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43 #include <sys/types.h>
57 #include "gromacs/fileio/confio.h"
61 #include "grompp-impl.h"
62 #include "gromacs/random/random.h"
63 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
65 #include "gromacs/fileio/futil.h"
66 #include "gromacs/commandline/pargs.h"
68 #include "gromacs/gmxana/sortwater.h"
70 #include "gmx_fatal.h"
73 #include "gromacs/fileio/gmxfio.h"
74 #include "gromacs/fileio/trnio.h"
75 #include "gromacs/fileio/tpxio.h"
76 #include "gromacs/fileio/trxio.h"
77 #include "vsite_parm.h"
81 #include "gromacs/fileio/enxio.h"
83 #include "compute_io.h"
84 #include "gpp_atomtype.h"
85 #include "mtop_util.h"
87 #include "calc_verletbuf.h"
91 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
96 /* For all the molecule types */
97 for (i = 0; i < nrmols; i++)
99 n += mols[i].plist[ifunc].nr;
100 mols[i].plist[ifunc].nr = 0;
105 static int check_atom_names(const char *fn1, const char *fn2,
106 gmx_mtop_t *mtop, t_atoms *at)
108 int mb, m, i, j, nmismatch;
110 #define MAXMISMATCH 20
112 if (mtop->natoms != at->nr)
114 gmx_incons("comparing atom names");
119 for (mb = 0; mb < mtop->nmolblock; mb++)
121 tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
122 for (m = 0; m < mtop->molblock[mb].nmol; m++)
124 for (j = 0; j < tat->nr; j++)
126 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
128 if (nmismatch < MAXMISMATCH)
131 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
132 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
134 else if (nmismatch == MAXMISMATCH)
136 fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
148 static void check_eg_vs_cg(gmx_mtop_t *mtop)
150 int astart, mb, m, cg, j, firstj;
151 unsigned char firsteg, eg;
154 /* Go through all the charge groups and make sure all their
155 * atoms are in the same energy group.
159 for (mb = 0; mb < mtop->nmolblock; mb++)
161 molt = &mtop->moltype[mtop->molblock[mb].type];
162 for (m = 0; m < mtop->molblock[mb].nmol; m++)
164 for (cg = 0; cg < molt->cgs.nr; cg++)
166 /* Get the energy group of the first atom in this charge group */
167 firstj = astart + molt->cgs.index[cg];
168 firsteg = ggrpnr(&mtop->groups, egcENER, firstj);
169 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
171 eg = ggrpnr(&mtop->groups, egcENER, astart+j);
174 gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
175 firstj+1, astart+j+1, cg+1, *molt->name);
179 astart += molt->atoms.nr;
184 static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
187 char warn_buf[STRLEN];
190 for (cg = 0; cg < cgs->nr; cg++)
192 maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
195 if (maxsize > MAX_CHARGEGROUP_SIZE)
197 gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
199 else if (maxsize > 10)
201 set_warning_line(wi, topfn, -1);
203 "The largest charge group contains %d atoms.\n"
204 "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
205 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
206 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
208 warning_note(wi, warn_buf);
212 static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
214 /* This check is not intended to ensure accurate integration,
215 * rather it is to signal mistakes in the mdp settings.
216 * A common mistake is to forget to turn on constraints
217 * for MD after energy minimization with flexible bonds.
218 * This check can also detect too large time steps for flexible water
219 * models, but such errors will often be masked by the constraints
220 * mdp options, which turns flexible water into water with bond constraints,
221 * but without an angle constraint. Unfortunately such incorrect use
222 * of water models can not easily be detected without checking
223 * for specific model names.
225 * The stability limit of leap-frog or velocity verlet is 4.44 steps
226 * per oscillational period.
227 * But accurate bonds distributions are lost far before that limit.
228 * To allow relatively common schemes (although not common with Gromacs)
229 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
230 * we set the note limit to 10.
232 int min_steps_warn = 5;
233 int min_steps_note = 10;
236 gmx_moltype_t *moltype, *w_moltype;
238 t_ilist *ilist, *ilb, *ilc, *ils;
240 int i, a1, a2, w_a1, w_a2, j;
241 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
242 gmx_bool bFound, bWater, bWarn;
243 char warn_buf[STRLEN];
245 ip = mtop->ffparams.iparams;
247 twopi2 = sqr(2*M_PI);
249 limit2 = sqr(min_steps_note*dt);
255 for (molt = 0; molt < mtop->nmoltype; molt++)
257 moltype = &mtop->moltype[molt];
258 atom = moltype->atoms.atom;
259 ilist = moltype->ilist;
260 ilc = &ilist[F_CONSTR];
261 ils = &ilist[F_SETTLE];
262 for (ftype = 0; ftype < F_NRE; ftype++)
264 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
270 for (i = 0; i < ilb->nr; i += 3)
272 fc = ip[ilb->iatoms[i]].harmonic.krA;
273 re = ip[ilb->iatoms[i]].harmonic.rA;
274 if (ftype == F_G96BONDS)
276 /* Convert squared sqaure fc to harmonic fc */
279 a1 = ilb->iatoms[i+1];
280 a2 = ilb->iatoms[i+2];
283 if (fc > 0 && m1 > 0 && m2 > 0)
285 period2 = twopi2*m1*m2/((m1 + m2)*fc);
289 period2 = GMX_FLOAT_MAX;
293 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
294 fc, m1, m2, sqrt(period2));
296 if (period2 < limit2)
299 for (j = 0; j < ilc->nr; j += 3)
301 if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
302 (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
307 for (j = 0; j < ils->nr; j += 4)
309 if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
310 (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
316 (w_moltype == NULL || period2 < w_period2))
328 if (w_moltype != NULL)
330 bWarn = (w_period2 < sqr(min_steps_warn*dt));
331 /* A check that would recognize most water models */
332 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
333 w_moltype->atoms.nr <= 5);
334 sprintf(warn_buf, "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
337 w_a1+1, *w_moltype->atoms.atomname[w_a1],
338 w_a2+1, *w_moltype->atoms.atomname[w_a2],
339 sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
341 "Maybe you asked for fexible water." :
342 "Maybe you forgot to change the constraints mdp option.");
345 warning(wi, warn_buf);
349 warning_note(wi, warn_buf);
354 static void check_vel(gmx_mtop_t *mtop, rvec v[])
356 gmx_mtop_atomloop_all_t aloop;
360 aloop = gmx_mtop_atomloop_all_init(mtop);
361 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
363 if (atom->ptype == eptShell ||
364 atom->ptype == eptBond ||
365 atom->ptype == eptVSite)
372 static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
377 for (mb = 0; mb < mtop->nmolblock; mb++)
379 nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
385 /* This routine reorders the molecule type array
386 * in the order of use in the molblocks,
387 * unused molecule types are deleted.
389 static void renumber_moltypes(gmx_mtop_t *sys,
390 int *nmolinfo, t_molinfo **molinfo)
392 int *order, norder, i;
396 snew(order, *nmolinfo);
398 for (mb = 0; mb < sys->nmolblock; mb++)
400 for (i = 0; i < norder; i++)
402 if (order[i] == sys->molblock[mb].type)
409 /* This type did not occur yet, add it */
410 order[norder] = sys->molblock[mb].type;
411 /* Renumber the moltype in the topology */
414 sys->molblock[mb].type = i;
417 /* We still need to reorder the molinfo structs */
419 for (mi = 0; mi < *nmolinfo; mi++)
421 for (i = 0; i < norder; i++)
430 done_mi(&(*molinfo)[mi]);
434 minew[i] = (*molinfo)[mi];
443 static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
448 mtop->nmoltype = nmi;
449 snew(mtop->moltype, nmi);
450 for (m = 0; m < nmi; m++)
452 molt = &mtop->moltype[m];
453 molt->name = mi[m].name;
454 molt->atoms = mi[m].atoms;
455 /* ilists are copied later */
456 molt->cgs = mi[m].cgs;
457 molt->excls = mi[m].excls;
462 new_status(const char *topfile, const char *topppfile, const char *confin,
463 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
464 gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
465 gpp_atomtype_t atype, gmx_mtop_t *sys,
466 int *nmi, t_molinfo **mi, t_params plist[],
467 int *comb, double *reppow, real *fudgeQQ,
471 t_molinfo *molinfo = NULL;
473 gmx_molblock_t *molblock, *molbs;
475 int mb, i, nrmols, nmismatch;
477 gmx_bool bGB = FALSE;
478 char warn_buf[STRLEN];
482 /* Set gmx_boolean for GB */
483 if (ir->implicit_solvent)
488 /* TOPOLOGY processing */
489 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
490 plist, comb, reppow, fudgeQQ,
491 atype, &nrmols, &molinfo, ir,
492 &nmolblock, &molblock, bGB,
496 snew(sys->molblock, nmolblock);
499 for (mb = 0; mb < nmolblock; mb++)
501 if (sys->nmolblock > 0 &&
502 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
504 /* Merge consecutive blocks with the same molecule type */
505 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
506 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
508 else if (molblock[mb].nmol > 0)
510 /* Add a new molblock to the topology */
511 molbs = &sys->molblock[sys->nmolblock];
512 *molbs = molblock[mb];
513 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
514 molbs->nposres_xA = 0;
515 molbs->nposres_xB = 0;
516 sys->natoms += molbs->nmol*molbs->natoms_mol;
520 if (sys->nmolblock == 0)
522 gmx_fatal(FARGS, "No molecules were defined in the system");
525 renumber_moltypes(sys, &nrmols, &molinfo);
529 convert_harmonics(nrmols, molinfo, atype);
532 if (ir->eDisre == edrNone)
534 i = rm_interactions(F_DISRES, nrmols, molinfo);
537 set_warning_line(wi, "unknown", -1);
538 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
539 warning_note(wi, warn_buf);
542 if (opts->bOrire == FALSE)
544 i = rm_interactions(F_ORIRES, nrmols, molinfo);
547 set_warning_line(wi, "unknown", -1);
548 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
549 warning_note(wi, warn_buf);
553 /* Copy structures from msys to sys */
554 molinfo2mtop(nrmols, molinfo, sys);
556 gmx_mtop_finalize(sys);
558 /* COORDINATE file processing */
561 fprintf(stderr, "processing coordinates...\n");
564 get_stx_coordnum(confin, &state->natoms);
565 if (state->natoms != sys->natoms)
567 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
568 " does not match topology (%s, %d)",
569 confin, state->natoms, topfile, sys->natoms);
573 /* make space for coordinates and velocities */
576 init_t_atoms(confat, state->natoms, FALSE);
577 init_state(state, state->natoms, 0, 0, 0, 0);
578 read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
579 /* This call fixes the box shape for runs with pressure scaling */
580 set_box_rel(ir, state);
582 nmismatch = check_atom_names(topfile, confin, sys, confat);
583 free_t_atoms(confat, TRUE);
588 sprintf(buf, "%d non-matching atom name%s\n"
589 "atom names from %s will be used\n"
590 "atom names from %s will be ignored\n",
591 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
596 fprintf(stderr, "double-checking input for internal consistency...\n");
598 double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
604 gmx_mtop_atomloop_all_t aloop;
608 snew(mass, state->natoms);
609 aloop = gmx_mtop_atomloop_all_init(sys);
610 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
616 if (opts->seed == -1)
618 useed = (int)gmx_rng_make_seed();
619 fprintf(stderr, "Setting gen_seed to %u\n", useed);
621 maxwell_speed(opts->tempi, useed, sys, state->v);
623 stop_cm(stdout, state->natoms, mass, state->x, state->v);
631 static void copy_state(const char *slog, t_trxframe *fr,
632 gmx_bool bReadVel, t_state *state,
637 if (fr->not_ok & FRAME_NOT_OK)
639 gmx_fatal(FARGS, "Can not start from an incomplete frame");
643 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
647 for (i = 0; i < state->natoms; i++)
649 copy_rvec(fr->x[i], state->x[i]);
655 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
657 for (i = 0; i < state->natoms; i++)
659 copy_rvec(fr->v[i], state->v[i]);
664 copy_mat(fr->box, state->box);
667 *use_time = fr->time;
670 static void cont_status(const char *slog, const char *ener,
671 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
672 t_inputrec *ir, t_state *state,
674 const output_env_t oenv)
675 /* If fr_time == -1 read the last frame available which is complete */
683 bReadVel = (bNeedVel && !bGenVel);
686 "Reading Coordinates%s and Box size from old trajectory\n",
687 bReadVel ? ", Velocities" : "");
690 fprintf(stderr, "Will read whole trajectory\n");
694 fprintf(stderr, "Will read till time %g\n", fr_time);
700 fprintf(stderr, "Velocities generated: "
701 "ignoring velocities in input trajectory\n");
703 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
707 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
713 "WARNING: Did not find a frame with velocities in file %s,\n"
714 " all velocities will be set to zero!\n\n", slog);
715 for (i = 0; i < sys->natoms; i++)
717 clear_rvec(state->v[i]);
720 /* Search for a frame without velocities */
722 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
726 state->natoms = fr.natoms;
728 if (sys->natoms != state->natoms)
730 gmx_fatal(FARGS, "Number of atoms in Topology "
731 "is not the same as in Trajectory");
733 copy_state(slog, &fr, bReadVel, state, &use_time);
735 /* Find the appropriate frame */
736 while ((fr_time == -1 || fr.time < fr_time) &&
737 read_next_frame(oenv, fp, &fr))
739 copy_state(slog, &fr, bReadVel, state, &use_time);
744 /* Set the relative box lengths for preserving the box shape.
745 * Note that this call can lead to differences in the last bit
746 * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
748 set_box_rel(ir, state);
750 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
751 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
753 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
755 get_enx_state(ener, use_time, &sys->groups, ir, state);
756 preserve_box_shape(ir, state->box_rel, state->boxv);
760 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
762 int rc_scaling, int ePBC,
766 gmx_bool bFirst = TRUE, *hadAtom;
772 int natoms, npbcdim = 0;
773 char warn_buf[STRLEN], title[STRLEN];
774 int a, i, ai, j, k, mb, nat_molb;
775 gmx_molblock_t *molb;
779 get_stx_coordnum(fn, &natoms);
780 if (natoms != mtop->natoms)
782 sprintf(warn_buf, "The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.", fn, natoms, mtop->natoms, min(mtop->natoms, natoms), fn);
783 warning(wi, warn_buf);
787 init_t_atoms(&dumat, natoms, FALSE);
788 read_stx_conf(fn, title, &dumat, x, v, NULL, box);
790 npbcdim = ePBC2npbcdim(ePBC);
792 if (rc_scaling != erscNO)
794 copy_mat(box, invbox);
795 for (j = npbcdim; j < DIM; j++)
797 clear_rvec(invbox[j]);
800 m_inv_ur0(invbox, invbox);
803 /* Copy the reference coordinates to mtop */
807 snew(hadAtom, natoms);
808 for (mb = 0; mb < mtop->nmolblock; mb++)
810 molb = &mtop->molblock[mb];
811 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
812 pr = &(molinfo[molb->type].plist[F_POSRES]);
813 prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
814 if (pr->nr > 0 || prfb->nr > 0)
816 atom = mtop->moltype[molb->type].atoms.atom;
817 for (i = 0; (i < pr->nr); i++)
819 ai = pr->param[i].AI;
822 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
823 ai+1, *molinfo[molb->type].name, fn, natoms);
826 if (rc_scaling == erscCOM)
828 /* Determine the center of mass of the posres reference coordinates */
829 for (j = 0; j < npbcdim; j++)
831 sum[j] += atom[ai].m*x[a+ai][j];
833 totmass += atom[ai].m;
836 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
837 for (i = 0; (i < prfb->nr); i++)
839 ai = prfb->param[i].AI;
842 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
843 ai+1, *molinfo[molb->type].name, fn, natoms);
845 if (rc_scaling == erscCOM && hadAtom[ai] == FALSE)
847 /* Determine the center of mass of the posres reference coordinates */
848 for (j = 0; j < npbcdim; j++)
850 sum[j] += atom[ai].m*x[a+ai][j];
852 totmass += atom[ai].m;
857 molb->nposres_xA = nat_molb;
858 snew(molb->posres_xA, molb->nposres_xA);
859 for (i = 0; i < nat_molb; i++)
861 copy_rvec(x[a+i], molb->posres_xA[i]);
866 molb->nposres_xB = nat_molb;
867 snew(molb->posres_xB, molb->nposres_xB);
868 for (i = 0; i < nat_molb; i++)
870 copy_rvec(x[a+i], molb->posres_xB[i]);
876 if (rc_scaling == erscCOM)
880 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
882 for (j = 0; j < npbcdim; j++)
884 com[j] = sum[j]/totmass;
886 fprintf(stderr, "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n", com[XX], com[YY], com[ZZ]);
889 if (rc_scaling != erscNO)
891 assert(npbcdim <= DIM);
893 for (mb = 0; mb < mtop->nmolblock; mb++)
895 molb = &mtop->molblock[mb];
896 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
897 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
899 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
900 for (i = 0; i < nat_molb; i++)
902 for (j = 0; j < npbcdim; j++)
904 if (rc_scaling == erscALL)
906 /* Convert from Cartesian to crystal coordinates */
907 xp[i][j] *= invbox[j][j];
908 for (k = j+1; k < npbcdim; k++)
910 xp[i][j] += invbox[k][j]*xp[i][k];
913 else if (rc_scaling == erscCOM)
915 /* Subtract the center of mass */
923 if (rc_scaling == erscCOM)
925 /* Convert the COM from Cartesian to crystal coordinates */
926 for (j = 0; j < npbcdim; j++)
928 com[j] *= invbox[j][j];
929 for (k = j+1; k < npbcdim; k++)
931 com[j] += invbox[k][j]*com[k];
937 free_t_atoms(&dumat, TRUE);
943 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
944 char *fnA, char *fnB,
945 int rc_scaling, int ePBC,
951 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
952 if (strcmp(fnA, fnB) != 0)
954 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
958 static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
959 t_inputrec *ir, warninp_t wi)
962 char warn_buf[STRLEN];
966 fprintf(stderr, "Searching the wall atom type(s)\n");
968 for (i = 0; i < ir->nwall; i++)
970 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
971 if (ir->wall_atomtype[i] == NOTSET)
973 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
974 warning_error(wi, warn_buf);
979 static int nrdf_internal(t_atoms *atoms)
984 for (i = 0; i < atoms->nr; i++)
986 /* Vsite ptype might not be set here yet, so also check the mass */
987 if ((atoms->atom[i].ptype == eptAtom ||
988 atoms->atom[i].ptype == eptNucleus)
989 && atoms->atom[i].m > 0)
996 case 0: nrdf = 0; break;
997 case 1: nrdf = 0; break;
998 case 2: nrdf = 1; break;
999 default: nrdf = nmass*3 - 6; break;
1006 spline1d( double dx,
1018 for (i = 1; i < n-1; i++)
1020 p = 0.5*y2[i-1]+2.0;
1022 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1023 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1028 for (i = n-2; i >= 0; i--)
1030 y2[i] = y2[i]*y2[i+1]+u[i];
1036 interpolate1d( double xmin,
1049 a = (xmin+(ix+1)*dx-x)/dx;
1050 b = (x-xmin-ix*dx)/dx;
1052 *y = a*ya[ix]+b*ya[ix+1]+((a*a*a-a)*y2a[ix]+(b*b*b-b)*y2a[ix+1])*(dx*dx)/6.0;
1053 *y1 = (ya[ix+1]-ya[ix])/dx-(3.0*a*a-1.0)/6.0*dx*y2a[ix]+(3.0*b*b-1.0)/6.0*dx*y2a[ix+1];
1058 setup_cmap (int grid_spacing,
1061 gmx_cmap_t * cmap_grid)
1063 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1065 int i, j, k, ii, jj, kk, idx;
1067 double dx, xmin, v, v1, v2, v12;
1070 snew(tmp_u, 2*grid_spacing);
1071 snew(tmp_u2, 2*grid_spacing);
1072 snew(tmp_yy, 2*grid_spacing);
1073 snew(tmp_y1, 2*grid_spacing);
1074 snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
1075 snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
1077 dx = 360.0/grid_spacing;
1078 xmin = -180.0-dx*grid_spacing/2;
1080 for (kk = 0; kk < nc; kk++)
1082 /* Compute an offset depending on which cmap we are using
1083 * Offset will be the map number multiplied with the
1084 * grid_spacing * grid_spacing * 2
1086 offset = kk * grid_spacing * grid_spacing * 2;
1088 for (i = 0; i < 2*grid_spacing; i++)
1090 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1092 for (j = 0; j < 2*grid_spacing; j++)
1094 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1095 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1099 for (i = 0; i < 2*grid_spacing; i++)
1101 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1104 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1106 ii = i-grid_spacing/2;
1109 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1111 jj = j-grid_spacing/2;
1114 for (k = 0; k < 2*grid_spacing; k++)
1116 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1117 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1120 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1121 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1122 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1123 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1125 idx = ii*grid_spacing+jj;
1126 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1127 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1128 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1129 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1135 void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1139 cmap_grid->ngrid = ngrid;
1140 cmap_grid->grid_spacing = grid_spacing;
1141 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1143 snew(cmap_grid->cmapdata, ngrid);
1145 for (i = 0; i < cmap_grid->ngrid; i++)
1147 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
1152 static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1154 int count, count_mol, i, mb;
1155 gmx_molblock_t *molb;
1160 for (mb = 0; mb < mtop->nmolblock; mb++)
1163 molb = &mtop->molblock[mb];
1164 plist = mi[molb->type].plist;
1166 for (i = 0; i < F_NRE; i++)
1170 count_mol += 3*plist[i].nr;
1172 else if (interaction_function[i].flags & IF_CONSTRAINT)
1174 count_mol += plist[i].nr;
1178 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1181 "Molecule type '%s' has %d constraints.\n"
1182 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1183 *mi[molb->type].name, count_mol,
1184 nrdf_internal(&mi[molb->type].atoms));
1187 count += molb->nmol*count_mol;
1193 static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1195 int i, nmiss, natoms, mt;
1197 const t_atoms *atoms;
1200 for (mt = 0; mt < sys->nmoltype; mt++)
1202 atoms = &sys->moltype[mt].atoms;
1205 for (i = 0; i < natoms; i++)
1207 q = atoms->atom[i].q;
1208 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1209 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1210 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1211 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1212 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1215 fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1216 get_atomtype_name(atoms->atom[i].type, atype), q);
1224 gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.", nmiss);
1229 static void check_gbsa_params(gpp_atomtype_t atype)
1233 /* If we are doing GBSA, check that we got the parameters we need
1234 * This checking is to see if there are GBSA paratmeters for all
1235 * atoms in the force field. To go around this for testing purposes
1236 * comment out the nerror++ counter temporarily
1239 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1241 if (get_atomtype_radius(i, atype) < 0 ||
1242 get_atomtype_vol(i, atype) < 0 ||
1243 get_atomtype_surftens(i, atype) < 0 ||
1244 get_atomtype_gb_radius(i, atype) < 0 ||
1245 get_atomtype_S_hct(i, atype) < 0)
1247 fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1248 get_atomtype_name(i, atype));
1255 gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.", nmiss);
1260 static real calc_temp(const gmx_mtop_t *mtop,
1261 const t_inputrec *ir,
1265 gmx_mtop_atomloop_all_t aloop;
1272 aloop = gmx_mtop_atomloop_all_init(mtop);
1273 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
1275 sum_mv2 += atom->m*norm2(v[a]);
1279 for (g = 0; g < ir->opts.ngtc; g++)
1281 nrdf += ir->opts.nrdf[g];
1284 return sum_mv2/(nrdf*BOLTZ);
1287 static real get_max_reference_temp(const t_inputrec *ir,
1296 for (i = 0; i < ir->opts.ngtc; i++)
1298 if (ir->opts.tau_t[i] < 0)
1304 ref_t = max(ref_t, ir->opts.ref_t[i]);
1312 sprintf(buf, "Some temperature coupling groups do not use temperature coupling. We will assume their temperature is not more than %.3f K. If their temperature is higher, the energy error and the Verlet buffer might be underestimated.",
1320 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1327 verletbuf_list_setup_t ls;
1330 char warn_buf[STRLEN];
1332 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1334 /* Calculate the buffer size for simple atom vs atoms list */
1335 ls.cluster_size_i = 1;
1336 ls.cluster_size_j = 1;
1337 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1338 &ls, &n_nonlin_vsite, &rlist_1x1);
1340 /* Set the pair-list buffer size in ir */
1341 verletbuf_get_list_setup(FALSE, &ls);
1342 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1343 &ls, &n_nonlin_vsite, &ir->rlist);
1345 if (n_nonlin_vsite > 0)
1347 sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly.", n_nonlin_vsite);
1348 warning_note(wi, warn_buf);
1351 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1352 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
1354 ir->rlistlong = ir->rlist;
1355 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1356 ls.cluster_size_i, ls.cluster_size_j,
1357 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
1359 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1361 gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
1365 int gmx_grompp(int argc, char *argv[])
1367 static const char *desc[] = {
1368 "[THISMODULE] (the gromacs preprocessor)",
1369 "reads a molecular topology file, checks the validity of the",
1370 "file, expands the topology from a molecular description to an atomic",
1371 "description. The topology file contains information about",
1372 "molecule types and the number of molecules, the preprocessor",
1373 "copies each molecule as needed. ",
1374 "There is no limitation on the number of molecule types. ",
1375 "Bonds and bond-angles can be converted into constraints, separately",
1376 "for hydrogens and heavy atoms.",
1377 "Then a coordinate file is read and velocities can be generated",
1378 "from a Maxwellian distribution if requested.",
1379 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1380 "(eg. number of MD steps, time step, cut-off), and others such as",
1381 "NEMD parameters, which are corrected so that the net acceleration",
1383 "Eventually a binary file is produced that can serve as the sole input",
1384 "file for the MD program.[PAR]",
1386 "[THISMODULE] uses the atom names from the topology file. The atom names",
1387 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1388 "warnings when they do not match the atom names in the topology.",
1389 "Note that the atom names are irrelevant for the simulation as",
1390 "only the atom types are used for generating interaction parameters.[PAR]",
1392 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1393 "etc. The preprocessor supports the following keywords:[PAR]",
1394 "#ifdef VARIABLE[BR]",
1395 "#ifndef VARIABLE[BR]",
1398 "#define VARIABLE[BR]",
1399 "#undef VARIABLE[BR]"
1400 "#include \"filename\"[BR]",
1401 "#include <filename>[PAR]",
1402 "The functioning of these statements in your topology may be modulated by",
1403 "using the following two flags in your [TT].mdp[tt] file:[PAR]",
1404 "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
1405 "include = -I/home/john/doe[tt][BR]",
1406 "For further information a C-programming textbook may help you out.",
1407 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1408 "topology file written out so that you can verify its contents.[PAR]",
1410 /* cpp has been unnecessary for some time, hasn't it?
1411 "If your system does not have a C-preprocessor, you can still",
1412 "use [TT]grompp[tt], but you do not have access to the features ",
1413 "from the cpp. Command line options to the C-preprocessor can be given",
1414 "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
1417 "When using position restraints a file with restraint coordinates",
1418 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1419 "with respect to the conformation from the [TT]-c[tt] option.",
1420 "For free energy calculation the the coordinates for the B topology",
1421 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1422 "those of the A topology.[PAR]",
1424 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1425 "The last frame with coordinates and velocities will be read,",
1426 "unless the [TT]-time[tt] option is used. Only if this information",
1427 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1428 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1429 "in your [TT].mdp[tt] file. An energy file can be supplied with",
1430 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1433 "[THISMODULE] can be used to restart simulations (preserving",
1434 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1435 "However, for simply changing the number of run steps to extend",
1436 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1437 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1438 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1439 "like output frequency, then supplying the checkpoint file to",
1440 "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
1441 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1443 "By default, all bonded interactions which have constant energy due to",
1444 "virtual site constructions will be removed. If this constant energy is",
1445 "not zero, this will result in a shift in the total energy. All bonded",
1446 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1447 "all constraints for distances which will be constant anyway because",
1448 "of virtual site constructions will be removed. If any constraints remain",
1449 "which involve virtual sites, a fatal error will result.[PAR]"
1451 "To verify your run input file, please take note of all warnings",
1452 "on the screen, and correct where necessary. Do also look at the contents",
1453 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1454 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1455 "with the [TT]-debug[tt] option which will give you more information",
1456 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1457 "can see the contents of the run input file with the [gmx-dump]",
1458 "program. [gmx-check] can be used to compare the contents of two",
1459 "run input files.[PAR]"
1461 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1462 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1463 "harmless, but usually they are not. The user is advised to carefully",
1464 "interpret the output messages before attempting to bypass them with",
1471 gpp_atomtype_t atype;
1473 int natoms, nvsite, comb, mt;
1477 real max_spacing, fudgeQQ;
1479 char fn[STRLEN], fnB[STRLEN];
1480 const char *mdparin;
1482 gmx_bool bNeedVel, bGenVel;
1483 gmx_bool have_atomnumber;
1485 t_params *gb_plist = NULL;
1486 gmx_genborn_t *born = NULL;
1488 gmx_bool bVerbose = FALSE;
1490 char warn_buf[STRLEN];
1494 { efMDP, NULL, NULL, ffREAD },
1495 { efMDP, "-po", "mdout", ffWRITE },
1496 { efSTX, "-c", NULL, ffREAD },
1497 { efSTX, "-r", NULL, ffOPTRD },
1498 { efSTX, "-rb", NULL, ffOPTRD },
1499 { efNDX, NULL, NULL, ffOPTRD },
1500 { efTOP, NULL, NULL, ffREAD },
1501 { efTOP, "-pp", "processed", ffOPTWR },
1502 { efTPX, "-o", NULL, ffWRITE },
1503 { efTRN, "-t", NULL, ffOPTRD },
1504 { efEDR, "-e", NULL, ffOPTRD },
1505 { efTRN, "-ref", "rotref", ffOPTRW }
1507 #define NFILE asize(fnm)
1509 /* Command line options */
1510 static gmx_bool bRenum = TRUE;
1511 static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1512 static int i, maxwarn = 0;
1513 static real fr_time = -1;
1515 { "-v", FALSE, etBOOL, {&bVerbose},
1516 "Be loud and noisy" },
1517 { "-time", FALSE, etREAL, {&fr_time},
1518 "Take frame at or first after this time." },
1519 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1520 "Remove constant bonded interactions with virtual sites" },
1521 { "-maxwarn", FALSE, etINT, {&maxwarn},
1522 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1523 { "-zero", FALSE, etBOOL, {&bZero},
1524 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1525 { "-renum", FALSE, etBOOL, {&bRenum},
1526 "Renumber atomtypes and minimize number of atomtypes" }
1529 /* Initiate some variables */
1534 /* Parse the command line */
1535 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1536 asize(desc), desc, 0, NULL, &oenv))
1541 wi = init_warning(TRUE, maxwarn);
1543 /* PARAMETER file processing */
1544 mdparin = opt2fn("-f", NFILE, fnm);
1545 set_warning_line(wi, mdparin, -1);
1546 get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
1550 fprintf(stderr, "checking input for internal consistency...\n");
1552 check_ir(mdparin, ir, opts, wi);
1554 if (ir->ld_seed == -1)
1556 ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
1557 fprintf(stderr, "Setting the LD random seed to %"GMX_PRId64 "\n", ir->ld_seed);
1560 if (ir->expandedvals->lmc_seed == -1)
1562 ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
1563 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1566 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1567 bGenVel = (bNeedVel && opts->bGenVel);
1568 if (bGenVel && ir->bContinuation)
1571 "Generating velocities is inconsistent with attempting "
1572 "to continue a previous run. Choose only one of "
1573 "gen-vel = yes and continuation = yes.");
1574 warning_error(wi, warn_buf);
1580 atype = init_atomtype();
1583 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1586 strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
1587 if (!gmx_fexist(fn))
1589 gmx_fatal(FARGS, "%s does not exist", fn);
1591 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1592 opts, ir, bZero, bGenVel, bVerbose, &state,
1593 atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
1599 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1603 /* set parameters for virtual site construction (not for vsiten) */
1604 for (mt = 0; mt < sys->nmoltype; mt++)
1607 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1609 /* now throw away all obsolete bonds, angles and dihedrals: */
1610 /* note: constraints are ALWAYS removed */
1613 for (mt = 0; mt < sys->nmoltype; mt++)
1615 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1619 if (ir->cutoff_scheme == ecutsVERLET)
1621 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1622 ecutscheme_names[ir->cutoff_scheme]);
1624 /* Remove all charge groups */
1625 gmx_mtop_remove_chargegroups(sys);
1628 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1630 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1632 sprintf(warn_buf, "Can not do %s with %s, use %s",
1633 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1634 warning_error(wi, warn_buf);
1636 if (ir->bPeriodicMols)
1638 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1639 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1640 warning_error(wi, warn_buf);
1644 if (EI_SD (ir->eI) && ir->etc != etcNO)
1646 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1649 /* If we are doing QM/MM, check that we got the atom numbers */
1650 have_atomnumber = TRUE;
1651 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1653 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1655 if (!have_atomnumber && ir->bQMMM)
1659 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1660 "field you are using does not contain atom numbers fields. This is an\n"
1661 "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
1662 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1663 "an integer just before the mass column in ffXXXnb.itp.\n"
1664 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1669 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1671 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1673 /** \TODO check size of ex+hy width against box size */
1676 /* Check for errors in the input now, since they might cause problems
1677 * during processing further down.
1679 check_warning_error(wi, FARGS);
1681 if (opt2bSet("-r", NFILE, fnm))
1683 sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
1687 sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
1689 if (opt2bSet("-rb", NFILE, fnm))
1691 sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
1698 if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
1702 fprintf(stderr, "Reading position restraint coords from %s", fn);
1703 if (strcmp(fn, fnB) == 0)
1705 fprintf(stderr, "\n");
1709 fprintf(stderr, " and %s\n", fnB);
1712 gen_posres(sys, mi, fn, fnB,
1713 ir->refcoord_scaling, ir->ePBC,
1714 ir->posres_com, ir->posres_comB,
1718 /* If we are using CMAP, setup the pre-interpolation grid */
1719 if (plist->ncmap > 0)
1721 init_cmap_grid(&sys->ffparams.cmap_grid, plist->nc, plist->grid_spacing);
1722 setup_cmap(plist->grid_spacing, plist->nc, plist->cmap, &sys->ffparams.cmap_grid);
1725 set_wall_atomtype(atype, opts, ir, wi);
1728 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1729 ntype = get_atomtype_ntypes(atype);
1732 if (ir->implicit_solvent != eisNO)
1734 /* Now we have renumbered the atom types, we can check the GBSA params */
1735 check_gbsa_params(atype);
1737 /* Check that all atoms that have charge and/or LJ-parameters also have
1738 * sensible GB-parameters
1740 check_gbsa_params_charged(sys, atype);
1743 /* PELA: Copy the atomtype data to the topology atomtype list */
1744 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1748 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1753 fprintf(stderr, "converting bonded parameters...\n");
1756 ntype = get_atomtype_ntypes(atype);
1757 convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
1761 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1764 /* set ptype to VSite for virtual sites */
1765 for (mt = 0; mt < sys->nmoltype; mt++)
1767 set_vsites_ptype(FALSE, &sys->moltype[mt]);
1771 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1773 /* Check velocity for virtual sites and shells */
1776 check_vel(sys, state.v);
1782 for (i = 0; i < sys->nmoltype; i++)
1784 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
1787 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
1789 check_bonds_timestep(sys, ir->delta_t, wi);
1792 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
1794 warning_note(wi, "Zero-step energy minimization will alter the coordinates before calculating the energy. If you just want the energy of a single point, try zero-step MD (with unconstrained_start = yes). To do multiple single-point energy evaluations of different configurations of the same topology, use mdrun -rerun.");
1797 check_warning_error(wi, FARGS);
1801 fprintf(stderr, "initialising group options...\n");
1803 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
1805 bGenVel ? state.v : NULL,
1808 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
1811 if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
1815 if (EI_MD(ir->eI) && ir->etc == etcNO)
1819 buffer_temp = opts->tempi;
1823 buffer_temp = calc_temp(sys, ir, state.v);
1825 if (buffer_temp > 0)
1827 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
1828 warning_note(wi, warn_buf);
1832 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1833 (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
1834 warning_note(wi, warn_buf);
1839 buffer_temp = get_max_reference_temp(ir, wi);
1842 if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
1844 /* NVE with initial T=0: we add a fixed ratio to rlist.
1845 * Since we don't actually use verletbuf_tol, we set it to -1
1846 * so it can't be misused later.
1848 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
1849 ir->verletbuf_tol = -1;
1853 /* We warn for NVE simulations with >1(.1)% drift tolerance */
1854 const real drift_tol = 0.01;
1857 /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
1858 * the safe side with constraints (without constraints: 3 DOF).
1860 ener_runtime = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
1862 if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
1864 ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
1866 sprintf(warn_buf, "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an NVE simulation of length %g ps, which can give a final drift of %d%%. For conserving energy to %d%%, you might need to set verlet-buffer-tolerance to %.1e.",
1867 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
1868 (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
1869 (int)(100*drift_tol + 0.5),
1870 drift_tol*ener_runtime);
1871 warning_note(wi, warn_buf);
1874 set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
1879 /* Init the temperature coupling state */
1880 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1884 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
1886 check_eg_vs_cg(sys);
1890 pr_symtab(debug, 0, "After index", &sys->symtab);
1893 triple_check(mdparin, ir, sys, wi);
1894 close_symtab(&sys->symtab);
1897 pr_symtab(debug, 0, "After close", &sys->symtab);
1900 /* make exclusions between QM atoms */
1903 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1905 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1909 generate_qmexcl(sys, ir, wi);
1913 if (ftp2bSet(efTRN, NFILE, fnm))
1917 fprintf(stderr, "getting data from old trajectory ...\n");
1919 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
1920 bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
1923 if (ir->ePBC == epbcXY && ir->nwall != 2)
1925 clear_rvec(state.box[ZZ]);
1928 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1930 set_warning_line(wi, mdparin, -1);
1931 check_chargegroup_radii(sys, ir, state.x, wi);
1934 if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1936 /* Calculate the optimal grid dimensions */
1937 copy_mat(state.box, box);
1938 if (ir->ePBC == epbcXY && ir->nwall == 2)
1940 svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
1942 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
1944 /* Mark fourier_spacing as not used */
1945 ir->fourier_spacing = 0;
1947 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
1949 set_warning_line(wi, mdparin, -1);
1950 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
1952 max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
1953 &(ir->nkx), &(ir->nky), &(ir->nkz));
1956 /* MRS: eventually figure out better logic for initializing the fep
1957 values that makes declaring the lambda and declaring the state not
1958 potentially conflict if not handled correctly. */
1959 if (ir->efep != efepNO)
1961 if (EVDW_PME(ir->vdwtype))
1963 gmx_fatal(FARGS, "LJ-PME not implemented together with free energy calculations!");
1966 state.fep_state = ir->fepvals->init_fep_state;
1967 for (i = 0; i < efptNR; i++)
1969 /* init_lambda trumps state definitions*/
1970 if (ir->fepvals->init_lambda >= 0)
1972 state.lambda[i] = ir->fepvals->init_lambda;
1976 if (ir->fepvals->all_lambda[i] == NULL)
1978 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
1982 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
1988 if (ir->ePull != epullNO)
1990 set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
1995 set_reference_positions(ir->rot, state.x, state.box,
1996 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
2000 /* reset_multinr(sys); */
2002 if (EEL_PME(ir->coulombtype))
2004 float ratio = pme_load_estimate(sys, ir, state.box);
2005 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2006 /* With free energy we might need to do PME both for the A and B state
2007 * charges. This will double the cost, but the optimal performance will
2008 * then probably be at a slightly larger cut-off and grid spacing.
2010 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2011 (ir->efep != efepNO && ratio > 2.0/3.0))
2014 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2015 "and for highly parallel simulations between 0.25 and 0.33,\n"
2016 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2017 if (ir->efep != efepNO)
2020 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2026 char warn_buf[STRLEN];
2027 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
2028 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2031 set_warning_line(wi, mdparin, -1);
2032 warning_note(wi, warn_buf);
2036 printf("%s\n", warn_buf);
2042 fprintf(stderr, "writing run input file...\n");
2045 done_warning(wi, FARGS);
2046 write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
2048 done_atomtype(atype);
2049 done_mtop(sys, TRUE);
2050 done_inputrec_strings();