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39 #include "gromacs/legacyheaders/constr.h"
44 #include "gromacs/essentialdynamics/edsam.h"
45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/pdbio.h"
48 #include "gromacs/legacyheaders/copyrite.h"
49 #include "gromacs/legacyheaders/domdec.h"
50 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
51 #include "gromacs/legacyheaders/macros.h"
52 #include "gromacs/legacyheaders/mdrun.h"
53 #include "gromacs/legacyheaders/names.h"
54 #include "gromacs/legacyheaders/nrnb.h"
55 #include "gromacs/legacyheaders/splitter.h"
56 #include "gromacs/legacyheaders/txtdump.h"
57 #include "gromacs/legacyheaders/types/commrec.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/pbcutil/pbc.h"
60 #include "gromacs/pulling/pull.h"
61 #include "gromacs/topology/block.h"
62 #include "gromacs/topology/invblock.h"
63 #include "gromacs/topology/mtop_util.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/smalloc.h"
67 typedef struct gmx_constr {
68 int ncon_tot; /* The total number of constraints */
69 int nflexcon; /* The number of flexible constraints */
70 int n_at2con_mt; /* The size of at2con = #moltypes */
71 t_blocka *at2con_mt; /* A list of atoms to constraints */
72 int n_at2settle_mt; /* The size of at2settle = #moltypes */
73 int **at2settle_mt; /* A list of atoms to settles */
74 gmx_bool bInterCGsettles;
75 gmx_lincsdata_t lincsd; /* LINCS data */
76 gmx_shakedata_t shaked; /* SHAKE data */
77 gmx_settledata_t settled; /* SETTLE data */
78 int nblocks; /* The number of SHAKE blocks */
79 int *sblock; /* The SHAKE blocks */
80 int sblock_nalloc; /* The allocation size of sblock */
81 real *lagr; /* Lagrange multipliers for SHAKE */
82 int lagr_nalloc; /* The allocation size of lagr */
83 int maxwarn; /* The maximum number of warnings */
86 gmx_edsam_t ed; /* The essential dynamics data */
88 tensor *vir_r_m_dr_th; /* Thread local working data */
89 int *settle_error; /* Thread local working data */
91 gmx_mtop_t *warn_mtop; /* Only used for printing warnings */
99 /* delta_t should be used instead of ir->delta_t, to permit the time
100 step to be scaled by the calling code */
101 static void *init_vetavars(t_vetavars *vars,
102 gmx_bool constr_deriv,
103 real veta, real vetanew,
104 t_inputrec *ir, real delta_t,
105 gmx_ekindata_t *ekind, gmx_bool bPscal)
110 /* first, set the alpha integrator variable */
111 if ((ir->opts.nrdf[0] > 0) && bPscal)
113 vars->alpha = 1.0 + DIM/((double)ir->opts.nrdf[0]);
119 g = 0.5*veta*delta_t;
120 vars->rscale = exp(g)*series_sinhx(g);
121 g = -0.25*vars->alpha*veta*delta_t;
122 vars->vscale = exp(g)*series_sinhx(g);
123 vars->rvscale = vars->vscale*vars->rscale;
124 vars->veta = vetanew;
128 snew(vars->vscale_nhc, ir->opts.ngtc);
129 if ((ekind == NULL) || (!bPscal))
131 for (i = 0; i < ir->opts.ngtc; i++)
133 vars->vscale_nhc[i] = 1;
138 for (i = 0; i < ir->opts.ngtc; i++)
140 vars->vscale_nhc[i] = ekind->tcstat[i].vscale_nhc;
146 vars->vscale_nhc = NULL;
152 static void free_vetavars(t_vetavars *vars)
154 if (vars->vscale_nhc != NULL)
156 sfree(vars->vscale_nhc);
160 static int pcomp(const void *p1, const void *p2)
163 atom_id min1, min2, max1, max2;
164 t_sortblock *a1 = (t_sortblock *)p1;
165 t_sortblock *a2 = (t_sortblock *)p2;
167 db = a1->blocknr-a2->blocknr;
174 min1 = min(a1->iatom[1], a1->iatom[2]);
175 max1 = max(a1->iatom[1], a1->iatom[2]);
176 min2 = min(a2->iatom[1], a2->iatom[2]);
177 max2 = max(a2->iatom[1], a2->iatom[2]);
189 int n_flexible_constraints(struct gmx_constr *constr)
195 nflexcon = constr->nflexcon;
205 static void clear_constraint_quantity_nonlocal(gmx_domdec_t *dd, rvec *q)
207 int nonlocal_at_start, nonlocal_at_end, at;
209 dd_get_constraint_range(dd, &nonlocal_at_start, &nonlocal_at_end);
211 for (at = nonlocal_at_start; at < nonlocal_at_end; at++)
217 void too_many_constraint_warnings(int eConstrAlg, int warncount)
219 const char *abort = "- aborting to avoid logfile runaway.\n"
220 "This normally happens when your system is not sufficiently equilibrated,"
221 "or if you are changing lambda too fast in free energy simulations.\n";
224 "Too many %s warnings (%d)\n"
225 "If you know what you are doing you can %s"
226 "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
227 "but normally it is better to fix the problem",
228 (eConstrAlg == econtLINCS) ? "LINCS" : "SETTLE", warncount,
229 (eConstrAlg == econtLINCS) ?
230 "adjust the lincs warning threshold in your mdp file\nor " : "\n");
233 static void write_constr_pdb(const char *fn, const char *title,
235 int start, int homenr, t_commrec *cr,
236 rvec x[], matrix box)
240 int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
245 if (DOMAINDECOMP(cr))
248 dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
255 sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
259 sprintf(fname, "%s.pdb", fn);
262 out = gmx_fio_fopen(fname, "w");
264 fprintf(out, "TITLE %s\n", title);
265 gmx_write_pdb_box(out, -1, box);
266 for (i = start; i < start+homenr; i++)
270 if (i >= dd->nat_home && i < dd_ac0)
274 ii = dd->gatindex[i];
280 gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
281 gmx_fprintf_pdb_atomline(out, epdbATOM, ii+1, anm, ' ', resnm, ' ', resnr, ' ',
282 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 0.0, "");
284 fprintf(out, "TER\n");
289 static void dump_confs(FILE *fplog, gmx_int64_t step, gmx_mtop_t *mtop,
290 int start, int homenr, t_commrec *cr,
291 rvec x[], rvec xprime[], matrix box)
293 char buf[256], buf2[22];
295 char *env = getenv("GMX_SUPPRESS_DUMP");
301 sprintf(buf, "step%sb", gmx_step_str(step, buf2));
302 write_constr_pdb(buf, "initial coordinates",
303 mtop, start, homenr, cr, x, box);
304 sprintf(buf, "step%sc", gmx_step_str(step, buf2));
305 write_constr_pdb(buf, "coordinates after constraining",
306 mtop, start, homenr, cr, xprime, box);
309 fprintf(fplog, "Wrote pdb files with previous and current coordinates\n");
311 fprintf(stderr, "Wrote pdb files with previous and current coordinates\n");
314 static void pr_sortblock(FILE *fp, const char *title, int nsb, t_sortblock sb[])
318 fprintf(fp, "%s\n", title);
319 for (i = 0; (i < nsb); i++)
321 fprintf(fp, "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n",
322 i, sb[i].iatom[0], sb[i].iatom[1], sb[i].iatom[2],
327 gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
328 struct gmx_constr *constr,
329 t_idef *idef, t_inputrec *ir, gmx_ekindata_t *ekind,
331 gmx_int64_t step, int delta_step,
334 rvec *x, rvec *xprime, rvec *min_proj,
335 gmx_bool bMolPBC, matrix box,
336 real lambda, real *dvdlambda,
337 rvec *v, tensor *vir,
338 t_nrnb *nrnb, int econq, gmx_bool bPscal,
339 real veta, real vetanew)
342 int start, homenr, nrend;
344 int ncons, settle_error;
348 real invdt, vir_fac, t;
351 t_pbc pbc, *pbc_null;
356 if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
358 gmx_incons("constrain called for forces displacements while not doing energy minimization, can not do this while the LINCS and SETTLE constraint connection matrices are mass weighted");
366 nrend = start+homenr;
368 scaled_delta_t = step_scaling * ir->delta_t;
370 /* set constants for pressure control integration */
371 init_vetavars(&vetavar, econq != econqCoord,
372 veta, vetanew, ir, scaled_delta_t, ekind, bPscal);
374 /* Prepare time step for use in constraint implementations, and
375 avoid generating inf when ir->delta_t = 0. */
376 if (ir->delta_t == 0)
382 invdt = 1.0/scaled_delta_t;
385 if (ir->efep != efepNO && EI_DYNAMICS(ir->eI))
387 /* Set the constraint lengths for the step at which this configuration
388 * is meant to be. The invmasses should not be changed.
390 lambda += delta_step*ir->fepvals->delta_lambda;
395 clear_mat(vir_r_m_dr);
400 settle = &idef->il[F_SETTLE];
401 nsettle = settle->nr/(1+NRAL(F_SETTLE));
405 nth = gmx_omp_nthreads_get(emntSETTLE);
412 if (nth > 1 && constr->vir_r_m_dr_th == NULL)
414 snew(constr->vir_r_m_dr_th, nth);
415 snew(constr->settle_error, nth);
420 /* We do not need full pbc when constraints do not cross charge groups,
421 * i.e. when dd->constraint_comm==NULL.
422 * Note that PBC for constraints is different from PBC for bondeds.
423 * For constraints there is both forward and backward communication.
425 if (ir->ePBC != epbcNONE &&
426 (cr->dd || bMolPBC) && !(cr->dd && cr->dd->constraint_comm == NULL))
428 /* With pbc=screw the screw has been changed to a shift
429 * by the constraint coordinate communication routine,
430 * so that here we can use normal pbc.
432 pbc_null = set_pbc_dd(&pbc, ir->ePBC, cr->dd, FALSE, box);
439 /* Communicate the coordinates required for the non-local constraints
440 * for LINCS and/or SETTLE.
444 dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
448 /* We need to initialize the non-local components of v.
449 * We never actually use these values, but we do increment them,
450 * so we should avoid uninitialized variables and overflows.
452 clear_constraint_quantity_nonlocal(cr->dd, v);
456 if (constr->lincsd != NULL)
458 bOK = constrain_lincs(fplog, bLog, bEner, ir, step, constr->lincsd, md, cr,
460 box, pbc_null, lambda, dvdlambda,
461 invdt, v, vir != NULL, vir_r_m_dr,
463 constr->maxwarn, &constr->warncount_lincs);
464 if (!bOK && constr->maxwarn >= 0)
468 fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
469 econstr_names[econtLINCS], gmx_step_str(step, buf));
475 if (constr->nblocks > 0)
480 bOK = bshakef(fplog, constr->shaked,
481 md->invmass, constr->nblocks, constr->sblock,
482 idef, ir, x, xprime, nrnb,
483 constr->lagr, lambda, dvdlambda,
484 invdt, v, vir != NULL, vir_r_m_dr,
485 constr->maxwarn >= 0, econq, &vetavar);
488 bOK = bshakef(fplog, constr->shaked,
489 md->invmass, constr->nblocks, constr->sblock,
490 idef, ir, x, min_proj, nrnb,
491 constr->lagr, lambda, dvdlambda,
492 invdt, NULL, vir != NULL, vir_r_m_dr,
493 constr->maxwarn >= 0, econq, &vetavar);
496 gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
500 if (!bOK && constr->maxwarn >= 0)
504 fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
505 econstr_names[econtSHAKE], gmx_step_str(step, buf));
513 int calcvir_atom_end;
517 calcvir_atom_end = 0;
521 calcvir_atom_end = md->homenr;
527 #pragma omp parallel for num_threads(nth) schedule(static)
528 for (th = 0; th < nth; th++)
530 int start_th, end_th;
534 clear_mat(constr->vir_r_m_dr_th[th]);
537 start_th = (nsettle* th )/nth;
538 end_th = (nsettle*(th+1))/nth;
539 if (start_th >= 0 && end_th - start_th > 0)
541 csettle(constr->settled,
543 settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
546 invdt, v ? v[0] : NULL, calcvir_atom_end,
547 th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
548 th == 0 ? &settle_error : &constr->settle_error[th],
552 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
555 inc_nrnb(nrnb, eNR_CONSTR_V, nsettle*3);
559 inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle*3);
565 case econqForceDispl:
566 #pragma omp parallel for num_threads(nth) schedule(static)
567 for (th = 0; th < nth; th++)
569 int start_th, end_th;
573 clear_mat(constr->vir_r_m_dr_th[th]);
576 start_th = (nsettle* th )/nth;
577 end_th = (nsettle*(th+1))/nth;
579 if (start_th >= 0 && end_th - start_th > 0)
581 settle_proj(constr->settled, econq,
583 settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
586 xprime, min_proj, calcvir_atom_end,
587 th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
591 /* This is an overestimate */
592 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
594 case econqDeriv_FlexCon:
595 /* Nothing to do, since the are no flexible constraints in settles */
598 gmx_incons("Unknown constraint quantity for settle");
604 /* Combine virial and error info of the other threads */
605 for (i = 1; i < nth; i++)
607 m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
608 settle_error = constr->settle_error[i];
611 if (econq == econqCoord && settle_error >= 0)
614 if (constr->maxwarn >= 0)
618 "\nstep " "%"GMX_PRId64 ": Water molecule starting at atom %d can not be "
619 "settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
620 step, ddglatnr(cr->dd, settle->iatoms[settle_error*(1+NRAL(F_SETTLE))+1]));
623 fprintf(fplog, "%s", buf);
625 fprintf(stderr, "%s", buf);
626 constr->warncount_settle++;
627 if (constr->warncount_settle > constr->maxwarn)
629 too_many_constraint_warnings(-1, constr->warncount_settle);
636 free_vetavars(&vetavar);
640 /* The normal uses of constrain() pass step_scaling = 1.0.
641 * The call to constrain() for SD1 that passes step_scaling =
642 * 0.5 also passes vir = NULL, so cannot reach this
643 * assertion. This assertion should remain until someone knows
644 * that this path works for their intended purpose, and then
645 * they can use scaled_delta_t instead of ir->delta_t
647 assert(gmx_within_tol(step_scaling, 1.0, GMX_REAL_EPS));
651 vir_fac = 0.5/(ir->delta_t*ir->delta_t);
654 vir_fac = 0.5/ir->delta_t;
657 case econqForceDispl:
662 gmx_incons("Unsupported constraint quantity for virial");
667 vir_fac *= 2; /* only constraining over half the distance here */
669 for (i = 0; i < DIM; i++)
671 for (j = 0; j < DIM; j++)
673 (*vir)[i][j] = vir_fac*vir_r_m_dr[i][j];
680 dump_confs(fplog, step, constr->warn_mtop, start, homenr, cr, x, xprime, box);
683 if (econq == econqCoord)
685 if (ir->ePull == epullCONSTRAINT)
687 if (EI_DYNAMICS(ir->eI))
689 t = ir->init_t + (step + delta_step)*ir->delta_t;
695 set_pbc(&pbc, ir->ePBC, box);
696 pull_constraint(ir->pull, md, &pbc, cr, ir->delta_t, t, x, xprime, v, *vir);
698 if (constr->ed && delta_step > 0)
700 /* apply the essential dynamcs constraints here */
701 do_edsam(ir, step, cr, xprime, v, box, constr->ed);
708 real *constr_rmsd_data(struct gmx_constr *constr)
712 return lincs_rmsd_data(constr->lincsd);
720 real constr_rmsd(struct gmx_constr *constr, gmx_bool bSD2)
724 return lincs_rmsd(constr->lincsd, bSD2);
732 static void make_shake_sblock_serial(struct gmx_constr *constr,
733 t_idef *idef, t_mdatoms *md)
742 /* Since we are processing the local topology,
743 * the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
745 ncons = idef->il[F_CONSTR].nr/3;
747 init_blocka(&sblocks);
748 gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
751 bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
752 nblocks=blocks->multinr[idef->nodeid] - bstart;
755 constr->nblocks = sblocks.nr;
758 fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
759 ncons, bstart, constr->nblocks);
762 /* Calculate block number for each atom */
763 inv_sblock = make_invblocka(&sblocks, md->nr);
765 done_blocka(&sblocks);
767 /* Store the block number in temp array and
768 * sort the constraints in order of the sblock number
769 * and the atom numbers, really sorting a segment of the array!
772 pr_idef(fplog, 0, "Before Sort", idef);
774 iatom = idef->il[F_CONSTR].iatoms;
776 for (i = 0; (i < ncons); i++, iatom += 3)
778 for (m = 0; (m < 3); m++)
780 sb[i].iatom[m] = iatom[m];
782 sb[i].blocknr = inv_sblock[iatom[1]];
785 /* Now sort the blocks */
788 pr_sortblock(debug, "Before sorting", ncons, sb);
789 fprintf(debug, "Going to sort constraints\n");
792 qsort(sb, ncons, (size_t)sizeof(*sb), pcomp);
796 pr_sortblock(debug, "After sorting", ncons, sb);
799 iatom = idef->il[F_CONSTR].iatoms;
800 for (i = 0; (i < ncons); i++, iatom += 3)
802 for (m = 0; (m < 3); m++)
804 iatom[m] = sb[i].iatom[m];
808 pr_idef(fplog, 0, "After Sort", idef);
812 snew(constr->sblock, constr->nblocks+1);
814 for (i = 0; (i < ncons); i++)
816 if (sb[i].blocknr != bnr)
819 constr->sblock[j++] = 3*i;
823 constr->sblock[j++] = 3*ncons;
825 if (j != (constr->nblocks+1))
827 fprintf(stderr, "bstart: %d\n", bstart);
828 fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
829 j, constr->nblocks, ncons);
830 for (i = 0; (i < ncons); i++)
832 fprintf(stderr, "i: %5d sb[i].blocknr: %5d\n", i, sb[i].blocknr);
834 for (j = 0; (j <= constr->nblocks); j++)
836 fprintf(stderr, "sblock[%3d]=%5d\n", j, (int)constr->sblock[j]);
838 gmx_fatal(FARGS, "DEATH HORROR: "
839 "sblocks does not match idef->il[F_CONSTR]");
845 static void make_shake_sblock_dd(struct gmx_constr *constr,
846 t_ilist *ilcon, t_block *cgs,
852 if (dd->ncg_home+1 > constr->sblock_nalloc)
854 constr->sblock_nalloc = over_alloc_dd(dd->ncg_home+1);
855 srenew(constr->sblock, constr->sblock_nalloc);
859 iatom = ilcon->iatoms;
862 for (c = 0; c < ncons; c++)
864 if (c == 0 || iatom[1] >= cgs->index[cg+1])
866 constr->sblock[constr->nblocks++] = 3*c;
867 while (iatom[1] >= cgs->index[cg+1])
874 constr->sblock[constr->nblocks] = 3*ncons;
877 t_blocka make_at2con(int start, int natoms,
878 t_ilist *ilist, t_iparams *iparams,
879 gmx_bool bDynamics, int *nflexiblecons)
881 int *count, ncon, con, con_tot, nflexcon, ftype, i, a;
888 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
890 ncon = ilist[ftype].nr/3;
891 ia = ilist[ftype].iatoms;
892 for (con = 0; con < ncon; con++)
894 bFlexCon = (iparams[ia[0]].constr.dA == 0 &&
895 iparams[ia[0]].constr.dB == 0);
900 if (bDynamics || !bFlexCon)
902 for (i = 1; i < 3; i++)
911 *nflexiblecons = nflexcon;
914 at2con.nalloc_index = at2con.nr+1;
915 snew(at2con.index, at2con.nalloc_index);
917 for (a = 0; a < natoms; a++)
919 at2con.index[a+1] = at2con.index[a] + count[a];
922 at2con.nra = at2con.index[natoms];
923 at2con.nalloc_a = at2con.nra;
924 snew(at2con.a, at2con.nalloc_a);
926 /* The F_CONSTRNC constraints have constraint numbers
927 * that continue after the last F_CONSTR constraint.
930 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
932 ncon = ilist[ftype].nr/3;
933 ia = ilist[ftype].iatoms;
934 for (con = 0; con < ncon; con++)
936 bFlexCon = (iparams[ia[0]].constr.dA == 0 &&
937 iparams[ia[0]].constr.dB == 0);
938 if (bDynamics || !bFlexCon)
940 for (i = 1; i < 3; i++)
943 at2con.a[at2con.index[a]+count[a]++] = con_tot;
956 static int *make_at2settle(int natoms, const t_ilist *ilist)
962 /* Set all to no settle */
963 for (a = 0; a < natoms; a++)
968 stride = 1 + NRAL(F_SETTLE);
970 for (s = 0; s < ilist->nr; s += stride)
972 at2s[ilist->iatoms[s+1]] = s/stride;
973 at2s[ilist->iatoms[s+2]] = s/stride;
974 at2s[ilist->iatoms[s+3]] = s/stride;
980 void set_constraints(struct gmx_constr *constr,
981 gmx_localtop_t *top, t_inputrec *ir,
982 t_mdatoms *md, t_commrec *cr)
991 if (constr->ncon_tot > 0)
993 /* We are using the local topology,
994 * so there are only F_CONSTR constraints.
996 ncons = idef->il[F_CONSTR].nr/3;
998 /* With DD we might also need to call LINCS with ncons=0 for
999 * communicating coordinates to other nodes that do have constraints.
1001 if (ir->eConstrAlg == econtLINCS)
1003 set_lincs(idef, md, EI_DYNAMICS(ir->eI), cr, constr->lincsd);
1005 if (ir->eConstrAlg == econtSHAKE)
1009 make_shake_sblock_dd(constr, &idef->il[F_CONSTR], &top->cgs, cr->dd);
1013 make_shake_sblock_serial(constr, idef, md);
1015 if (ncons > constr->lagr_nalloc)
1017 constr->lagr_nalloc = over_alloc_dd(ncons);
1018 srenew(constr->lagr, constr->lagr_nalloc);
1023 if (idef->il[F_SETTLE].nr > 0 && constr->settled == NULL)
1025 settle = &idef->il[F_SETTLE];
1026 iO = settle->iatoms[1];
1027 iH = settle->iatoms[2];
1029 settle_init(md->massT[iO], md->massT[iH],
1030 md->invmass[iO], md->invmass[iH],
1031 idef->iparams[settle->iatoms[0]].settle.doh,
1032 idef->iparams[settle->iatoms[0]].settle.dhh);
1035 /* Make a selection of the local atoms for essential dynamics */
1036 if (constr->ed && cr->dd)
1038 dd_make_local_ed_indices(cr->dd, constr->ed);
1042 static void constr_recur(t_blocka *at2con,
1043 t_ilist *ilist, t_iparams *iparams, gmx_bool bTopB,
1044 int at, int depth, int nc, int *path,
1045 real r0, real r1, real *r2max,
1057 ncon1 = ilist[F_CONSTR].nr/3;
1058 ia1 = ilist[F_CONSTR].iatoms;
1059 ia2 = ilist[F_CONSTRNC].iatoms;
1061 /* Loop over all constraints connected to this atom */
1062 for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
1065 /* Do not walk over already used constraints */
1067 for (a1 = 0; a1 < depth; a1++)
1069 if (con == path[a1])
1076 ia = constr_iatomptr(ncon1, ia1, ia2, con);
1077 /* Flexible constraints currently have length 0, which is incorrect */
1080 len = iparams[ia[0]].constr.dA;
1084 len = iparams[ia[0]].constr.dB;
1086 /* In the worst case the bond directions alternate */
1097 /* Assume angles of 120 degrees between all bonds */
1098 if (rn0*rn0 + rn1*rn1 + rn0*rn1 > *r2max)
1100 *r2max = rn0*rn0 + rn1*rn1 + r0*rn1;
1103 fprintf(debug, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
1104 for (a1 = 0; a1 < depth; a1++)
1106 fprintf(debug, " %d %5.3f",
1108 iparams[constr_iatomptr(ncon1, ia1, ia2, con)[0]].constr.dA);
1110 fprintf(debug, " %d %5.3f\n", con, len);
1113 /* Limit the number of recursions to 1000*nc,
1114 * so a call does not take more than a second,
1115 * even for highly connected systems.
1117 if (depth + 1 < nc && *count < 1000*nc)
1129 constr_recur(at2con, ilist, iparams,
1130 bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
1137 static real constr_r_max_moltype(gmx_moltype_t *molt, t_iparams *iparams,
1140 int natoms, nflexcon, *path, at, count;
1143 real r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
1145 if (molt->ilist[F_CONSTR].nr == 0 &&
1146 molt->ilist[F_CONSTRNC].nr == 0)
1151 natoms = molt->atoms.nr;
1153 at2con = make_at2con(0, natoms, molt->ilist, iparams,
1154 EI_DYNAMICS(ir->eI), &nflexcon);
1155 snew(path, 1+ir->nProjOrder);
1156 for (at = 0; at < 1+ir->nProjOrder; at++)
1162 for (at = 0; at < natoms; at++)
1168 constr_recur(&at2con, molt->ilist, iparams,
1169 FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxA, &count);
1171 if (ir->efep == efepNO)
1173 rmax = sqrt(r2maxA);
1178 for (at = 0; at < natoms; at++)
1183 constr_recur(&at2con, molt->ilist, iparams,
1184 TRUE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxB, &count);
1186 lam0 = ir->fepvals->init_lambda;
1187 if (EI_DYNAMICS(ir->eI))
1189 lam0 += ir->init_step*ir->fepvals->delta_lambda;
1191 rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
1192 if (EI_DYNAMICS(ir->eI))
1194 lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
1195 rmax = max(rmax, (1 - lam1)*sqrt(r2maxA) + lam1*sqrt(r2maxB));
1199 done_blocka(&at2con);
1205 real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir)
1211 for (mt = 0; mt < mtop->nmoltype; mt++)
1214 constr_r_max_moltype(&mtop->moltype[mt],
1215 mtop->ffparams.iparams, ir));
1220 fprintf(fplog, "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm\n", 1+ir->nProjOrder, rmax);
1226 gmx_constr_t init_constraints(FILE *fplog,
1227 gmx_mtop_t *mtop, t_inputrec *ir,
1228 gmx_edsam_t ed, t_state *state,
1231 int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
1232 struct gmx_constr *constr;
1235 gmx_mtop_ilistloop_t iloop;
1238 gmx_mtop_ftype_count(mtop, F_CONSTR) +
1239 gmx_mtop_ftype_count(mtop, F_CONSTRNC);
1240 nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
1242 if (ncon+nset == 0 && ir->ePull != epullCONSTRAINT && ed == NULL)
1249 constr->ncon_tot = ncon;
1250 constr->nflexcon = 0;
1253 constr->n_at2con_mt = mtop->nmoltype;
1254 snew(constr->at2con_mt, constr->n_at2con_mt);
1255 for (mt = 0; mt < mtop->nmoltype; mt++)
1257 constr->at2con_mt[mt] = make_at2con(0, mtop->moltype[mt].atoms.nr,
1258 mtop->moltype[mt].ilist,
1259 mtop->ffparams.iparams,
1260 EI_DYNAMICS(ir->eI), &nflexcon);
1261 for (i = 0; i < mtop->nmolblock; i++)
1263 if (mtop->molblock[i].type == mt)
1265 constr->nflexcon += mtop->molblock[i].nmol*nflexcon;
1270 if (constr->nflexcon > 0)
1274 fprintf(fplog, "There are %d flexible constraints\n",
1276 if (ir->fc_stepsize == 0)
1279 "WARNING: step size for flexible constraining = 0\n"
1280 " All flexible constraints will be rigid.\n"
1281 " Will try to keep all flexible constraints at their original length,\n"
1282 " but the lengths may exhibit some drift.\n\n");
1283 constr->nflexcon = 0;
1286 if (constr->nflexcon > 0)
1288 please_cite(fplog, "Hess2002");
1292 if (ir->eConstrAlg == econtLINCS)
1294 constr->lincsd = init_lincs(fplog, mtop,
1295 constr->nflexcon, constr->at2con_mt,
1296 DOMAINDECOMP(cr) && cr->dd->bInterCGcons,
1297 ir->nLincsIter, ir->nProjOrder);
1300 if (ir->eConstrAlg == econtSHAKE)
1302 if (DOMAINDECOMP(cr) && cr->dd->bInterCGcons)
1304 gmx_fatal(FARGS, "SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS");
1306 if (constr->nflexcon)
1308 gmx_fatal(FARGS, "For this system also velocities and/or forces need to be constrained, this can not be done with SHAKE, you should select LINCS");
1310 please_cite(fplog, "Ryckaert77a");
1313 please_cite(fplog, "Barth95a");
1316 constr->shaked = shake_init();
1322 please_cite(fplog, "Miyamoto92a");
1324 constr->bInterCGsettles = inter_charge_group_settles(mtop);
1326 /* Check that we have only one settle type */
1328 iloop = gmx_mtop_ilistloop_init(mtop);
1329 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
1331 for (i = 0; i < ilist[F_SETTLE].nr; i += 4)
1333 if (settle_type == -1)
1335 settle_type = ilist[F_SETTLE].iatoms[i];
1337 else if (ilist[F_SETTLE].iatoms[i] != settle_type)
1340 "The [molecules] section of your topology specifies more than one block of\n"
1341 "a [moleculetype] with a [settles] block. Only one such is allowed. If you\n"
1342 "are trying to partition your solvent into different *groups* (e.g. for\n"
1343 "freezing, T-coupling, etc.) then you are using the wrong approach. Index\n"
1344 "files specify groups. Otherwise, you may wish to change the least-used\n"
1345 "block of molecules with SETTLE constraints into 3 normal constraints.");
1350 constr->n_at2settle_mt = mtop->nmoltype;
1351 snew(constr->at2settle_mt, constr->n_at2settle_mt);
1352 for (mt = 0; mt < mtop->nmoltype; mt++)
1354 constr->at2settle_mt[mt] =
1355 make_at2settle(mtop->moltype[mt].atoms.nr,
1356 &mtop->moltype[mt].ilist[F_SETTLE]);
1360 constr->maxwarn = 999;
1361 env = getenv("GMX_MAXCONSTRWARN");
1364 constr->maxwarn = 0;
1365 sscanf(env, "%d", &constr->maxwarn);
1369 "Setting the maximum number of constraint warnings to %d\n",
1375 "Setting the maximum number of constraint warnings to %d\n",
1379 if (constr->maxwarn < 0 && fplog)
1381 fprintf(fplog, "maxwarn < 0, will not stop on constraint errors\n");
1383 constr->warncount_lincs = 0;
1384 constr->warncount_settle = 0;
1386 /* Initialize the essential dynamics sampling.
1387 * Put the pointer to the ED struct in constr */
1389 if (ed != NULL || state->edsamstate.nED > 0)
1391 init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
1394 constr->warn_mtop = mtop;
1399 const t_blocka *atom2constraints_moltype(gmx_constr_t constr)
1401 return constr->at2con_mt;
1404 const int **atom2settle_moltype(gmx_constr_t constr)
1406 return (const int **)constr->at2settle_mt;
1410 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop)
1412 const gmx_moltype_t *molt;
1416 int nat, *at2cg, cg, a, ftype, i;
1420 for (mb = 0; mb < mtop->nmolblock && !bInterCG; mb++)
1422 molt = &mtop->moltype[mtop->molblock[mb].type];
1424 if (molt->ilist[F_CONSTR].nr > 0 ||
1425 molt->ilist[F_CONSTRNC].nr > 0 ||
1426 molt->ilist[F_SETTLE].nr > 0)
1429 snew(at2cg, molt->atoms.nr);
1430 for (cg = 0; cg < cgs->nr; cg++)
1432 for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
1438 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
1440 il = &molt->ilist[ftype];
1441 for (i = 0; i < il->nr && !bInterCG; i += 1+NRAL(ftype))
1443 if (at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+2]])
1457 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop)
1459 const gmx_moltype_t *molt;
1463 int nat, *at2cg, cg, a, ftype, i;
1467 for (mb = 0; mb < mtop->nmolblock && !bInterCG; mb++)
1469 molt = &mtop->moltype[mtop->molblock[mb].type];
1471 if (molt->ilist[F_SETTLE].nr > 0)
1474 snew(at2cg, molt->atoms.nr);
1475 for (cg = 0; cg < cgs->nr; cg++)
1477 for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
1483 for (ftype = F_SETTLE; ftype <= F_SETTLE; ftype++)
1485 il = &molt->ilist[ftype];
1486 for (i = 0; i < il->nr && !bInterCG; i += 1+NRAL(F_SETTLE))
1488 if (at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+2]] ||
1489 at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+3]])
1503 /* helper functions for andersen temperature control, because the
1504 * gmx_constr construct is only defined in constr.c. Return the list
1505 * of blocks (get_sblock) and the number of blocks (get_nblocks). */
1507 extern int *get_sblock(struct gmx_constr *constr)
1509 return constr->sblock;
1512 extern int get_nblocks(struct gmx_constr *constr)
1514 return constr->nblocks;