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43 #include <sys/types.h>
50 #include "gromacs/legacyheaders/macros.h"
54 #include "gromacs/fileio/confio.h"
56 #include "gromacs/legacyheaders/names.h"
57 #include "grompp-impl.h"
58 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/legacyheaders/splitter.h"
62 #include "gromacs/gmxpreprocess/sortwater.h"
64 #include "gromacs/legacyheaders/warninp.h"
65 #include "gromacs/fileio/gmxfio.h"
66 #include "gromacs/fileio/trnio.h"
67 #include "gromacs/fileio/tpxio.h"
68 #include "gromacs/fileio/trxio.h"
69 #include "vsite_parm.h"
70 #include "gromacs/legacyheaders/txtdump.h"
71 #include "gromacs/legacyheaders/calcgrid.h"
73 #include "gromacs/fileio/enxio.h"
74 #include "gromacs/legacyheaders/perf_est.h"
75 #include "compute_io.h"
76 #include "gpp_atomtype.h"
77 #include "gromacs/topology/mtop_util.h"
78 #include "gromacs/legacyheaders/genborn.h"
79 #include "calc_verletbuf.h"
81 #include "gromacs/imd/imd.h"
82 #include "gromacs/utility/cstringutil.h"
84 #include "gromacs/commandline/pargs.h"
85 #include "gromacs/pbcutil/pbc.h"
86 #include "gromacs/random/random.h"
87 #include "gromacs/topology/symtab.h"
88 #include "gromacs/topology/topology.h"
89 #include "gromacs/utility/fatalerror.h"
90 #include "gromacs/utility/smalloc.h"
92 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
97 /* For all the molecule types */
98 for (i = 0; i < nrmols; i++)
100 n += mols[i].plist[ifunc].nr;
101 mols[i].plist[ifunc].nr = 0;
106 static int check_atom_names(const char *fn1, const char *fn2,
107 gmx_mtop_t *mtop, t_atoms *at)
109 int mb, m, i, j, nmismatch;
111 #define MAXMISMATCH 20
113 if (mtop->natoms != at->nr)
115 gmx_incons("comparing atom names");
120 for (mb = 0; mb < mtop->nmolblock; mb++)
122 tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
123 for (m = 0; m < mtop->molblock[mb].nmol; m++)
125 for (j = 0; j < tat->nr; j++)
127 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
129 if (nmismatch < MAXMISMATCH)
132 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
133 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
135 else if (nmismatch == MAXMISMATCH)
137 fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
149 static void check_eg_vs_cg(gmx_mtop_t *mtop)
151 int astart, mb, m, cg, j, firstj;
152 unsigned char firsteg, eg;
155 /* Go through all the charge groups and make sure all their
156 * atoms are in the same energy group.
160 for (mb = 0; mb < mtop->nmolblock; mb++)
162 molt = &mtop->moltype[mtop->molblock[mb].type];
163 for (m = 0; m < mtop->molblock[mb].nmol; m++)
165 for (cg = 0; cg < molt->cgs.nr; cg++)
167 /* Get the energy group of the first atom in this charge group */
168 firstj = astart + molt->cgs.index[cg];
169 firsteg = ggrpnr(&mtop->groups, egcENER, firstj);
170 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
172 eg = ggrpnr(&mtop->groups, egcENER, astart+j);
175 gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
176 firstj+1, astart+j+1, cg+1, *molt->name);
180 astart += molt->atoms.nr;
185 static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
188 char warn_buf[STRLEN];
191 for (cg = 0; cg < cgs->nr; cg++)
193 maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
196 if (maxsize > MAX_CHARGEGROUP_SIZE)
198 gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
200 else if (maxsize > 10)
202 set_warning_line(wi, topfn, -1);
204 "The largest charge group contains %d atoms.\n"
205 "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"
206 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
207 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
209 warning_note(wi, warn_buf);
213 static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
215 /* This check is not intended to ensure accurate integration,
216 * rather it is to signal mistakes in the mdp settings.
217 * A common mistake is to forget to turn on constraints
218 * for MD after energy minimization with flexible bonds.
219 * This check can also detect too large time steps for flexible water
220 * models, but such errors will often be masked by the constraints
221 * mdp options, which turns flexible water into water with bond constraints,
222 * but without an angle constraint. Unfortunately such incorrect use
223 * of water models can not easily be detected without checking
224 * for specific model names.
226 * The stability limit of leap-frog or velocity verlet is 4.44 steps
227 * per oscillational period.
228 * But accurate bonds distributions are lost far before that limit.
229 * To allow relatively common schemes (although not common with Gromacs)
230 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
231 * we set the note limit to 10.
233 int min_steps_warn = 5;
234 int min_steps_note = 10;
237 gmx_moltype_t *moltype, *w_moltype;
239 t_ilist *ilist, *ilb, *ilc, *ils;
241 int i, a1, a2, w_a1, w_a2, j;
242 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
243 gmx_bool bFound, bWater, bWarn;
244 char warn_buf[STRLEN];
246 ip = mtop->ffparams.iparams;
248 twopi2 = sqr(2*M_PI);
250 limit2 = sqr(min_steps_note*dt);
256 for (molt = 0; molt < mtop->nmoltype; molt++)
258 moltype = &mtop->moltype[molt];
259 atom = moltype->atoms.atom;
260 ilist = moltype->ilist;
261 ilc = &ilist[F_CONSTR];
262 ils = &ilist[F_SETTLE];
263 for (ftype = 0; ftype < F_NRE; ftype++)
265 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
271 for (i = 0; i < ilb->nr; i += 3)
273 fc = ip[ilb->iatoms[i]].harmonic.krA;
274 re = ip[ilb->iatoms[i]].harmonic.rA;
275 if (ftype == F_G96BONDS)
277 /* Convert squared sqaure fc to harmonic fc */
280 a1 = ilb->iatoms[i+1];
281 a2 = ilb->iatoms[i+2];
284 if (fc > 0 && m1 > 0 && m2 > 0)
286 period2 = twopi2*m1*m2/((m1 + m2)*fc);
290 period2 = GMX_FLOAT_MAX;
294 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
295 fc, m1, m2, sqrt(period2));
297 if (period2 < limit2)
300 for (j = 0; j < ilc->nr; j += 3)
302 if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
303 (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
308 for (j = 0; j < ils->nr; j += 4)
310 if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
311 (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
317 (w_moltype == NULL || period2 < w_period2))
329 if (w_moltype != NULL)
331 bWarn = (w_period2 < sqr(min_steps_warn*dt));
332 /* A check that would recognize most water models */
333 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
334 w_moltype->atoms.nr <= 5);
335 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"
338 w_a1+1, *w_moltype->atoms.atomname[w_a1],
339 w_a2+1, *w_moltype->atoms.atomname[w_a2],
340 sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
342 "Maybe you asked for fexible water." :
343 "Maybe you forgot to change the constraints mdp option.");
346 warning(wi, warn_buf);
350 warning_note(wi, warn_buf);
355 static void check_vel(gmx_mtop_t *mtop, rvec v[])
357 gmx_mtop_atomloop_all_t aloop;
361 aloop = gmx_mtop_atomloop_all_init(mtop);
362 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
364 if (atom->ptype == eptShell ||
365 atom->ptype == eptBond ||
366 atom->ptype == eptVSite)
373 static void check_shells_inputrec(gmx_mtop_t *mtop,
377 gmx_mtop_atomloop_all_t aloop;
380 char warn_buf[STRLEN];
382 aloop = gmx_mtop_atomloop_all_init(mtop);
383 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
385 if (atom->ptype == eptShell ||
386 atom->ptype == eptBond)
391 if (IR_TWINRANGE(*ir) && (nshells > 0))
393 snprintf(warn_buf, STRLEN,
394 "The combination of using shells and a twin-range cut-off is not supported");
395 warning_error(wi, warn_buf);
397 if ((nshells > 0) && (ir->nstcalcenergy != 1))
399 set_warning_line(wi, "unknown", -1);
400 snprintf(warn_buf, STRLEN,
401 "There are %d shells, changing nstcalcenergy from %d to 1",
402 nshells, ir->nstcalcenergy);
403 ir->nstcalcenergy = 1;
404 warning(wi, warn_buf);
408 static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
413 for (mb = 0; mb < mtop->nmolblock; mb++)
415 nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
421 /* This routine reorders the molecule type array
422 * in the order of use in the molblocks,
423 * unused molecule types are deleted.
425 static void renumber_moltypes(gmx_mtop_t *sys,
426 int *nmolinfo, t_molinfo **molinfo)
428 int *order, norder, i;
432 snew(order, *nmolinfo);
434 for (mb = 0; mb < sys->nmolblock; mb++)
436 for (i = 0; i < norder; i++)
438 if (order[i] == sys->molblock[mb].type)
445 /* This type did not occur yet, add it */
446 order[norder] = sys->molblock[mb].type;
447 /* Renumber the moltype in the topology */
450 sys->molblock[mb].type = i;
453 /* We still need to reorder the molinfo structs */
455 for (mi = 0; mi < *nmolinfo; mi++)
457 for (i = 0; i < norder; i++)
466 done_mi(&(*molinfo)[mi]);
470 minew[i] = (*molinfo)[mi];
479 static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
484 mtop->nmoltype = nmi;
485 snew(mtop->moltype, nmi);
486 for (m = 0; m < nmi; m++)
488 molt = &mtop->moltype[m];
489 molt->name = mi[m].name;
490 molt->atoms = mi[m].atoms;
491 /* ilists are copied later */
492 molt->cgs = mi[m].cgs;
493 molt->excls = mi[m].excls;
498 new_status(const char *topfile, const char *topppfile, const char *confin,
499 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
500 gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
501 gpp_atomtype_t atype, gmx_mtop_t *sys,
502 int *nmi, t_molinfo **mi, t_params plist[],
503 int *comb, double *reppow, real *fudgeQQ,
507 t_molinfo *molinfo = NULL;
509 gmx_molblock_t *molblock, *molbs;
511 int mb, i, nrmols, nmismatch;
513 gmx_bool bGB = FALSE;
514 char warn_buf[STRLEN];
518 /* Set gmx_boolean for GB */
519 if (ir->implicit_solvent)
524 /* TOPOLOGY processing */
525 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
526 plist, comb, reppow, fudgeQQ,
527 atype, &nrmols, &molinfo, ir,
528 &nmolblock, &molblock, bGB,
532 snew(sys->molblock, nmolblock);
535 for (mb = 0; mb < nmolblock; mb++)
537 if (sys->nmolblock > 0 &&
538 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
540 /* Merge consecutive blocks with the same molecule type */
541 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
542 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
544 else if (molblock[mb].nmol > 0)
546 /* Add a new molblock to the topology */
547 molbs = &sys->molblock[sys->nmolblock];
548 *molbs = molblock[mb];
549 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
550 molbs->nposres_xA = 0;
551 molbs->nposres_xB = 0;
552 sys->natoms += molbs->nmol*molbs->natoms_mol;
556 if (sys->nmolblock == 0)
558 gmx_fatal(FARGS, "No molecules were defined in the system");
561 renumber_moltypes(sys, &nrmols, &molinfo);
565 convert_harmonics(nrmols, molinfo, atype);
568 if (ir->eDisre == edrNone)
570 i = rm_interactions(F_DISRES, nrmols, molinfo);
573 set_warning_line(wi, "unknown", -1);
574 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
575 warning_note(wi, warn_buf);
578 if (opts->bOrire == FALSE)
580 i = rm_interactions(F_ORIRES, nrmols, molinfo);
583 set_warning_line(wi, "unknown", -1);
584 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
585 warning_note(wi, warn_buf);
589 /* Copy structures from msys to sys */
590 molinfo2mtop(nrmols, molinfo, sys);
592 gmx_mtop_finalize(sys);
594 /* COORDINATE file processing */
597 fprintf(stderr, "processing coordinates...\n");
600 get_stx_coordnum(confin, &state->natoms);
601 if (state->natoms != sys->natoms)
603 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
604 " does not match topology (%s, %d)",
605 confin, state->natoms, topfile, sys->natoms);
609 /* make space for coordinates and velocities */
612 init_t_atoms(confat, state->natoms, FALSE);
613 init_state(state, state->natoms, 0, 0, 0, 0);
614 read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
615 /* This call fixes the box shape for runs with pressure scaling */
616 set_box_rel(ir, state);
618 nmismatch = check_atom_names(topfile, confin, sys, confat);
619 free_t_atoms(confat, TRUE);
624 sprintf(buf, "%d non-matching atom name%s\n"
625 "atom names from %s will be used\n"
626 "atom names from %s will be ignored\n",
627 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
632 fprintf(stderr, "double-checking input for internal consistency...\n");
634 double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
640 gmx_mtop_atomloop_all_t aloop;
644 snew(mass, state->natoms);
645 aloop = gmx_mtop_atomloop_all_init(sys);
646 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
652 if (opts->seed == -1)
654 useed = (int)gmx_rng_make_seed();
655 fprintf(stderr, "Setting gen_seed to %u\n", useed);
657 maxwell_speed(opts->tempi, useed, sys, state->v);
659 stop_cm(stdout, state->natoms, mass, state->x, state->v);
667 static void copy_state(const char *slog, t_trxframe *fr,
668 gmx_bool bReadVel, t_state *state,
673 if (fr->not_ok & FRAME_NOT_OK)
675 gmx_fatal(FARGS, "Can not start from an incomplete frame");
679 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
683 for (i = 0; i < state->natoms; i++)
685 copy_rvec(fr->x[i], state->x[i]);
691 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
693 for (i = 0; i < state->natoms; i++)
695 copy_rvec(fr->v[i], state->v[i]);
700 copy_mat(fr->box, state->box);
703 *use_time = fr->time;
706 static void cont_status(const char *slog, const char *ener,
707 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
708 t_inputrec *ir, t_state *state,
710 const output_env_t oenv)
711 /* If fr_time == -1 read the last frame available which is complete */
719 bReadVel = (bNeedVel && !bGenVel);
722 "Reading Coordinates%s and Box size from old trajectory\n",
723 bReadVel ? ", Velocities" : "");
726 fprintf(stderr, "Will read whole trajectory\n");
730 fprintf(stderr, "Will read till time %g\n", fr_time);
736 fprintf(stderr, "Velocities generated: "
737 "ignoring velocities in input trajectory\n");
739 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
743 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
749 "WARNING: Did not find a frame with velocities in file %s,\n"
750 " all velocities will be set to zero!\n\n", slog);
751 for (i = 0; i < sys->natoms; i++)
753 clear_rvec(state->v[i]);
756 /* Search for a frame without velocities */
758 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
762 state->natoms = fr.natoms;
764 if (sys->natoms != state->natoms)
766 gmx_fatal(FARGS, "Number of atoms in Topology "
767 "is not the same as in Trajectory");
769 copy_state(slog, &fr, bReadVel, state, &use_time);
771 /* Find the appropriate frame */
772 while ((fr_time == -1 || fr.time < fr_time) &&
773 read_next_frame(oenv, fp, &fr))
775 copy_state(slog, &fr, bReadVel, state, &use_time);
780 /* Set the relative box lengths for preserving the box shape.
781 * Note that this call can lead to differences in the last bit
782 * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
784 set_box_rel(ir, state);
786 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
787 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
789 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
791 get_enx_state(ener, use_time, &sys->groups, ir, state);
792 preserve_box_shape(ir, state->box_rel, state->boxv);
796 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
798 int rc_scaling, int ePBC,
802 gmx_bool bFirst = TRUE, *hadAtom;
808 int natoms, npbcdim = 0;
809 char warn_buf[STRLEN], title[STRLEN];
810 int a, i, ai, j, k, mb, nat_molb;
811 gmx_molblock_t *molb;
815 get_stx_coordnum(fn, &natoms);
816 if (natoms != mtop->natoms)
818 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);
819 warning(wi, warn_buf);
823 init_t_atoms(&dumat, natoms, FALSE);
824 read_stx_conf(fn, title, &dumat, x, v, NULL, box);
826 npbcdim = ePBC2npbcdim(ePBC);
828 if (rc_scaling != erscNO)
830 copy_mat(box, invbox);
831 for (j = npbcdim; j < DIM; j++)
833 clear_rvec(invbox[j]);
836 m_inv_ur0(invbox, invbox);
839 /* Copy the reference coordinates to mtop */
843 snew(hadAtom, natoms);
844 for (mb = 0; mb < mtop->nmolblock; mb++)
846 molb = &mtop->molblock[mb];
847 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
848 pr = &(molinfo[molb->type].plist[F_POSRES]);
849 prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
850 if (pr->nr > 0 || prfb->nr > 0)
852 atom = mtop->moltype[molb->type].atoms.atom;
853 for (i = 0; (i < pr->nr); i++)
855 ai = pr->param[i].AI;
858 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
859 ai+1, *molinfo[molb->type].name, fn, natoms);
862 if (rc_scaling == erscCOM)
864 /* Determine the center of mass of the posres reference coordinates */
865 for (j = 0; j < npbcdim; j++)
867 sum[j] += atom[ai].m*x[a+ai][j];
869 totmass += atom[ai].m;
872 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
873 for (i = 0; (i < prfb->nr); i++)
875 ai = prfb->param[i].AI;
878 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
879 ai+1, *molinfo[molb->type].name, fn, natoms);
881 if (rc_scaling == erscCOM && hadAtom[ai] == FALSE)
883 /* Determine the center of mass of the posres reference coordinates */
884 for (j = 0; j < npbcdim; j++)
886 sum[j] += atom[ai].m*x[a+ai][j];
888 totmass += atom[ai].m;
893 molb->nposres_xA = nat_molb;
894 snew(molb->posres_xA, molb->nposres_xA);
895 for (i = 0; i < nat_molb; i++)
897 copy_rvec(x[a+i], molb->posres_xA[i]);
902 molb->nposres_xB = nat_molb;
903 snew(molb->posres_xB, molb->nposres_xB);
904 for (i = 0; i < nat_molb; i++)
906 copy_rvec(x[a+i], molb->posres_xB[i]);
912 if (rc_scaling == erscCOM)
916 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
918 for (j = 0; j < npbcdim; j++)
920 com[j] = sum[j]/totmass;
922 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]);
925 if (rc_scaling != erscNO)
927 assert(npbcdim <= DIM);
929 for (mb = 0; mb < mtop->nmolblock; mb++)
931 molb = &mtop->molblock[mb];
932 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
933 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
935 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
936 for (i = 0; i < nat_molb; i++)
938 for (j = 0; j < npbcdim; j++)
940 if (rc_scaling == erscALL)
942 /* Convert from Cartesian to crystal coordinates */
943 xp[i][j] *= invbox[j][j];
944 for (k = j+1; k < npbcdim; k++)
946 xp[i][j] += invbox[k][j]*xp[i][k];
949 else if (rc_scaling == erscCOM)
951 /* Subtract the center of mass */
959 if (rc_scaling == erscCOM)
961 /* Convert the COM from Cartesian to crystal coordinates */
962 for (j = 0; j < npbcdim; j++)
964 com[j] *= invbox[j][j];
965 for (k = j+1; k < npbcdim; k++)
967 com[j] += invbox[k][j]*com[k];
973 free_t_atoms(&dumat, TRUE);
979 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
980 char *fnA, char *fnB,
981 int rc_scaling, int ePBC,
987 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
988 /* It is safer to simply read the b-state posres rather than trying
989 * to be smart and copy the positions.
991 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
994 static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
995 t_inputrec *ir, warninp_t wi)
998 char warn_buf[STRLEN];
1002 fprintf(stderr, "Searching the wall atom type(s)\n");
1004 for (i = 0; i < ir->nwall; i++)
1006 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
1007 if (ir->wall_atomtype[i] == NOTSET)
1009 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
1010 warning_error(wi, warn_buf);
1015 static int nrdf_internal(t_atoms *atoms)
1020 for (i = 0; i < atoms->nr; i++)
1022 /* Vsite ptype might not be set here yet, so also check the mass */
1023 if ((atoms->atom[i].ptype == eptAtom ||
1024 atoms->atom[i].ptype == eptNucleus)
1025 && atoms->atom[i].m > 0)
1032 case 0: nrdf = 0; break;
1033 case 1: nrdf = 0; break;
1034 case 2: nrdf = 1; break;
1035 default: nrdf = nmass*3 - 6; break;
1042 spline1d( double dx,
1054 for (i = 1; i < n-1; i++)
1056 p = 0.5*y2[i-1]+2.0;
1058 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1059 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1064 for (i = n-2; i >= 0; i--)
1066 y2[i] = y2[i]*y2[i+1]+u[i];
1072 interpolate1d( double xmin,
1085 a = (xmin+(ix+1)*dx-x)/dx;
1086 b = (x-xmin-ix*dx)/dx;
1088 *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;
1089 *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];
1094 setup_cmap (int grid_spacing,
1097 gmx_cmap_t * cmap_grid)
1099 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1101 int i, j, k, ii, jj, kk, idx;
1103 double dx, xmin, v, v1, v2, v12;
1106 snew(tmp_u, 2*grid_spacing);
1107 snew(tmp_u2, 2*grid_spacing);
1108 snew(tmp_yy, 2*grid_spacing);
1109 snew(tmp_y1, 2*grid_spacing);
1110 snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
1111 snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
1113 dx = 360.0/grid_spacing;
1114 xmin = -180.0-dx*grid_spacing/2;
1116 for (kk = 0; kk < nc; kk++)
1118 /* Compute an offset depending on which cmap we are using
1119 * Offset will be the map number multiplied with the
1120 * grid_spacing * grid_spacing * 2
1122 offset = kk * grid_spacing * grid_spacing * 2;
1124 for (i = 0; i < 2*grid_spacing; i++)
1126 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1128 for (j = 0; j < 2*grid_spacing; j++)
1130 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1131 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1135 for (i = 0; i < 2*grid_spacing; i++)
1137 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1140 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1142 ii = i-grid_spacing/2;
1145 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1147 jj = j-grid_spacing/2;
1150 for (k = 0; k < 2*grid_spacing; k++)
1152 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1153 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1156 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1157 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1158 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1159 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1161 idx = ii*grid_spacing+jj;
1162 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1163 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1164 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1165 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1171 void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1175 cmap_grid->ngrid = ngrid;
1176 cmap_grid->grid_spacing = grid_spacing;
1177 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1179 snew(cmap_grid->cmapdata, ngrid);
1181 for (i = 0; i < cmap_grid->ngrid; i++)
1183 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
1188 static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1190 int count, count_mol, i, mb;
1191 gmx_molblock_t *molb;
1196 for (mb = 0; mb < mtop->nmolblock; mb++)
1199 molb = &mtop->molblock[mb];
1200 plist = mi[molb->type].plist;
1202 for (i = 0; i < F_NRE; i++)
1206 count_mol += 3*plist[i].nr;
1208 else if (interaction_function[i].flags & IF_CONSTRAINT)
1210 count_mol += plist[i].nr;
1214 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1217 "Molecule type '%s' has %d constraints.\n"
1218 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1219 *mi[molb->type].name, count_mol,
1220 nrdf_internal(&mi[molb->type].atoms));
1223 count += molb->nmol*count_mol;
1229 static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1231 int i, nmiss, natoms, mt;
1233 const t_atoms *atoms;
1236 for (mt = 0; mt < sys->nmoltype; mt++)
1238 atoms = &sys->moltype[mt].atoms;
1241 for (i = 0; i < natoms; i++)
1243 q = atoms->atom[i].q;
1244 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1245 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1246 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1247 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1248 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1251 fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1252 get_atomtype_name(atoms->atom[i].type, atype), q);
1260 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);
1265 static void check_gbsa_params(gpp_atomtype_t atype)
1269 /* If we are doing GBSA, check that we got the parameters we need
1270 * This checking is to see if there are GBSA paratmeters for all
1271 * atoms in the force field. To go around this for testing purposes
1272 * comment out the nerror++ counter temporarily
1275 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1277 if (get_atomtype_radius(i, atype) < 0 ||
1278 get_atomtype_vol(i, atype) < 0 ||
1279 get_atomtype_surftens(i, atype) < 0 ||
1280 get_atomtype_gb_radius(i, atype) < 0 ||
1281 get_atomtype_S_hct(i, atype) < 0)
1283 fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1284 get_atomtype_name(i, atype));
1291 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);
1296 static real calc_temp(const gmx_mtop_t *mtop,
1297 const t_inputrec *ir,
1301 gmx_mtop_atomloop_all_t aloop;
1308 aloop = gmx_mtop_atomloop_all_init(mtop);
1309 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
1311 sum_mv2 += atom->m*norm2(v[a]);
1315 for (g = 0; g < ir->opts.ngtc; g++)
1317 nrdf += ir->opts.nrdf[g];
1320 return sum_mv2/(nrdf*BOLTZ);
1323 static real get_max_reference_temp(const t_inputrec *ir,
1332 for (i = 0; i < ir->opts.ngtc; i++)
1334 if (ir->opts.tau_t[i] < 0)
1340 ref_t = max(ref_t, ir->opts.ref_t[i]);
1348 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.",
1356 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1363 verletbuf_list_setup_t ls;
1366 char warn_buf[STRLEN];
1368 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1370 /* Calculate the buffer size for simple atom vs atoms list */
1371 ls.cluster_size_i = 1;
1372 ls.cluster_size_j = 1;
1373 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1374 &ls, &n_nonlin_vsite, &rlist_1x1);
1376 /* Set the pair-list buffer size in ir */
1377 verletbuf_get_list_setup(FALSE, &ls);
1378 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1379 &ls, &n_nonlin_vsite, &ir->rlist);
1381 if (n_nonlin_vsite > 0)
1383 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);
1384 warning_note(wi, warn_buf);
1387 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1388 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
1390 ir->rlistlong = ir->rlist;
1391 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1392 ls.cluster_size_i, ls.cluster_size_j,
1393 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
1395 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1397 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)));
1401 int gmx_grompp(int argc, char *argv[])
1403 static const char *desc[] = {
1404 "[THISMODULE] (the gromacs preprocessor)",
1405 "reads a molecular topology file, checks the validity of the",
1406 "file, expands the topology from a molecular description to an atomic",
1407 "description. The topology file contains information about",
1408 "molecule types and the number of molecules, the preprocessor",
1409 "copies each molecule as needed. ",
1410 "There is no limitation on the number of molecule types. ",
1411 "Bonds and bond-angles can be converted into constraints, separately",
1412 "for hydrogens and heavy atoms.",
1413 "Then a coordinate file is read and velocities can be generated",
1414 "from a Maxwellian distribution if requested.",
1415 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1416 "(eg. number of MD steps, time step, cut-off), and others such as",
1417 "NEMD parameters, which are corrected so that the net acceleration",
1419 "Eventually a binary file is produced that can serve as the sole input",
1420 "file for the MD program.[PAR]",
1422 "[THISMODULE] uses the atom names from the topology file. The atom names",
1423 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1424 "warnings when they do not match the atom names in the topology.",
1425 "Note that the atom names are irrelevant for the simulation as",
1426 "only the atom types are used for generating interaction parameters.[PAR]",
1428 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1429 "etc. The preprocessor supports the following keywords:[PAR]",
1430 "#ifdef VARIABLE[BR]",
1431 "#ifndef VARIABLE[BR]",
1434 "#define VARIABLE[BR]",
1435 "#undef VARIABLE[BR]"
1436 "#include \"filename\"[BR]",
1437 "#include <filename>[PAR]",
1438 "The functioning of these statements in your topology may be modulated by",
1439 "using the following two flags in your [TT].mdp[tt] file:[PAR]",
1440 "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
1441 "include = -I/home/john/doe[tt][BR]",
1442 "For further information a C-programming textbook may help you out.",
1443 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1444 "topology file written out so that you can verify its contents.[PAR]",
1446 /* cpp has been unnecessary for some time, hasn't it?
1447 "If your system does not have a C-preprocessor, you can still",
1448 "use [TT]grompp[tt], but you do not have access to the features ",
1449 "from the cpp. Command line options to the C-preprocessor can be given",
1450 "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
1453 "When using position restraints a file with restraint coordinates",
1454 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1455 "with respect to the conformation from the [TT]-c[tt] option.",
1456 "For free energy calculation the the coordinates for the B topology",
1457 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1458 "those of the A topology.[PAR]",
1460 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1461 "The last frame with coordinates and velocities will be read,",
1462 "unless the [TT]-time[tt] option is used. Only if this information",
1463 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1464 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1465 "in your [TT].mdp[tt] file. An energy file can be supplied with",
1466 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1469 "[THISMODULE] can be used to restart simulations (preserving",
1470 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1471 "However, for simply changing the number of run steps to extend",
1472 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1473 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1474 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1475 "like output frequency, then supplying the checkpoint file to",
1476 "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
1477 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1479 "By default, all bonded interactions which have constant energy due to",
1480 "virtual site constructions will be removed. If this constant energy is",
1481 "not zero, this will result in a shift in the total energy. All bonded",
1482 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1483 "all constraints for distances which will be constant anyway because",
1484 "of virtual site constructions will be removed. If any constraints remain",
1485 "which involve virtual sites, a fatal error will result.[PAR]"
1487 "To verify your run input file, please take note of all warnings",
1488 "on the screen, and correct where necessary. Do also look at the contents",
1489 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1490 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1491 "with the [TT]-debug[tt] option which will give you more information",
1492 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1493 "can see the contents of the run input file with the [gmx-dump]",
1494 "program. [gmx-check] can be used to compare the contents of two",
1495 "run input files.[PAR]"
1497 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1498 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1499 "harmless, but usually they are not. The user is advised to carefully",
1500 "interpret the output messages before attempting to bypass them with",
1507 gpp_atomtype_t atype;
1509 int natoms, nvsite, comb, mt;
1513 real max_spacing, fudgeQQ;
1515 char fn[STRLEN], fnB[STRLEN];
1516 const char *mdparin;
1518 gmx_bool bNeedVel, bGenVel;
1519 gmx_bool have_atomnumber;
1521 t_params *gb_plist = NULL;
1522 gmx_genborn_t *born = NULL;
1524 gmx_bool bVerbose = FALSE;
1526 char warn_buf[STRLEN];
1528 t_atoms IMDatoms; /* Atoms to be operated on interactively (IMD) */
1531 { efMDP, NULL, NULL, ffREAD },
1532 { efMDP, "-po", "mdout", ffWRITE },
1533 { efSTX, "-c", NULL, ffREAD },
1534 { efSTX, "-r", NULL, ffOPTRD },
1535 { efSTX, "-rb", NULL, ffOPTRD },
1536 { efNDX, NULL, NULL, ffOPTRD },
1537 { efTOP, NULL, NULL, ffREAD },
1538 { efTOP, "-pp", "processed", ffOPTWR },
1539 { efTPX, "-o", NULL, ffWRITE },
1540 { efTRN, "-t", NULL, ffOPTRD },
1541 { efEDR, "-e", NULL, ffOPTRD },
1542 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1543 { efGRO, "-imd", "imdgroup", ffOPTWR },
1544 { efTRN, "-ref", "rotref", ffOPTRW }
1546 #define NFILE asize(fnm)
1548 /* Command line options */
1549 static gmx_bool bRenum = TRUE;
1550 static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1551 static int i, maxwarn = 0;
1552 static real fr_time = -1;
1554 { "-v", FALSE, etBOOL, {&bVerbose},
1555 "Be loud and noisy" },
1556 { "-time", FALSE, etREAL, {&fr_time},
1557 "Take frame at or first after this time." },
1558 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1559 "Remove constant bonded interactions with virtual sites" },
1560 { "-maxwarn", FALSE, etINT, {&maxwarn},
1561 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1562 { "-zero", FALSE, etBOOL, {&bZero},
1563 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1564 { "-renum", FALSE, etBOOL, {&bRenum},
1565 "Renumber atomtypes and minimize number of atomtypes" }
1568 /* Initiate some variables */
1573 /* Parse the command line */
1574 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1575 asize(desc), desc, 0, NULL, &oenv))
1580 wi = init_warning(TRUE, maxwarn);
1582 /* PARAMETER file processing */
1583 mdparin = opt2fn("-f", NFILE, fnm);
1584 set_warning_line(wi, mdparin, -1);
1585 get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
1589 fprintf(stderr, "checking input for internal consistency...\n");
1591 check_ir(mdparin, ir, opts, wi);
1593 if (ir->ld_seed == -1)
1595 ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
1596 fprintf(stderr, "Setting the LD random seed to %"GMX_PRId64 "\n", ir->ld_seed);
1599 if (ir->expandedvals->lmc_seed == -1)
1601 ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
1602 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1605 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1606 bGenVel = (bNeedVel && opts->bGenVel);
1607 if (bGenVel && ir->bContinuation)
1610 "Generating velocities is inconsistent with attempting "
1611 "to continue a previous run. Choose only one of "
1612 "gen-vel = yes and continuation = yes.");
1613 warning_error(wi, warn_buf);
1619 atype = init_atomtype();
1622 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1625 strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
1626 if (!gmx_fexist(fn))
1628 gmx_fatal(FARGS, "%s does not exist", fn);
1630 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1631 opts, ir, bZero, bGenVel, bVerbose, &state,
1632 atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
1638 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1642 /* set parameters for virtual site construction (not for vsiten) */
1643 for (mt = 0; mt < sys->nmoltype; mt++)
1646 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1648 /* now throw away all obsolete bonds, angles and dihedrals: */
1649 /* note: constraints are ALWAYS removed */
1652 for (mt = 0; mt < sys->nmoltype; mt++)
1654 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1658 if (nvsite && ir->eI == eiNM)
1660 gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
1663 if (ir->cutoff_scheme == ecutsVERLET)
1665 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1666 ecutscheme_names[ir->cutoff_scheme]);
1668 /* Remove all charge groups */
1669 gmx_mtop_remove_chargegroups(sys);
1672 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1674 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1676 sprintf(warn_buf, "Can not do %s with %s, use %s",
1677 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1678 warning_error(wi, warn_buf);
1680 if (ir->bPeriodicMols)
1682 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1683 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1684 warning_error(wi, warn_buf);
1688 if (EI_SD (ir->eI) && ir->etc != etcNO)
1690 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1693 /* If we are doing QM/MM, check that we got the atom numbers */
1694 have_atomnumber = TRUE;
1695 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1697 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1699 if (!have_atomnumber && ir->bQMMM)
1703 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1704 "field you are using does not contain atom numbers fields. This is an\n"
1705 "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
1706 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1707 "an integer just before the mass column in ffXXXnb.itp.\n"
1708 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1713 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1715 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1717 /** TODO check size of ex+hy width against box size */
1720 /* Check for errors in the input now, since they might cause problems
1721 * during processing further down.
1723 check_warning_error(wi, FARGS);
1725 if (opt2bSet("-r", NFILE, fnm))
1727 sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
1731 sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
1733 if (opt2bSet("-rb", NFILE, fnm))
1735 sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
1742 if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
1746 fprintf(stderr, "Reading position restraint coords from %s", fn);
1747 if (strcmp(fn, fnB) == 0)
1749 fprintf(stderr, "\n");
1753 fprintf(stderr, " and %s\n", fnB);
1756 gen_posres(sys, mi, fn, fnB,
1757 ir->refcoord_scaling, ir->ePBC,
1758 ir->posres_com, ir->posres_comB,
1762 /* If we are using CMAP, setup the pre-interpolation grid */
1763 if (plist[F_CMAP].ncmap > 0)
1765 init_cmap_grid(&sys->ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
1766 setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys->ffparams.cmap_grid);
1769 set_wall_atomtype(atype, opts, ir, wi);
1772 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1773 ntype = get_atomtype_ntypes(atype);
1776 if (ir->implicit_solvent != eisNO)
1778 /* Now we have renumbered the atom types, we can check the GBSA params */
1779 check_gbsa_params(atype);
1781 /* Check that all atoms that have charge and/or LJ-parameters also have
1782 * sensible GB-parameters
1784 check_gbsa_params_charged(sys, atype);
1787 /* PELA: Copy the atomtype data to the topology atomtype list */
1788 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1792 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1797 fprintf(stderr, "converting bonded parameters...\n");
1800 ntype = get_atomtype_ntypes(atype);
1801 convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
1805 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1808 /* set ptype to VSite for virtual sites */
1809 for (mt = 0; mt < sys->nmoltype; mt++)
1811 set_vsites_ptype(FALSE, &sys->moltype[mt]);
1815 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1817 /* Check velocity for virtual sites and shells */
1820 check_vel(sys, state.v);
1823 /* check for shells and inpurecs */
1824 check_shells_inputrec(sys, ir, wi);
1829 for (i = 0; i < sys->nmoltype; i++)
1831 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
1834 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
1836 check_bonds_timestep(sys, ir->delta_t, wi);
1839 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
1841 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.");
1844 check_warning_error(wi, FARGS);
1848 fprintf(stderr, "initialising group options...\n");
1850 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
1852 bGenVel ? state.v : NULL,
1855 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
1858 if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
1862 if (EI_MD(ir->eI) && ir->etc == etcNO)
1866 buffer_temp = opts->tempi;
1870 buffer_temp = calc_temp(sys, ir, state.v);
1872 if (buffer_temp > 0)
1874 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
1875 warning_note(wi, warn_buf);
1879 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1880 (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
1881 warning_note(wi, warn_buf);
1886 buffer_temp = get_max_reference_temp(ir, wi);
1889 if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
1891 /* NVE with initial T=0: we add a fixed ratio to rlist.
1892 * Since we don't actually use verletbuf_tol, we set it to -1
1893 * so it can't be misused later.
1895 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
1896 ir->verletbuf_tol = -1;
1900 /* We warn for NVE simulations with >1(.1)% drift tolerance */
1901 const real drift_tol = 0.01;
1904 /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
1905 * the safe side with constraints (without constraints: 3 DOF).
1907 ener_runtime = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
1909 if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
1911 ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
1913 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.",
1914 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
1915 (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
1916 (int)(100*drift_tol + 0.5),
1917 drift_tol*ener_runtime);
1918 warning_note(wi, warn_buf);
1921 set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
1926 /* Init the temperature coupling state */
1927 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1931 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
1933 check_eg_vs_cg(sys);
1937 pr_symtab(debug, 0, "After index", &sys->symtab);
1940 triple_check(mdparin, ir, sys, wi);
1941 close_symtab(&sys->symtab);
1944 pr_symtab(debug, 0, "After close", &sys->symtab);
1947 /* make exclusions between QM atoms */
1950 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1952 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1956 generate_qmexcl(sys, ir, wi);
1960 if (ftp2bSet(efTRN, NFILE, fnm))
1964 fprintf(stderr, "getting data from old trajectory ...\n");
1966 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
1967 bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
1970 if (ir->ePBC == epbcXY && ir->nwall != 2)
1972 clear_rvec(state.box[ZZ]);
1975 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1977 set_warning_line(wi, mdparin, -1);
1978 check_chargegroup_radii(sys, ir, state.x, wi);
1981 if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1983 /* Calculate the optimal grid dimensions */
1984 copy_mat(state.box, box);
1985 if (ir->ePBC == epbcXY && ir->nwall == 2)
1987 svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
1989 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
1991 /* Mark fourier_spacing as not used */
1992 ir->fourier_spacing = 0;
1994 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
1996 set_warning_line(wi, mdparin, -1);
1997 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
1999 max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
2000 &(ir->nkx), &(ir->nky), &(ir->nkz));
2003 /* MRS: eventually figure out better logic for initializing the fep
2004 values that makes declaring the lambda and declaring the state not
2005 potentially conflict if not handled correctly. */
2006 if (ir->efep != efepNO)
2008 state.fep_state = ir->fepvals->init_fep_state;
2009 for (i = 0; i < efptNR; i++)
2011 /* init_lambda trumps state definitions*/
2012 if (ir->fepvals->init_lambda >= 0)
2014 state.lambda[i] = ir->fepvals->init_lambda;
2018 if (ir->fepvals->all_lambda[i] == NULL)
2020 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
2024 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
2030 if (ir->ePull != epullNO)
2032 set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
2037 set_reference_positions(ir->rot, state.x, state.box,
2038 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
2042 /* reset_multinr(sys); */
2044 if (EEL_PME(ir->coulombtype))
2046 float ratio = pme_load_estimate(sys, ir, state.box);
2047 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2048 /* With free energy we might need to do PME both for the A and B state
2049 * charges. This will double the cost, but the optimal performance will
2050 * then probably be at a slightly larger cut-off and grid spacing.
2052 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2053 (ir->efep != efepNO && ratio > 2.0/3.0))
2056 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2057 "and for highly parallel simulations between 0.25 and 0.33,\n"
2058 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2059 if (ir->efep != efepNO)
2062 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2068 char warn_buf[STRLEN];
2069 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
2070 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2073 set_warning_line(wi, mdparin, -1);
2074 warning_note(wi, warn_buf);
2078 printf("%s\n", warn_buf);
2084 fprintf(stderr, "writing run input file...\n");
2087 done_warning(wi, FARGS);
2088 write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
2090 /* Output IMD group, if bIMD is TRUE */
2091 write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
2093 done_atomtype(atype);
2094 done_mtop(sys, TRUE);
2095 done_inputrec_strings();