, dist = 0.0, ang = 0.0;
3673 double max_nhb, aver_nhb, aver_dist;
3674 int h = 0, i = 0, j, k = 0, l, start, end, id, ja, ogrp, nsel;
3676 int xj, yj, zj, aj, xjj, yjj, zjj;
3677 int xk, yk, zk, ak, xkk, ykk, zkk;
3678 gmx_bool bSelected, bHBmap, bStop, bTwo, was, bBox, bTric;
3679 int *adist, *rdist, *aptr, *rprt;
3680 int grp, nabin, nrbin, bin, resdist, ihb;
3682 t_hbdata *hb, *hbptr;
3683 FILE *fp, *fpins = NULL, *fpnhb = NULL;
3685 t_ncell *icell, *jcell, *kcell;
3687 unsigned char *datable;
3692 int ii, jj, hh, actual_nThreads;
3694 gmx_bool bGem, bNN, bParallel;
3695 t_gemParams *params = NULL;
3696 gmx_bool bEdge_yjj, bEdge_xjj, bOMP;
3698 t_hbdata **p_hb = NULL; /* one per thread, then merge after the frame loop */
3699 int **p_adist = NULL, **p_rdist = NULL; /* a histogram for each thread. */
3708 ppa = add_acf_pargs(&npargs, pa);
3710 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
3711 ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
3716 /* NN-loop? If so, what estimator to use ?*/
3718 /* Outcommented for now DvdS 2010-07-13
3719 while (NN < NN_NR && gmx_strcasecmp(NNtype[0], NNtype[NN])!=0)
3722 gmx_fatal(FARGS, "Invalid NN-loop type.");
3725 for (i = 2; bNN == FALSE && i < NN_NR; i++)
3727 bNN = bNN || NN == i;
3730 if (NN > NN_NONE && bMerge)
3735 /* geminate recombination? If so, which flavor? */
3737 while (gemmode < gemNR && gmx_strcasecmp(gemType[0], gemType[gemmode]) != 0)
3741 if (gemmode == gemNR)
3743 gmx_fatal(FARGS, "Invalid recombination type.");
3747 for (i = 2; bGem == FALSE && i < gemNR; i++)
3749 bGem = bGem || gemmode == i;
3754 printf("Geminate recombination: %s\n", gemType[gemmode]);
3757 if (gemmode != gemDD)
3759 printf("Turning off -contact option...\n");
3765 if (gemmode == gemDD)
3767 printf("Turning on -contact option...\n");
3773 if (gemmode == gemAA)
3775 printf("Turning off -merge option...\n");
3781 if (gemmode != gemAA)
3783 printf("Turning on -merge option...\n");
3791 ccut = cos(acut*DEG2RAD);
3797 gmx_fatal(FARGS, "Can not analyze selected contacts.");
3801 gmx_fatal(FARGS, "Can not analyze contact between H and A: turn off -noda");
3805 /* Initiate main data structure! */
3806 bHBmap = (opt2bSet("-ac", NFILE, fnm) ||
3807 opt2bSet("-life", NFILE, fnm) ||
3808 opt2bSet("-hbn", NFILE, fnm) ||
3809 opt2bSet("-hbm", NFILE, fnm) ||
3812 if (opt2bSet("-nhbdist", NFILE, fnm))
3814 const char *leg[MAXHH+1] = { "0 HBs", "1 HB", "2 HBs", "3 HBs", "Total" };
3815 fpnhb = xvgropen(opt2fn("-nhbdist", NFILE, fnm),
3816 "Number of donor-H with N HBs", output_env_get_xvgr_tlabel(oenv), "N", oenv);
3817 xvgr_legend(fpnhb, asize(leg), leg, oenv);
3820 hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
3823 read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
3825 snew(grpnames, grNR);
3828 /* Make Donor-Acceptor table */
3829 snew(datable, top.atoms.nr);
3830 gen_datable(index[0], isize[0], datable, top.atoms.nr);
3834 /* analyze selected hydrogen bonds */
3835 printf("Select group with selected atoms:\n");
3836 get_index(&(top.atoms), opt2fn("-sel", NFILE, fnm),
3837 1, &nsel, index, grpnames);
3840 gmx_fatal(FARGS, "Number of atoms in group '%s' not a multiple of 3\n"
3841 "and therefore cannot contain triplets of "
3842 "Donor-Hydrogen-Acceptor", grpnames[0]);
3846 for (i = 0; (i < nsel); i += 3)
3848 int dd = index[0][i];
3849 int aa = index[0][i+2];
3850 /* int */ hh = index[0][i+1];
3851 add_dh (&hb->d, dd, hh, i, datable);
3852 add_acc(&hb->a, aa, i);
3853 /* Should this be here ? */
3854 snew(hb->d.dptr, top.atoms.nr);
3855 snew(hb->a.aptr, top.atoms.nr);
3856 add_hbond(hb, dd, aa, hh, gr0, gr0, 0, bMerge, 0, bContact, peri);
3858 printf("Analyzing %d selected hydrogen bonds from '%s'\n",
3859 isize[0], grpnames[0]);
3863 /* analyze all hydrogen bonds: get group(s) */
3864 printf("Specify 2 groups to analyze:\n");
3865 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
3866 2, isize, index, grpnames);
3868 /* check if we have two identical or two non-overlapping groups */
3869 bTwo = isize[0] != isize[1];
3870 for (i = 0; (i < isize[0]) && !bTwo; i++)
3872 bTwo = index[0][i] != index[1][i];
3876 printf("Checking for overlap in atoms between %s and %s\n",
3877 grpnames[0], grpnames[1]);
3878 for (i = 0; i < isize[1]; i++)
3880 if (ISINGRP(datable[index[1][i]]))
3882 gmx_fatal(FARGS, "Partial overlap between groups '%s' and '%s'",
3883 grpnames[0], grpnames[1]);
3887 printf("Checking for overlap in atoms between %s and %s\n",
3888 grpnames[0],grpnames[1]);
3889 for (i=0; i<isize[0]; i++)
3890 for (j=0; j<isize[1]; j++)
3891 if (index[0][i] == index[1][j])
3892 gmx_fatal(FARGS,"Partial overlap between groups '%s' and '%s'",
3893 grpnames[0],grpnames[1]);
3898 printf("Calculating %s "
3899 "between %s (%d atoms) and %s (%d atoms)\n",
3900 bContact ? "contacts" : "hydrogen bonds",
3901 grpnames[0], isize[0], grpnames[1], isize[1]);
3905 fprintf(stderr, "Calculating %s in %s (%d atoms)\n",
3906 bContact ? "contacts" : "hydrogen bonds", grpnames[0], isize[0]);
3911 /* search donors and acceptors in groups */
3912 snew(datable, top.atoms.nr);
3913 for (i = 0; (i < grNR); i++)
3915 if ( ((i == gr0) && !bSelected ) ||
3916 ((i == gr1) && bTwo ))
3918 gen_datable(index[i], isize[i], datable, top.atoms.nr);
3921 search_acceptors(&top, isize[i], index[i], &hb->a, i,
3922 bNitAcc, TRUE, (bTwo && (i == gr0)) || !bTwo, datable);
3923 search_donors (&top, isize[i], index[i], &hb->d, i,
3924 TRUE, (bTwo && (i == gr1)) || !bTwo, datable);
3928 search_acceptors(&top, isize[i], index[i], &hb->a, i, bNitAcc, FALSE, TRUE, datable);
3929 search_donors (&top, isize[i], index[i], &hb->d, i, FALSE, TRUE, datable);
3933 clear_datable_grp(datable, top.atoms.nr);
3938 printf("Found %d donors and %d acceptors\n", hb->d.nrd, hb->a.nra);
3940 snew(donors[gr0D], dons[gr0D].nrd);*/
3944 printf("Making hbmap structure...");
3945 /* Generate hbond data structure */
3950 #ifdef HAVE_NN_LOOPS
3959 printf("Making per structure...");
3960 /* Generate hbond data structure */
3967 if (hb->d.nrd + hb->a.nra == 0)
3969 printf("No Donors or Acceptors found\n");
3976 printf("No Donors found\n");
3981 printf("No Acceptors found\n");
3987 gmx_fatal(FARGS, "Nothing to be done");
3996 /* get index group with atom for shell */
3999 printf("Select atom for shell (1 atom):\n");
4000 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
4001 1, &shisz, &shidx, &shgrpnm);
4004 printf("group contains %d atoms, should be 1 (one)\n", shisz);
4009 printf("Will calculate hydrogen bonds within a shell "
4010 "of %g nm around atom %i\n", rshell, shatom+1);
4013 /* Analyze trajectory */
4014 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
4015 if (natoms > top.atoms.nr)
4017 gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
4018 top.atoms.nr, natoms);
4021 bBox = ir.ePBC != epbcNONE;
4022 grid = init_grid(bBox, box, (rcut > r2cut) ? rcut : r2cut, ngrid);
4025 snew(adist, nabin+1);
4026 snew(rdist, nrbin+1);
4030 gmx_fatal(FARGS, "Can't do geminate recombination without periodic box.");
4036 #define __ADIST adist
4037 #define __RDIST rdist
4039 #else /* GMX_OPENMP ================================================== \
4040 * Set up the OpenMP stuff, |
4041 * like the number of threads and such |
4042 * Also start the parallel loop. |
4044 #define __ADIST p_adist[threadNr]
4045 #define __RDIST p_rdist[threadNr]
4046 #define __HBDATA p_hb[threadNr]
4050 bParallel = !bSelected;
4054 actual_nThreads = min((nThreads <= 0) ? INT_MAX : nThreads, gmx_omp_get_max_threads());
4056 gmx_omp_set_num_threads(actual_nThreads);
4057 printf("Frame loop parallelized with OpenMP using %i threads.\n", actual_nThreads);
4062 actual_nThreads = 1;
4065 snew(p_hb, actual_nThreads);
4066 snew(p_adist, actual_nThreads);
4067 snew(p_rdist, actual_nThreads);
4068 for (i = 0; i < actual_nThreads; i++)
4071 snew(p_adist[i], nabin+1);
4072 snew(p_rdist[i], nrbin+1);
4074 p_hb[i]->max_frames = 0;
4075 p_hb[i]->nhb = NULL;
4076 p_hb[i]->ndist = NULL;
4077 p_hb[i]->n_bound = NULL;
4078 p_hb[i]->time = NULL;
4079 p_hb[i]->nhx = NULL;
4081 p_hb[i]->bHBmap = hb->bHBmap;
4082 p_hb[i]->bDAnr = hb->bDAnr;
4083 p_hb[i]->bGem = hb->bGem;
4084 p_hb[i]->wordlen = hb->wordlen;
4085 p_hb[i]->nframes = hb->nframes;
4086 p_hb[i]->maxhydro = hb->maxhydro;
4087 p_hb[i]->danr = hb->danr;
4090 p_hb[i]->hbmap = hb->hbmap;
4091 p_hb[i]->time = hb->time; /* This may need re-syncing at every frame. */
4092 p_hb[i]->per = hb->per;
4094 #ifdef HAVE_NN_LOOPS
4095 p_hb[i]->hbE = hb->hbE;
4099 p_hb[i]->nrdist = 0;
4103 /* Make a thread pool here,
4104 * instead of forking anew at every frame. */
4106 #pragma omp parallel \
4108 private(j, h, ii, jj, hh, E, \
4109 xi, yi, zi, xj, yj, zj, threadNr, \
4110 dist, ang, peri, icell, jcell, \
4111 grp, ogrp, ai, aj, xjj, yjj, zjj, \
4112 xk, yk, zk, ihb, id, resdist, \
4113 xkk, ykk, zkk, kcell, ak, k, bTric, \
4114 bEdge_xjj, bEdge_yjj) \
4116 { /* Start of parallel region */
4117 threadNr = gmx_omp_get_thread_num();
4122 bTric = bBox && TRICLINIC(box);
4126 sync_hbdata(p_hb[threadNr], nframes);
4130 build_grid(hb, x, x[shatom], bBox, box, hbox, (rcut > r2cut) ? rcut : r2cut,
4131 rshell, ngrid, grid);
4132 reset_nhbonds(&(hb->d));
4134 if (debug && bDebug)
4136 dump_grid(debug, ngrid, grid);
4139 add_frames(hb, nframes);
4140 init_hbframe(hb, nframes, output_env_conv_time(oenv, t));
4144 count_da_grid(ngrid, grid, hb->danr[nframes]);
4150 p_hb[threadNr]->time = hb->time; /* This pointer may have changed. */
4155 #ifdef HAVE_NN_LOOPS /* Unlock this feature when testing */
4156 /* Loop over all atom pairs and estimate interaction energy */
4160 addFramesNN(hb, nframes);
4164 #pragma omp for schedule(dynamic)
4165 for (i = 0; i < hb->d.nrd; i++)
4167 for (j = 0; j < hb->a.nra; j++)
4170 h < (bContact ? 1 : hb->d.nhydro[i]);
4173 if (i == hb->d.nrd || j == hb->a.nra)
4175 gmx_fatal(FARGS, "out of bounds");
4178 /* Get the real atom ids */
4181 hh = hb->d.hydro[i][h];
4183 /* Estimate the energy from the geometry */
4184 E = calcHbEnergy(ii, jj, hh, x, NN, box, hbox, &(hb->d));
4185 /* Store the energy */
4186 storeHbEnergy(hb, i, j, h, E, nframes);
4190 #endif /* HAVE_NN_LOOPS */
4199 /* Do not parallelize this just yet. */
4201 for (ii = 0; (ii < nsel); ii++)
4203 int dd = index[0][i];
4204 int aa = index[0][i+2];
4205 /* int */ hh = index[0][i+1];
4206 ihb = is_hbond(hb, ii, ii, dd, aa, rcut, r2cut, ccut, x, bBox, box,
4207 hbox, &dist, &ang, bDA, &h, bContact, bMerge, &peri);
4211 /* add to index if not already there */
4213 add_hbond(hb, dd, aa, hh, ii, ii, nframes, bMerge, ihb, bContact, peri);
4217 } /* if (bSelected) */
4225 calcBoxProjection(box, hb->per->P);
4228 /* loop over all gridcells (xi,yi,zi) */
4229 /* Removed confusing macro, DvdS 27/12/98 */
4232 /* The outer grid loop will have to do for now. */
4233 #pragma omp for schedule(dynamic)
4234 for (xi = 0; xi < ngrid[XX]; xi++)
4236 for (yi = 0; (yi < ngrid[YY]); yi++)
4238 for (zi = 0; (zi < ngrid[ZZ]); zi++)
4241 /* loop over donor groups gr0 (always) and gr1 (if necessary) */
4242 for (grp = gr0; (grp <= (bTwo ? gr1 : gr0)); grp++)
4244 icell = &(grid[zi][yi][xi].d[grp]);
4255 /* loop over all hydrogen atoms from group (grp)
4256 * in this gridcell (icell)
4258 for (ai = 0; (ai < icell->nr); ai++)
4260 i = icell->atoms[ai];
4262 /* loop over all adjacent gridcells (xj,yj,zj) */
4263 for (zjj = grid_loop_begin(ngrid[ZZ], zi, bTric, FALSE);
4264 zjj <= grid_loop_end(ngrid[ZZ], zi, bTric, FALSE);
4267 zj = grid_mod(zjj, ngrid[ZZ]);
4268 bEdge_yjj = (zj == 0) || (zj == ngrid[ZZ] - 1);
4269 for (yjj = grid_loop_begin(ngrid[YY], yi, bTric, bEdge_yjj);
4270 yjj <= grid_loop_end(ngrid[YY], yi, bTric, bEdge_yjj);
4273 yj = grid_mod(yjj, ngrid[YY]);
4275 (yj == 0) || (yj == ngrid[YY] - 1) ||
4276 (zj == 0) || (zj == ngrid[ZZ] - 1);
4277 for (xjj = grid_loop_begin(ngrid[XX], xi, bTric, bEdge_xjj);
4278 xjj <= grid_loop_end(ngrid[XX], xi, bTric, bEdge_xjj);
4281 xj = grid_mod(xjj, ngrid[XX]);
4282 jcell = &(grid[zj][yj][xj].a[ogrp]);
4283 /* loop over acceptor atoms from other group (ogrp)
4284 * in this adjacent gridcell (jcell)
4286 for (aj = 0; (aj < jcell->nr); aj++)
4288 j = jcell->atoms[aj];
4290 /* check if this once was a h-bond */
4292 ihb = is_hbond(__HBDATA, grp, ogrp, i, j, rcut, r2cut, ccut, x, bBox, box,
4293 hbox, &dist, &ang, bDA, &h, bContact, bMerge, &peri);
4297 /* add to index if not already there */
4299 add_hbond(__HBDATA, i, j, h, grp, ogrp, nframes, bMerge, ihb, bContact, peri);
4301 /* make angle and distance distributions */
4302 if (ihb == hbHB && !bContact)
4306 gmx_fatal(FARGS, "distance is higher than what is allowed for an hbond: %f", dist);
4309 __ADIST[(int)( ang/abin)]++;
4310 __RDIST[(int)(dist/rbin)]++;
4314 if ((id = donor_index(&hb->d, grp, i)) == NOTSET)
4316 gmx_fatal(FARGS, "Invalid donor %d", i);
4318 if ((ia = acceptor_index(&hb->a, ogrp, j)) == NOTSET)
4320 gmx_fatal(FARGS, "Invalid acceptor %d", j);
4322 resdist = abs(top.atoms.atom[i].resind-
4323 top.atoms.atom[j].resind);
4324 if (resdist >= max_hx)
4328 __HBDATA->nhx[nframes][resdist]++;
4339 } /* for xi,yi,zi */
4342 } /* if (bSelected) {...} else */
4345 /* Better wait for all threads to finnish using x[] before updating it. */
4348 #pragma omp critical
4350 /* Sum up histograms and counts from p_hb[] into hb */
4353 hb->nhb[k] += p_hb[threadNr]->nhb[k];
4354 hb->ndist[k] += p_hb[threadNr]->ndist[k];
4355 for (j = 0; j < max_hx; j++)
4357 hb->nhx[k][j] += p_hb[threadNr]->nhx[k][j];
4362 /* Here are a handful of single constructs
4363 * to share the workload a bit. The most
4364 * important one is of course the last one,
4365 * where there's a potential bottleneck in form
4372 analyse_donor_props(opt2fn_null("-don", NFILE, fnm), hb, k, t, oenv);
4380 do_nhb_dist(fpnhb, hb, t);
4383 } /* if (bNN) {...} else + */
4387 trrStatus = (read_next_x(oenv, status, &t, x, box));
4397 #pragma omp critical
4399 hb->nrhb += p_hb[threadNr]->nrhb;
4400 hb->nrdist += p_hb[threadNr]->nrdist;
4402 /* Free parallel datastructures */
4403 sfree(p_hb[threadNr]->nhb);
4404 sfree(p_hb[threadNr]->ndist);
4405 sfree(p_hb[threadNr]->nhx);
4408 for (i = 0; i < nabin; i++)
4410 for (j = 0; j < actual_nThreads; j++)
4413 adist[i] += p_adist[j][i];
4417 for (i = 0; i <= nrbin; i++)
4419 for (j = 0; j < actual_nThreads; j++)
4421 rdist[i] += p_rdist[j][i];
4425 sfree(p_adist[threadNr]);
4426 sfree(p_rdist[threadNr]);
4428 } /* End of parallel region */
4435 if (nframes < 2 && (opt2bSet("-ac", NFILE, fnm) || opt2bSet("-life", NFILE, fnm)))
4437 gmx_fatal(FARGS, "Cannot calculate autocorrelation of life times with less than two frames");
4440 free_grid(ngrid, &grid);
4448 /* Compute maximum possible number of different hbonds */
4455 max_nhb = 0.5*(hb->d.nrd*hb->a.nra);
4457 /* Added support for -contact below.
4458 * - Erik Marklund, May 29-31, 2006 */
4459 /* Changed contact code.
4460 * - Erik Marklund, June 29, 2006 */
4465 printf("No %s found!!\n", bContact ? "contacts" : "hydrogen bonds");
4469 printf("Found %d different %s in trajectory\n"
4470 "Found %d different atom-pairs within %s distance\n",
4471 hb->nrhb, bContact ? "contacts" : "hydrogen bonds",
4472 hb->nrdist, (r2cut > 0) ? "second cut-off" : "hydrogen bonding");
4474 /*Control the pHist.*/
4478 merge_hb(hb, bTwo, bContact);
4481 if (opt2bSet("-hbn", NFILE, fnm))
4483 dump_hbmap(hb, NFILE, fnm, bTwo, bContact, isize, index, grpnames, &top.atoms);
4486 /* Moved the call to merge_hb() to a line BEFORE dump_hbmap
4487 * to make the -hbn and -hmb output match eachother.
4488 * - Erik Marklund, May 30, 2006 */
4491 /* Print out number of hbonds and distances */
4494 fp = xvgropen(opt2fn("-num", NFILE, fnm), bContact ? "Contacts" :
4495 "Hydrogen Bonds", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
4497 snew(leg[0], STRLEN);
4498 snew(leg[1], STRLEN);
4499 sprintf(leg[0], "%s", bContact ? "Contacts" : "Hydrogen bonds");
4500 sprintf(leg[1], "Pairs within %g nm", (r2cut > 0) ? r2cut : rcut);
4501 xvgr_legend(fp, 2, (const char**)leg, oenv);
4505 for (i = 0; (i < nframes); i++)
4507 fprintf(fp, "%10g %10d %10d\n", hb->time[i], hb->nhb[i], hb->ndist[i]);
4508 aver_nhb += hb->nhb[i];
4509 aver_dist += hb->ndist[i];
4512 aver_nhb /= nframes;
4513 aver_dist /= nframes;
4514 /* Print HB distance distribution */
4515 if (opt2bSet("-dist", NFILE, fnm))
4520 for (i = 0; i < nrbin; i++)
4525 fp = xvgropen(opt2fn("-dist", NFILE, fnm),
4526 "Hydrogen Bond Distribution",
4528 "Donor - Acceptor Distance (nm)" :
4529 "Hydrogen - Acceptor Distance (nm)", "", oenv);
4530 for (i = 0; i < nrbin; i++)
4532 fprintf(fp, "%10g %10g\n", (i+0.5)*rbin, rdist[i]/(rbin*(real)sum));
4537 /* Print HB angle distribution */
4538 if (opt2bSet("-ang", NFILE, fnm))
4543 for (i = 0; i < nabin; i++)
4548 fp = xvgropen(opt2fn("-ang", NFILE, fnm),
4549 "Hydrogen Bond Distribution",
4550 "Hydrogen - Donor - Acceptor Angle (\\SO\\N)", "", oenv);
4551 for (i = 0; i < nabin; i++)
4553 fprintf(fp, "%10g %10g\n", (i+0.5)*abin, adist[i]/(abin*(real)sum));
4558 /* Print HB in alpha-helix */
4559 if (opt2bSet("-hx", NFILE, fnm))
4561 fp = xvgropen(opt2fn("-hx", NFILE, fnm),
4562 "Hydrogen Bonds", output_env_get_xvgr_tlabel(oenv), "Count", oenv);
4563 xvgr_legend(fp, NRHXTYPES, hxtypenames, oenv);
4564 for (i = 0; i < nframes; i++)
4566 fprintf(fp, "%10g", hb->time[i]);
4567 for (j = 0; j < max_hx; j++)
4569 fprintf(fp, " %6d", hb->nhx[i][j]);
4577 printf("Average number of %s per timeframe %.3f out of %g possible\n",
4578 bContact ? "contacts" : "hbonds",
4579 bContact ? aver_dist : aver_nhb, max_nhb);
4582 /* Do Autocorrelation etc. */
4586 Added support for -contact in ac and hbm calculations below.
4587 - Erik Marklund, May 29, 2006
4591 if (opt2bSet("-ac", NFILE, fnm) || opt2bSet("-life", NFILE, fnm))
4593 please_cite(stdout, "Spoel2006b");
4595 if (opt2bSet("-ac", NFILE, fnm))
4597 char *gemstring = NULL;
4601 params = init_gemParams(rcut, D, hb->time, hb->nframes/2, nFitPoints, fit_start, fit_end,
4602 gemBallistic, nBalExp);
4605 gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
4608 gemstring = gmx_strdup(gemType[hb->per->gemtype]);
4609 do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
4610 bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
4611 gemstring, nThreads, NN, bBallistic, bGemFit);
4613 if (opt2bSet("-life", NFILE, fnm))
4615 do_hblife(opt2fn("-life", NFILE, fnm), hb, bMerge, bContact, oenv);
4617 if (opt2bSet("-hbm", NFILE, fnm))
4620 int id, ia, hh, x, y;
4621 mat.flags = mat.y0 = 0;
4623 if ((nframes > 0) && (hb->nrhb > 0))
4628 snew(mat.matrix, mat.nx);
4629 for (x = 0; (x < mat.nx); x++)
4631 snew(mat.matrix[x], mat.ny);
4634 for (id = 0; (id < hb->d.nrd); id++)
4636 for (ia = 0; (ia < hb->a.nra); ia++)
4638 for (hh = 0; (hh < hb->maxhydro); hh++)
4640 if (hb->hbmap[id][ia])
4642 if (ISHB(hb->hbmap[id][ia]->history[hh]))
4644 /* Changed '<' into '<=' in the for-statement below.
4645 * It fixed the previously undiscovered bug that caused
4646 * the last occurance of an hbond/contact to not be
4647 * set in mat.matrix. Have a look at any old -hbm-output
4648 * and you will notice that the last column is allways empty.
4649 * - Erik Marklund May 30, 2006
4651 for (x = 0; (x <= hb->hbmap[id][ia]->nframes); x++)
4653 int nn0 = hb->hbmap[id][ia]->n0;
4654 range_check(y, 0, mat.ny);
4655 mat.matrix[x+nn0][y] = is_hb(hb->hbmap[id][ia]->h[hh], x);
4663 mat.axis_x = hb->time;
4664 snew(mat.axis_y, mat.ny);
4665 for (j = 0; j < mat.ny; j++)
4669 sprintf(mat.title, bContact ? "Contact Existence Map" :
4670 "Hydrogen Bond Existence Map");
4671 sprintf(mat.legend, bContact ? "Contacts" : "Hydrogen Bonds");
4672 sprintf(mat.label_x, "%s", output_env_get_xvgr_tlabel(oenv));
4673 sprintf(mat.label_y, bContact ? "Contact Index" : "Hydrogen Bond Index");
4674 mat.bDiscrete = TRUE;
4676 snew(mat.map, mat.nmap);
4677 for (i = 0; i < mat.nmap; i++)
4679 mat.map[i].code.c1 = hbmap[i];
4680 mat.map[i].desc = hbdesc[i];
4681 mat.map[i].rgb = hbrgb[i];
4683 fp = opt2FILE("-hbm", NFILE, fnm, "w");
4684 write_xpm_m(fp, mat);
4686 for (x = 0; x < mat.nx; x++)
4688 sfree(mat.matrix[x]);
4696 fprintf(stderr, "No hydrogen bonds/contacts found. No hydrogen bond map will be printed.\n");
4703 fprintf(stderr, "There were %i periodic shifts\n", hb->per->nper);
4704 fprintf(stderr, "Freeing pHist for all donors...\n");
4705 for (i = 0; i < hb->d.nrd; i++)
4707 fprintf(stderr, "\r%i", i);
4708 if (hb->per->pHist[i] != NULL)
4710 for (j = 0; j < hb->a.nra; j++)
4712 clearPshift(&(hb->per->pHist[i][j]));
4714 sfree(hb->per->pHist[i]);
4717 sfree(hb->per->pHist);
4718 sfree(hb->per->p2i);
4720 fprintf(stderr, "...done.\n");
4723 #ifdef HAVE_NN_LOOPS
4736 #define USE_THIS_GROUP(j) ( (j == gr0) || (bTwo && (j == gr1)) )
4738 fp = xvgropen(opt2fn("-dan", NFILE, fnm),
4739 "Donors and Acceptors", output_env_get_xvgr_tlabel(oenv), "Count", oenv);
4740 nleg = (bTwo ? 2 : 1)*2;
4741 snew(legnames, nleg);
4743 for (j = 0; j < grNR; j++)
4745 if (USE_THIS_GROUP(j) )
4747 sprintf(buf, "Donors %s", grpnames[j]);
4748 legnames[i++] = gmx_strdup(buf);
4749 sprintf(buf, "Acceptors %s", grpnames[j]);
4750 legnames[i++] = gmx_strdup(buf);
4755 gmx_incons("number of legend entries");
4757 xvgr_legend(fp, nleg, (const char**)legnames, oenv);
4758 for (i = 0; i < nframes; i++)
4760 fprintf(fp, "%10g", hb->time[i]);
4761 for (j = 0; (j < grNR); j++)
4763 if (USE_THIS_GROUP(j) )
4765 fprintf(fp, " %6d", hb->danr[i][j]);