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37 /* This file is completely threadsafe - keep it that way! */
48 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/utility/cstringutil.h"
50 #include "gromacs/fileio/confio.h"
51 #include "gromacs/math/vec.h"
54 #include "gpp_nextnb.h"
56 #include "gromacs/utility/fatalerror.h"
61 #define DIHEDRAL_WAS_SET_IN_RTP 0
62 static gmx_bool was_dihedral_set_in_rtp(t_param *dih)
64 return dih->c[MAXFORCEPARAM-1] == DIHEDRAL_WAS_SET_IN_RTP;
67 typedef gmx_bool (*peq)(t_param *p1, t_param *p2);
69 static int acomp(const void *a1, const void *a2)
76 if ((ac = (p1->AJ-p2->AJ)) != 0)
80 else if ((ac = (p1->AI-p2->AI)) != 0)
86 return (p1->AK-p2->AK);
90 static int pcomp(const void *a1, const void *a2)
97 if ((pc = (p1->AI-p2->AI)) != 0)
103 return (p1->AJ-p2->AJ);
107 static int dcomp(const void *d1, const void *d2)
114 /* First sort by J & K (the two central) atoms */
115 if ((dc = (p1->AJ-p2->AJ)) != 0)
119 else if ((dc = (p1->AK-p2->AK)) != 0)
123 /* Then make sure to put rtp dihedrals before generated ones */
124 else if (was_dihedral_set_in_rtp(p1) &&
125 !was_dihedral_set_in_rtp(p2))
129 else if (!was_dihedral_set_in_rtp(p1) &&
130 was_dihedral_set_in_rtp(p2))
134 /* Finally, sort by I and J (two outer) atoms */
135 else if ((dc = (p1->AI-p2->AI)) != 0)
141 return (p1->AL-p2->AL);
146 static gmx_bool is_dihedral_on_same_bond(t_param *p1, t_param *p2)
148 if (((p1->AJ == p2->AJ) && (p1->AK == p2->AK)) ||
149 ((p1->AJ == p2->AK) && (p1->AK == p2->AJ)))
160 static gmx_bool preq(t_param *p1, t_param *p2)
162 if ((p1->AI == p2->AI) && (p1->AJ == p2->AJ))
172 static void rm2par(t_param p[], int *np, peq eq)
185 for (i = 1; (i < (*np)); i++)
187 if (!eq(&p[i], &p[i-1]))
192 /* Index now holds pointers to all the non-equal params,
193 * this only works when p is sorted of course
195 for (i = 0; (i < nind); i++)
197 for (j = 0; (j < MAXATOMLIST); j++)
199 p[i].a[j] = p[index[i]].a[j];
201 for (j = 0; (j < MAXFORCEPARAM); j++)
203 p[i].c[j] = p[index[i]].c[j];
205 if (p[index[i]].a[0] == p[index[i]].a[1])
210 "Something VERY strange is going on in rm2par (gen_ad.c)\n"
211 "a[0] %d a[1] %d a[2] %d a[3] %d\n",
212 p[i].a[0], p[i].a[1], p[i].a[2], p[i].a[3]);
216 else if (index[i] > i)
218 /* Copy the string only if it comes from somewhere else
219 * otherwise we will end up copying a random (newly freed) pointer.
220 * Since the index is sorted we only have to test for index[i] > i.
222 strcpy(p[i].s, p[index[i]].s);
230 static void cppar(t_param p[], int np, t_params plist[], int ftype)
232 int i, j, nral, nrfp;
241 for (i = 0; (i < np); i++)
243 for (j = 0; (j < nral); j++)
245 ps->param[ps->nr].a[j] = p[i].a[j];
247 for (j = 0; (j < nrfp); j++)
249 ps->param[ps->nr].c[j] = p[i].c[j];
251 for (j = 0; (j < MAXSLEN); j++)
253 ps->param[ps->nr].s[j] = p[i].s[j];
259 static void cpparam(t_param *dest, t_param *src)
263 for (j = 0; (j < MAXATOMLIST); j++)
265 dest->a[j] = src->a[j];
267 for (j = 0; (j < MAXFORCEPARAM); j++)
269 dest->c[j] = src->c[j];
271 for (j = 0; (j < MAXSLEN); j++)
273 dest->s[j] = src->s[j];
277 static void set_p(t_param *p, atom_id ai[4], real *c, char *s)
281 for (j = 0; (j < 4); j++)
285 for (j = 0; (j < MAXFORCEPARAM); j++)
300 static int int_comp(const void *a, const void *b)
302 return (*(int *)a) - (*(int *)b);
305 static int atom_id_comp(const void *a, const void *b)
307 return (*(atom_id *)a) - (*(atom_id *)b);
310 static int eq_imp(atom_id a1[], atom_id a2[])
315 for (j = 0; (j < 4); j++)
320 qsort(b1, 4, (size_t)sizeof(b1[0]), int_comp);
321 qsort(b2, 4, (size_t)sizeof(b2[0]), int_comp);
323 for (j = 0; (j < 4); j++)
334 static int idcomp(const void *a, const void *b)
341 if ((d = (pa->a[0]-pb->a[0])) != 0)
345 else if ((d = (pa->a[3]-pb->a[3])) != 0)
349 else if ((d = (pa->a[1]-pb->a[1])) != 0)
355 return (int) (pa->a[2]-pb->a[2]);
359 static void sort_id(int nr, t_param ps[])
363 /* First swap order of atoms around if necessary */
364 for (i = 0; (i < nr); i++)
366 if (ps[i].a[3] < ps[i].a[0])
368 tmp = ps[i].a[3]; ps[i].a[3] = ps[i].a[0]; ps[i].a[0] = tmp;
369 tmp = ps[i].a[2]; ps[i].a[2] = ps[i].a[1]; ps[i].a[1] = tmp;
375 qsort(ps, nr, (size_t)sizeof(ps[0]), idcomp);
379 static int n_hydro(atom_id a[], char ***atomname)
384 for (i = 0; (i < 4); i += 3)
386 aname = *atomname[a[i]];
387 c0 = toupper(aname[0]);
392 else if (((int)strlen(aname) > 1) && (c0 >= '0') && (c0 <= '9'))
394 c1 = toupper(aname[1]);
404 /* Clean up the dihedrals (both generated and read from the .rtp
406 static void clean_dih(t_param *dih, int *ndih, t_param improper[], int nimproper,
407 t_atoms *atoms, gmx_bool bKeepAllGeneratedDihedrals,
408 gmx_bool bRemoveDihedralIfWithImproper)
413 /* Construct the list of the indices of the dihedrals
414 * (i.e. generated or read) that might be kept. */
415 snew(index, *ndih+1);
416 if (bKeepAllGeneratedDihedrals)
418 fprintf(stderr, "Keeping all generated dihedrals\n");
420 for (i = 0; i < nind; i++)
429 /* Check if generated dihedral i should be removed. The
430 * dihedrals have been sorted by dcomp() above, so all those
431 * on the same two central atoms are together, with those from
432 * the .rtp file preceding those that were automatically
433 * generated. We remove the latter if the former exist. */
434 for (i = 0; i < *ndih; i++)
436 /* Keep the dihedrals that were defined in the .rtp file,
437 * and the dihedrals that were generated and different
438 * from the last one (whether it was generated or not). */
439 if (was_dihedral_set_in_rtp(&dih[i]) ||
441 !is_dihedral_on_same_bond(&dih[i], &dih[i-1]))
450 for (i = 0; i < nind; i++)
452 gmx_bool bWasSetInRTP = was_dihedral_set_in_rtp(&dih[index[i]]);
453 gmx_bool bKeep = TRUE;
454 if (!bWasSetInRTP && bRemoveDihedralIfWithImproper)
456 /* Remove the dihedral if there is an improper on the same
458 for (j = 0; j < nimproper && bKeep; j++)
460 bKeep = !is_dihedral_on_same_bond(&dih[index[i]], &improper[j]);
466 /* If we don't want all dihedrals, we want to select the
467 * ones with the fewest hydrogens. Note that any generated
468 * dihedrals on the same bond as an .rtp dihedral may have
469 * been already pruned above in the construction of
470 * index[]. However, their parameters are still present,
471 * and l is looping over this dihedral and all of its
472 * pruned siblings. */
473 int bestl = index[i];
474 if (!bKeepAllGeneratedDihedrals && !bWasSetInRTP)
476 /* Minimum number of hydrogens for i and l atoms */
480 is_dihedral_on_same_bond(&dih[index[i]], &dih[l]));
483 int nh = n_hydro(dih[l].a, atoms->atomname);
497 cpparam(&dih[k], &dih[bestl]);
503 for (i = k; i < *ndih; i++)
505 strcpy(dih[i].s, "");
512 static int get_impropers(t_atoms *atoms, t_hackblock hb[], t_param **improper,
513 gmx_bool bAllowMissing)
516 t_rbondeds *impropers;
517 t_rbonded *hbimproper;
518 int nimproper, i, j, k, r, start, ninc, nalloc;
519 atom_id ai[MAXATOMLIST];
524 snew(*improper, nalloc);
526 /* Add all the impropers from the residue database to the list. */
531 for (i = 0; (i < atoms->nres); i++)
533 impropers = &hb[i].rb[ebtsIDIHS];
534 for (j = 0; (j < impropers->nb); j++)
537 for (k = 0; (k < 4) && !bStop; k++)
539 ai[k] = search_atom(impropers->b[j].a[k], start,
541 "improper", bAllowMissing);
542 if (ai[k] == NO_ATID)
549 if (nimproper == nalloc)
552 srenew(*improper, nalloc);
555 set_p(&((*improper)[nimproper]), ai, NULL, impropers->b[j].s);
559 while ((start < atoms->nr) && (atoms->atom[start].resind == i))
569 static int nb_dist(t_nextnb *nnb, int ai, int aj)
581 nrexcl = nnb->nrexcl[ai];
582 for (nre = 1; (nre < nnb->nrex); nre++)
585 for (nrx = 0; (nrx < nrexcl[nre]); nrx++)
587 if ((aj == a[nrx]) && (NRE == -1))
596 gmx_bool is_hydro(t_atoms *atoms, int ai)
598 return ((*(atoms->atomname[ai]))[0] == 'H');
601 static void get_atomnames_min(int n, char **anm,
602 int resind, t_atoms *atoms, atom_id *a)
606 /* Assume ascending residue numbering */
607 for (m = 0; m < n; m++)
609 if (atoms->atom[a[m]].resind < resind)
613 else if (atoms->atom[a[m]].resind > resind)
621 strcat(anm[m], *(atoms->atomname[a[m]]));
625 static void gen_excls(t_atoms *atoms, t_excls *excls, t_hackblock hb[],
626 gmx_bool bAllowMissing)
629 atom_id a, astart, i1, i2, itmp;
635 for (a = 0; a < atoms->nr; a++)
637 r = atoms->atom[a].resind;
638 if (a == atoms->nr-1 || atoms->atom[a+1].resind != r)
640 hbexcl = &hb[r].rb[ebtsEXCLS];
642 for (e = 0; e < hbexcl->nb; e++)
644 anm = hbexcl->b[e].a[0];
645 i1 = search_atom(anm, astart, atoms,
646 "exclusion", bAllowMissing);
647 anm = hbexcl->b[e].a[1];
648 i2 = search_atom(anm, astart, atoms,
649 "exclusion", bAllowMissing);
650 if (i1 != NO_ATID && i2 != NO_ATID)
658 srenew(excls[i1].e, excls[i1].nr+1);
659 excls[i1].e[excls[i1].nr] = i2;
668 for (a = 0; a < atoms->nr; a++)
672 qsort(excls[a].e, excls[a].nr, (size_t)sizeof(atom_id), atom_id_comp);
677 static void remove_excl(t_excls *excls, int remove)
681 for (i = remove+1; i < excls->nr; i++)
683 excls->e[i-1] = excls->e[i];
689 void clean_excls(t_nextnb *nnb, int nrexcl, t_excls excls[])
691 int i, j, j1, k, k1, l, l1, m, n, e;
696 /* extract all i-j-k-l neighbours from nnb struct */
697 for (i = 0; (i < nnb->nr); i++)
699 /* For all particles */
702 for (j = 0; (j < nnb->nrexcl[i][1]); j++)
704 /* For all first neighbours */
705 j1 = nnb->a[i][1][j];
707 for (e = 0; e < excl->nr; e++)
709 if (excl->e[e] == j1)
711 remove_excl(excl, e);
717 for (k = 0; (k < nnb->nrexcl[j1][1]); k++)
719 /* For all first neighbours of j1 */
720 k1 = nnb->a[j1][1][k];
722 for (e = 0; e < excl->nr; e++)
724 if (excl->e[e] == k1)
726 remove_excl(excl, e);
732 for (l = 0; (l < nnb->nrexcl[k1][1]); l++)
734 /* For all first neighbours of k1 */
735 l1 = nnb->a[k1][1][l];
737 for (e = 0; e < excl->nr; e++)
739 if (excl->e[e] == l1)
741 remove_excl(excl, e);
753 void generate_excls(t_nextnb *nnb, int nrexcl, t_excls excls[])
755 int i, j, j1, k, k1, l, l1, m, n, e, N;
758 for (N = 1; (N < min(nrexcl, nnb->nrex)); N++)
760 /* extract all i-j-k-l neighbours from nnb struct */
761 for (i = 0; (i < nnb->nr); i++)
763 /* For all particles */
766 excl->nr += nnb->nrexcl[i][N];
767 srenew(excl->e, excl->nr);
768 for (j = 0; (j < nnb->nrexcl[i][N]); j++)
770 /* For all first neighbours */
771 if (nnb->a[i][N][j] != i)
773 excl->e[n++] = nnb->a[i][N][j];
780 /* Generate pairs, angles and dihedrals from .rtp settings */
781 void gen_pad(t_nextnb *nnb, t_atoms *atoms, t_restp rtp[],
782 t_params plist[], t_excls excls[], t_hackblock hb[],
783 gmx_bool bAllowMissing)
785 t_param *ang, *dih, *pai, *improper;
786 t_rbondeds *hbang, *hbdih;
789 int res, minres, maxres;
790 int i, j, j1, k, k1, l, l1, m, n, i1, i2;
791 int ninc, maxang, maxdih, maxpai;
792 int nang, ndih, npai, nimproper, nbd;
794 gmx_bool bFound, bExcl;
796 /* These are the angles, dihedrals and pairs that we generate
797 * from the bonds. The ones that are already there from the rtp file
804 maxang = maxdih = maxpai = ninc;
810 for (i = 0; i < 4; i++)
817 gen_excls(atoms, excls, hb, bAllowMissing);
818 /* mark all entries as not matched yet */
819 for (i = 0; i < atoms->nres; i++)
821 for (j = 0; j < ebtsNR; j++)
823 for (k = 0; k < hb[i].rb[j].nb; k++)
825 hb[i].rb[j].b[k].match = FALSE;
831 /* Extract all i-j-k-l neighbours from nnb struct to generate all
832 * angles and dihedrals. */
833 for (i = 0; (i < nnb->nr); i++)
835 /* For all particles */
836 for (j = 0; (j < nnb->nrexcl[i][1]); j++)
838 /* For all first neighbours */
839 j1 = nnb->a[i][1][j];
840 for (k = 0; (k < nnb->nrexcl[j1][1]); k++)
842 /* For all first neighbours of j1 */
843 k1 = nnb->a[j1][1][k];
846 /* Generate every angle only once */
857 ang[nang].C0 = NOTSET;
858 ang[nang].C1 = NOTSET;
859 set_p_string(&(ang[nang]), "");
862 minres = atoms->atom[ang[nang].a[0]].resind;
864 for (m = 1; m < 3; m++)
866 minres = min(minres, atoms->atom[ang[nang].a[m]].resind);
867 maxres = max(maxres, atoms->atom[ang[nang].a[m]].resind);
869 res = 2*minres-maxres;
872 res += maxres-minres;
873 get_atomnames_min(3, anm, res, atoms, ang[nang].a);
874 hbang = &hb[res].rb[ebtsANGLES];
875 for (l = 0; (l < hbang->nb); l++)
877 if (strcmp(anm[1], hbang->b[l].AJ) == 0)
880 for (m = 0; m < 3; m += 2)
883 ((strcmp(anm[m], hbang->b[l].AI) == 0) &&
884 (strcmp(anm[2-m], hbang->b[l].AK) == 0)));
888 set_p_string(&(ang[nang]), hbang->b[l].s);
889 /* Mark that we found a match for this entry */
890 hbang->b[l].match = TRUE;
895 while (res < maxres);
899 /* Generate every dihedral, 1-4 exclusion and 1-4 interaction
903 for (l = 0; (l < nnb->nrexcl[k1][1]); l++)
905 /* For all first neighbours of k1 */
906 l1 = nnb->a[k1][1][l];
907 if ((l1 != i) && (l1 != j1))
918 for (m = 0; m < MAXFORCEPARAM; m++)
920 dih[ndih].c[m] = NOTSET;
922 set_p_string(&(dih[ndih]), "");
926 minres = atoms->atom[dih[ndih].a[0]].resind;
928 for (m = 1; m < 4; m++)
930 minres = min(minres, atoms->atom[dih[ndih].a[m]].resind);
931 maxres = max(maxres, atoms->atom[dih[ndih].a[m]].resind);
933 res = 2*minres-maxres;
936 res += maxres-minres;
937 get_atomnames_min(4, anm, res, atoms, dih[ndih].a);
938 hbdih = &hb[res].rb[ebtsPDIHS];
939 for (n = 0; (n < hbdih->nb); n++)
942 for (m = 0; m < 2; m++)
945 ((strcmp(anm[3*m], hbdih->b[n].AI) == 0) &&
946 (strcmp(anm[1+m], hbdih->b[n].AJ) == 0) &&
947 (strcmp(anm[2-m], hbdih->b[n].AK) == 0) &&
948 (strcmp(anm[3-3*m], hbdih->b[n].AL) == 0)));
952 set_p_string(&dih[ndih], hbdih->b[n].s);
953 /* Mark that we found a match for this entry */
954 hbdih->b[n].match = TRUE;
956 /* Set the last parameter to be able to see
957 if the dihedral was in the rtp list.
959 dih[ndih].c[MAXFORCEPARAM-1] = DIHEDRAL_WAS_SET_IN_RTP;
962 /* Set the next direct in case the rtp contains
963 multiple entries for this dihedral.
974 for (m = 0; m < MAXFORCEPARAM; m++)
976 dih[ndih].c[m] = NOTSET;
981 while (res < maxres);
994 for (m = 0; m < MAXFORCEPARAM; m++)
996 dih[ndih].c[m] = NOTSET;
998 set_p_string(&(dih[ndih]), "");
1002 nbd = nb_dist(nnb, i, l1);
1005 fprintf(debug, "Distance (%d-%d) = %d\n", i+1, l1+1, nbd);
1012 for (m = 0; m < excls[i1].nr; m++)
1014 bExcl = bExcl || excls[i1].e[m] == i2;
1018 if (rtp[0].bGenerateHH14Interactions ||
1019 !(is_hydro(atoms, i1) && is_hydro(atoms, i2)))
1024 srenew(pai, maxpai);
1028 pai[npai].C0 = NOTSET;
1029 pai[npai].C1 = NOTSET;
1030 set_p_string(&(pai[npai]), "");
1043 /* The above approach is great in that we double-check that e.g. an angle
1044 * really corresponds to three atoms connected by bonds, but this is not
1045 * generally true. Go through the angle and dihedral hackblocks to add
1046 * entries that we have not yet marked as matched when going through bonds.
1048 for (i = 0; i < atoms->nres; i++)
1050 /* Add remaining angles from hackblock */
1051 hbang = &hb[i].rb[ebtsANGLES];
1052 for (j = 0; j < hbang->nb; j++)
1054 if (hbang->b[j].match == TRUE)
1056 /* We already used this entry, continue to the next */
1059 /* Hm - entry not used, let's see if we can find all atoms */
1063 srenew(ang, maxang);
1066 for (k = 0; k < 3 && bFound; k++)
1068 p = hbang->b[j].a[k];
1075 else if (p[0] == '+')
1080 ang[nang].a[k] = search_res_atom(p, res, atoms, "angle", TRUE);
1081 bFound = (ang[nang].a[k] != NO_ATID);
1083 ang[nang].C0 = NOTSET;
1084 ang[nang].C1 = NOTSET;
1088 set_p_string(&(ang[nang]), hbang->b[j].s);
1089 hbang->b[j].match = TRUE;
1090 /* Incrementing nang means we save this angle */
1095 /* Add remaining dihedrals from hackblock */
1096 hbdih = &hb[i].rb[ebtsPDIHS];
1097 for (j = 0; j < hbdih->nb; j++)
1099 if (hbdih->b[j].match == TRUE)
1101 /* We already used this entry, continue to the next */
1104 /* Hm - entry not used, let's see if we can find all atoms */
1108 srenew(dih, maxdih);
1111 for (k = 0; k < 4 && bFound; k++)
1113 p = hbdih->b[j].a[k];
1120 else if (p[0] == '+')
1125 dih[ndih].a[k] = search_res_atom(p, res, atoms, "dihedral", TRUE);
1126 bFound = (dih[ndih].a[k] != NO_ATID);
1128 for (m = 0; m < MAXFORCEPARAM; m++)
1130 dih[ndih].c[m] = NOTSET;
1135 set_p_string(&(dih[ndih]), hbdih->b[j].s);
1136 hbdih->b[j].match = TRUE;
1137 /* Incrementing ndih means we save this dihedral */
1143 /* Sort angles with respect to j-i-k (middle atom first) */
1146 qsort(ang, nang, (size_t)sizeof(ang[0]), acomp);
1149 /* Sort dihedrals with respect to j-k-i-l (middle atoms first) */
1152 qsort(dih, ndih, (size_t)sizeof(dih[0]), dcomp);
1155 /* Sort the pairs */
1158 qsort(pai, npai, (size_t)sizeof(pai[0]), pcomp);
1162 /* Remove doubles, could occur in 6-rings, such as phenyls,
1163 maybe one does not want this when fudgeQQ < 1.
1165 fprintf(stderr, "Before cleaning: %d pairs\n", npai);
1166 rm2par(pai, &npai, preq);
1169 /* Get the impropers from the database */
1170 nimproper = get_impropers(atoms, hb, &improper, bAllowMissing);
1172 /* Sort the impropers */
1173 sort_id(nimproper, improper);
1177 fprintf(stderr, "Before cleaning: %d dihedrals\n", ndih);
1178 clean_dih(dih, &ndih, improper, nimproper, atoms,
1179 rtp[0].bKeepAllGeneratedDihedrals,
1180 rtp[0].bRemoveDihedralIfWithImproper);
1183 /* Now we have unique lists of angles and dihedrals
1184 * Copy them into the destination struct
1186 cppar(ang, nang, plist, F_ANGLES);
1187 cppar(dih, ndih, plist, F_PDIHS);
1188 cppar(improper, nimproper, plist, F_IDIHS);
1189 cppar(pai, npai, plist, F_LJ14);
1191 /* Remove all exclusions which are within nrexcl */
1192 clean_excls(nnb, rtp[0].nrexcl, excls);