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42 #include <sys/types.h>
66 #include "sortwater.h"
68 #include "gmx_fatal.h"
74 #include "vsite_parm.h"
80 #include "compute_io.h"
81 #include "gpp_atomtype.h"
82 #include "gpp_tomorse.h"
83 #include "mtop_util.h"
85 #include "calc_verletbuf.h"
87 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
92 /* For all the molecule types */
93 for (i = 0; i < nrmols; i++)
95 n += mols[i].plist[ifunc].nr;
96 mols[i].plist[ifunc].nr = 0;
101 static int check_atom_names(const char *fn1, const char *fn2,
102 gmx_mtop_t *mtop, t_atoms *at)
104 int mb, m, i, j, nmismatch;
106 #define MAXMISMATCH 20
108 if (mtop->natoms != at->nr)
110 gmx_incons("comparing atom names");
115 for (mb = 0; mb < mtop->nmolblock; mb++)
117 tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
118 for (m = 0; m < mtop->molblock[mb].nmol; m++)
120 for (j = 0; j < tat->nr; j++)
122 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
124 if (nmismatch < MAXMISMATCH)
127 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
128 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
130 else if (nmismatch == MAXMISMATCH)
132 fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
144 static void check_eg_vs_cg(gmx_mtop_t *mtop)
146 int astart, mb, m, cg, j, firstj;
147 unsigned char firsteg, eg;
150 /* Go through all the charge groups and make sure all their
151 * atoms are in the same energy group.
155 for (mb = 0; mb < mtop->nmolblock; mb++)
157 molt = &mtop->moltype[mtop->molblock[mb].type];
158 for (m = 0; m < mtop->molblock[mb].nmol; m++)
160 for (cg = 0; cg < molt->cgs.nr; cg++)
162 /* Get the energy group of the first atom in this charge group */
163 firstj = astart + molt->cgs.index[cg];
164 firsteg = ggrpnr(&mtop->groups, egcENER, firstj);
165 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
167 eg = ggrpnr(&mtop->groups, egcENER, astart+j);
170 gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
171 firstj+1, astart+j+1, cg+1, *molt->name);
175 astart += molt->atoms.nr;
180 static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
183 char warn_buf[STRLEN];
186 for (cg = 0; cg < cgs->nr; cg++)
188 maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
191 if (maxsize > MAX_CHARGEGROUP_SIZE)
193 gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
195 else if (maxsize > 10)
197 set_warning_line(wi, topfn, -1);
199 "The largest charge group contains %d atoms.\n"
200 "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"
201 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
202 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
204 warning_note(wi, warn_buf);
208 static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
210 /* This check is not intended to ensure accurate integration,
211 * rather it is to signal mistakes in the mdp settings.
212 * A common mistake is to forget to turn on constraints
213 * for MD after energy minimization with flexible bonds.
214 * This check can also detect too large time steps for flexible water
215 * models, but such errors will often be masked by the constraints
216 * mdp options, which turns flexible water into water with bond constraints,
217 * but without an angle constraint. Unfortunately such incorrect use
218 * of water models can not easily be detected without checking
219 * for specific model names.
221 * The stability limit of leap-frog or velocity verlet is 4.44 steps
222 * per oscillational period.
223 * But accurate bonds distributions are lost far before that limit.
224 * To allow relatively common schemes (although not common with Gromacs)
225 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
226 * we set the note limit to 10.
228 int min_steps_warn = 5;
229 int min_steps_note = 10;
232 gmx_moltype_t *moltype, *w_moltype;
234 t_ilist *ilist, *ilb, *ilc, *ils;
236 int i, a1, a2, w_a1, w_a2, j;
237 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
238 gmx_bool bFound, bWater, bWarn;
239 char warn_buf[STRLEN];
241 ip = mtop->ffparams.iparams;
243 twopi2 = sqr(2*M_PI);
245 limit2 = sqr(min_steps_note*dt);
251 for (molt = 0; molt < mtop->nmoltype; molt++)
253 moltype = &mtop->moltype[molt];
254 atom = moltype->atoms.atom;
255 ilist = moltype->ilist;
256 ilc = &ilist[F_CONSTR];
257 ils = &ilist[F_SETTLE];
258 for (ftype = 0; ftype < F_NRE; ftype++)
260 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
266 for (i = 0; i < ilb->nr; i += 3)
268 fc = ip[ilb->iatoms[i]].harmonic.krA;
269 re = ip[ilb->iatoms[i]].harmonic.rA;
270 if (ftype == F_G96BONDS)
272 /* Convert squared sqaure fc to harmonic fc */
275 a1 = ilb->iatoms[i+1];
276 a2 = ilb->iatoms[i+2];
279 if (fc > 0 && m1 > 0 && m2 > 0)
281 period2 = twopi2*m1*m2/((m1 + m2)*fc);
285 period2 = GMX_FLOAT_MAX;
289 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
290 fc, m1, m2, sqrt(period2));
292 if (period2 < limit2)
295 for (j = 0; j < ilc->nr; j += 3)
297 if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
298 (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
303 for (j = 0; j < ils->nr; j += 4)
305 if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
306 (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
312 (w_moltype == NULL || period2 < w_period2))
324 if (w_moltype != NULL)
326 bWarn = (w_period2 < sqr(min_steps_warn*dt));
327 /* A check that would recognize most water models */
328 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
329 w_moltype->atoms.nr <= 5);
330 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"
333 w_a1+1, *w_moltype->atoms.atomname[w_a1],
334 w_a2+1, *w_moltype->atoms.atomname[w_a2],
335 sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
337 "Maybe you asked for fexible water." :
338 "Maybe you forgot to change the constraints mdp option.");
341 warning(wi, warn_buf);
345 warning_note(wi, warn_buf);
350 static void check_vel(gmx_mtop_t *mtop, rvec v[])
352 gmx_mtop_atomloop_all_t aloop;
356 aloop = gmx_mtop_atomloop_all_init(mtop);
357 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
359 if (atom->ptype == eptShell ||
360 atom->ptype == eptBond ||
361 atom->ptype == eptVSite)
368 static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
373 for (mb = 0; mb < mtop->nmolblock; mb++)
375 nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
381 /* This routine reorders the molecule type array
382 * in the order of use in the molblocks,
383 * unused molecule types are deleted.
385 static void renumber_moltypes(gmx_mtop_t *sys,
386 int *nmolinfo, t_molinfo **molinfo)
388 int *order, norder, i;
392 snew(order, *nmolinfo);
394 for (mb = 0; mb < sys->nmolblock; mb++)
396 for (i = 0; i < norder; i++)
398 if (order[i] == sys->molblock[mb].type)
405 /* This type did not occur yet, add it */
406 order[norder] = sys->molblock[mb].type;
407 /* Renumber the moltype in the topology */
410 sys->molblock[mb].type = i;
413 /* We still need to reorder the molinfo structs */
415 for (mi = 0; mi < *nmolinfo; mi++)
417 for (i = 0; i < norder; i++)
426 done_mi(&(*molinfo)[mi]);
430 minew[i] = (*molinfo)[mi];
439 static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
444 mtop->nmoltype = nmi;
445 snew(mtop->moltype, nmi);
446 for (m = 0; m < nmi; m++)
448 molt = &mtop->moltype[m];
449 molt->name = mi[m].name;
450 molt->atoms = mi[m].atoms;
451 /* ilists are copied later */
452 molt->cgs = mi[m].cgs;
453 molt->excls = mi[m].excls;
458 new_status(const char *topfile, const char *topppfile, const char *confin,
459 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
460 gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
461 gpp_atomtype_t atype, gmx_mtop_t *sys,
462 int *nmi, t_molinfo **mi, t_params plist[],
463 int *comb, double *reppow, real *fudgeQQ,
467 t_molinfo *molinfo = NULL;
469 gmx_molblock_t *molblock, *molbs;
471 int mb, i, nrmols, nmismatch;
473 gmx_bool bGB = FALSE;
474 char warn_buf[STRLEN];
478 /* Set gmx_boolean for GB */
479 if (ir->implicit_solvent)
484 /* TOPOLOGY processing */
485 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
486 plist, comb, reppow, fudgeQQ,
487 atype, &nrmols, &molinfo, ir,
488 &nmolblock, &molblock, bGB,
492 snew(sys->molblock, nmolblock);
495 for (mb = 0; mb < nmolblock; mb++)
497 if (sys->nmolblock > 0 &&
498 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
500 /* Merge consecutive blocks with the same molecule type */
501 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
502 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
504 else if (molblock[mb].nmol > 0)
506 /* Add a new molblock to the topology */
507 molbs = &sys->molblock[sys->nmolblock];
508 *molbs = molblock[mb];
509 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
510 molbs->nposres_xA = 0;
511 molbs->nposres_xB = 0;
512 sys->natoms += molbs->nmol*molbs->natoms_mol;
516 if (sys->nmolblock == 0)
518 gmx_fatal(FARGS, "No molecules were defined in the system");
521 renumber_moltypes(sys, &nrmols, &molinfo);
525 convert_harmonics(nrmols, molinfo, atype);
528 if (ir->eDisre == edrNone)
530 i = rm_interactions(F_DISRES, nrmols, molinfo);
533 set_warning_line(wi, "unknown", -1);
534 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
535 warning_note(wi, warn_buf);
538 if (opts->bOrire == FALSE)
540 i = rm_interactions(F_ORIRES, nrmols, molinfo);
543 set_warning_line(wi, "unknown", -1);
544 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
545 warning_note(wi, warn_buf);
549 /* Copy structures from msys to sys */
550 molinfo2mtop(nrmols, molinfo, sys);
552 gmx_mtop_finalize(sys);
554 /* COORDINATE file processing */
557 fprintf(stderr, "processing coordinates...\n");
560 get_stx_coordnum(confin, &state->natoms);
561 if (state->natoms != sys->natoms)
563 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
564 " does not match topology (%s, %d)",
565 confin, state->natoms, topfile, sys->natoms);
569 /* make space for coordinates and velocities */
572 init_t_atoms(confat, state->natoms, FALSE);
573 init_state(state, state->natoms, 0, 0, 0, 0);
574 read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
575 /* This call fixes the box shape for runs with pressure scaling */
576 set_box_rel(ir, state);
578 nmismatch = check_atom_names(topfile, confin, sys, confat);
579 free_t_atoms(confat, TRUE);
584 sprintf(buf, "%d non-matching atom name%s\n"
585 "atom names from %s will be used\n"
586 "atom names from %s will be ignored\n",
587 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
592 fprintf(stderr, "double-checking input for internal consistency...\n");
594 double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
600 gmx_mtop_atomloop_all_t aloop;
603 snew(mass, state->natoms);
604 aloop = gmx_mtop_atomloop_all_init(sys);
605 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
610 if (opts->seed == -1)
612 opts->seed = make_seed();
613 fprintf(stderr, "Setting gen_seed to %d\n", opts->seed);
615 maxwell_speed(opts->tempi, opts->seed, sys, state->v);
617 stop_cm(stdout, state->natoms, mass, state->x, state->v);
625 static void copy_state(const char *slog, t_trxframe *fr,
626 gmx_bool bReadVel, t_state *state,
631 if (fr->not_ok & FRAME_NOT_OK)
633 gmx_fatal(FARGS, "Can not start from an incomplete frame");
637 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
641 for (i = 0; i < state->natoms; i++)
643 copy_rvec(fr->x[i], state->x[i]);
649 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
651 for (i = 0; i < state->natoms; i++)
653 copy_rvec(fr->v[i], state->v[i]);
658 copy_mat(fr->box, state->box);
661 *use_time = fr->time;
664 static void cont_status(const char *slog, const char *ener,
665 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
666 t_inputrec *ir, t_state *state,
668 const output_env_t oenv)
669 /* If fr_time == -1 read the last frame available which is complete */
677 bReadVel = (bNeedVel && !bGenVel);
680 "Reading Coordinates%s and Box size from old trajectory\n",
681 bReadVel ? ", Velocities" : "");
684 fprintf(stderr, "Will read whole trajectory\n");
688 fprintf(stderr, "Will read till time %g\n", fr_time);
694 fprintf(stderr, "Velocities generated: "
695 "ignoring velocities in input trajectory\n");
697 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
701 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
707 "WARNING: Did not find a frame with velocities in file %s,\n"
708 " all velocities will be set to zero!\n\n", slog);
709 for (i = 0; i < sys->natoms; i++)
711 clear_rvec(state->v[i]);
714 /* Search for a frame without velocities */
716 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
720 state->natoms = fr.natoms;
722 if (sys->natoms != state->natoms)
724 gmx_fatal(FARGS, "Number of atoms in Topology "
725 "is not the same as in Trajectory");
727 copy_state(slog, &fr, bReadVel, state, &use_time);
729 /* Find the appropriate frame */
730 while ((fr_time == -1 || fr.time < fr_time) &&
731 read_next_frame(oenv, fp, &fr))
733 copy_state(slog, &fr, bReadVel, state, &use_time);
738 /* Set the relative box lengths for preserving the box shape.
739 * Note that this call can lead to differences in the last bit
740 * with respect to using tpbconv to create a [TT].tpx[tt] file.
742 set_box_rel(ir, state);
744 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
745 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
747 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
749 get_enx_state(ener, use_time, &sys->groups, ir, state);
750 preserve_box_shape(ir, state->box_rel, state->boxv);
754 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
756 int rc_scaling, int ePBC,
760 gmx_bool bFirst = TRUE;
766 int natoms, npbcdim = 0;
767 char warn_buf[STRLEN], title[STRLEN];
768 int a, i, ai, j, k, mb, nat_molb;
769 gmx_molblock_t *molb;
773 get_stx_coordnum(fn, &natoms);
774 if (natoms != mtop->natoms)
776 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);
777 warning(wi, warn_buf);
781 init_t_atoms(&dumat, natoms, FALSE);
782 read_stx_conf(fn, title, &dumat, x, v, NULL, box);
784 npbcdim = ePBC2npbcdim(ePBC);
786 if (rc_scaling != erscNO)
788 copy_mat(box, invbox);
789 for (j = npbcdim; j < DIM; j++)
791 clear_rvec(invbox[j]);
794 m_inv_ur0(invbox, invbox);
797 /* Copy the reference coordinates to mtop */
801 for (mb = 0; mb < mtop->nmolblock; mb++)
803 molb = &mtop->molblock[mb];
804 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
805 pr = &(molinfo[molb->type].plist[F_POSRES]);
808 atom = mtop->moltype[molb->type].atoms.atom;
809 for (i = 0; (i < pr->nr); i++)
811 ai = pr->param[i].AI;
814 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
815 ai+1, *molinfo[molb->type].name, fn, natoms);
817 if (rc_scaling == erscCOM)
819 /* Determine the center of mass of the posres reference coordinates */
820 for (j = 0; j < npbcdim; j++)
822 sum[j] += atom[ai].m*x[a+ai][j];
824 totmass += atom[ai].m;
829 molb->nposres_xA = nat_molb;
830 snew(molb->posres_xA, molb->nposres_xA);
831 for (i = 0; i < nat_molb; i++)
833 copy_rvec(x[a+i], molb->posres_xA[i]);
838 molb->nposres_xB = nat_molb;
839 snew(molb->posres_xB, molb->nposres_xB);
840 for (i = 0; i < nat_molb; i++)
842 copy_rvec(x[a+i], molb->posres_xB[i]);
848 if (rc_scaling == erscCOM)
852 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
854 for (j = 0; j < npbcdim; j++)
856 com[j] = sum[j]/totmass;
858 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]);
861 if (rc_scaling != erscNO)
863 for (mb = 0; mb < mtop->nmolblock; mb++)
865 molb = &mtop->molblock[mb];
866 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
867 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
869 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
870 for (i = 0; i < nat_molb; i++)
872 for (j = 0; j < npbcdim; j++)
874 if (rc_scaling == erscALL)
876 /* Convert from Cartesian to crystal coordinates */
877 xp[i][j] *= invbox[j][j];
878 for (k = j+1; k < npbcdim; k++)
880 xp[i][j] += invbox[k][j]*xp[i][k];
883 else if (rc_scaling == erscCOM)
885 /* Subtract the center of mass */
893 if (rc_scaling == erscCOM)
895 /* Convert the COM from Cartesian to crystal coordinates */
896 for (j = 0; j < npbcdim; j++)
898 com[j] *= invbox[j][j];
899 for (k = j+1; k < npbcdim; k++)
901 com[j] += invbox[k][j]*com[k];
907 free_t_atoms(&dumat, TRUE);
912 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
913 char *fnA, char *fnB,
914 int rc_scaling, int ePBC,
920 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
921 if (strcmp(fnA, fnB) != 0)
923 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
927 static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
928 t_inputrec *ir, warninp_t wi)
931 char warn_buf[STRLEN];
935 fprintf(stderr, "Searching the wall atom type(s)\n");
937 for (i = 0; i < ir->nwall; i++)
939 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
940 if (ir->wall_atomtype[i] == NOTSET)
942 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
943 warning_error(wi, warn_buf);
948 static int nrdf_internal(t_atoms *atoms)
953 for (i = 0; i < atoms->nr; i++)
955 /* Vsite ptype might not be set here yet, so also check the mass */
956 if ((atoms->atom[i].ptype == eptAtom ||
957 atoms->atom[i].ptype == eptNucleus)
958 && atoms->atom[i].m > 0)
965 case 0: nrdf = 0; break;
966 case 1: nrdf = 0; break;
967 case 2: nrdf = 1; break;
968 default: nrdf = nmass*3 - 6; break;
987 for (i = 1; i < n-1; i++)
991 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
992 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
997 for (i = n-2; i >= 0; i--)
999 y2[i] = y2[i]*y2[i+1]+u[i];
1005 interpolate1d( double xmin,
1018 a = (xmin+(ix+1)*dx-x)/dx;
1019 b = (x-xmin-ix*dx)/dx;
1021 *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;
1022 *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];
1027 setup_cmap (int grid_spacing,
1030 gmx_cmap_t * cmap_grid)
1032 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1034 int i, j, k, ii, jj, kk, idx;
1036 double dx, xmin, v, v1, v2, v12;
1039 snew(tmp_u, 2*grid_spacing);
1040 snew(tmp_u2, 2*grid_spacing);
1041 snew(tmp_yy, 2*grid_spacing);
1042 snew(tmp_y1, 2*grid_spacing);
1043 snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
1044 snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
1046 dx = 360.0/grid_spacing;
1047 xmin = -180.0-dx*grid_spacing/2;
1049 for (kk = 0; kk < nc; kk++)
1051 /* Compute an offset depending on which cmap we are using
1052 * Offset will be the map number multiplied with the
1053 * grid_spacing * grid_spacing * 2
1055 offset = kk * grid_spacing * grid_spacing * 2;
1057 for (i = 0; i < 2*grid_spacing; i++)
1059 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1061 for (j = 0; j < 2*grid_spacing; j++)
1063 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1064 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1068 for (i = 0; i < 2*grid_spacing; i++)
1070 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1073 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1075 ii = i-grid_spacing/2;
1078 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1080 jj = j-grid_spacing/2;
1083 for (k = 0; k < 2*grid_spacing; k++)
1085 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1086 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1089 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1090 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1091 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1092 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1094 idx = ii*grid_spacing+jj;
1095 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1096 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1097 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1098 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1104 void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1108 cmap_grid->ngrid = ngrid;
1109 cmap_grid->grid_spacing = grid_spacing;
1110 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1112 snew(cmap_grid->cmapdata, ngrid);
1114 for (i = 0; i < cmap_grid->ngrid; i++)
1116 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
1121 static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1123 int count, count_mol, i, mb;
1124 gmx_molblock_t *molb;
1129 for (mb = 0; mb < mtop->nmolblock; mb++)
1132 molb = &mtop->molblock[mb];
1133 plist = mi[molb->type].plist;
1135 for (i = 0; i < F_NRE; i++)
1139 count_mol += 3*plist[i].nr;
1141 else if (interaction_function[i].flags & IF_CONSTRAINT)
1143 count_mol += plist[i].nr;
1147 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1150 "Molecule type '%s' has %d constraints.\n"
1151 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1152 *mi[molb->type].name, count_mol,
1153 nrdf_internal(&mi[molb->type].atoms));
1156 count += molb->nmol*count_mol;
1162 static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1164 int i, nmiss, natoms, mt;
1166 const t_atoms *atoms;
1169 for (mt = 0; mt < sys->nmoltype; mt++)
1171 atoms = &sys->moltype[mt].atoms;
1174 for (i = 0; i < natoms; i++)
1176 q = atoms->atom[i].q;
1177 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1178 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1179 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1180 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1181 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1184 fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1185 get_atomtype_name(atoms->atom[i].type, atype), q);
1193 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);
1198 static void check_gbsa_params(t_inputrec *ir, gpp_atomtype_t atype)
1202 /* If we are doing GBSA, check that we got the parameters we need
1203 * This checking is to see if there are GBSA paratmeters for all
1204 * atoms in the force field. To go around this for testing purposes
1205 * comment out the nerror++ counter temporarily
1208 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1210 if (get_atomtype_radius(i, atype) < 0 ||
1211 get_atomtype_vol(i, atype) < 0 ||
1212 get_atomtype_surftens(i, atype) < 0 ||
1213 get_atomtype_gb_radius(i, atype) < 0 ||
1214 get_atomtype_S_hct(i, atype) < 0)
1216 fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1217 get_atomtype_name(i, atype));
1224 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);
1229 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1232 real verletbuf_drift,
1237 verletbuf_list_setup_t ls;
1240 char warn_buf[STRLEN];
1243 for (i = 0; i < ir->opts.ngtc; i++)
1245 if (ir->opts.ref_t[i] < 0)
1247 warning(wi, "Some atom groups do not use temperature coupling. This cannot be accounted for in the energy drift estimation for the Verlet buffer size. The energy drift and the Verlet buffer might be underestimated.");
1251 ref_T = max(ref_T, ir->opts.ref_t[i]);
1255 printf("Determining Verlet buffer for an energy drift of %g kJ/mol/ps at %g K\n", verletbuf_drift, ref_T);
1257 for (i = 0; i < ir->opts.ngtc; i++)
1259 if (ir->opts.ref_t[i] >= 0 && ir->opts.ref_t[i] != ref_T)
1261 sprintf(warn_buf, "ref_T for group of %.1f DOFs is %g K, which is smaller than the maximum of %g K used for the buffer size calculation. The buffer size might be on the conservative (large) side.",
1262 ir->opts.nrdf[i], ir->opts.ref_t[i], ref_T);
1263 warning_note(wi, warn_buf);
1267 /* Calculate the buffer size for simple atom vs atoms list */
1268 ls.cluster_size_i = 1;
1269 ls.cluster_size_j = 1;
1270 calc_verlet_buffer_size(mtop, det(box), ir, verletbuf_drift,
1271 &ls, &n_nonlin_vsite, &rlist_1x1);
1273 /* Set the pair-list buffer size in ir */
1274 verletbuf_get_list_setup(FALSE, &ls);
1275 calc_verlet_buffer_size(mtop, det(box), ir, verletbuf_drift,
1276 &ls, &n_nonlin_vsite, &ir->rlist);
1278 if (n_nonlin_vsite > 0)
1280 sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy drift is approximated. In most cases this does not affect the energy drift significantly.", n_nonlin_vsite);
1281 warning_note(wi, warn_buf);
1284 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1285 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
1287 ir->rlistlong = ir->rlist;
1288 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1289 ls.cluster_size_i, ls.cluster_size_j,
1290 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
1292 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1294 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-drift.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
1298 int cmain (int argc, char *argv[])
1300 static const char *desc[] = {
1301 "The gromacs preprocessor",
1302 "reads a molecular topology file, checks the validity of the",
1303 "file, expands the topology from a molecular description to an atomic",
1304 "description. The topology file contains information about",
1305 "molecule types and the number of molecules, the preprocessor",
1306 "copies each molecule as needed. ",
1307 "There is no limitation on the number of molecule types. ",
1308 "Bonds and bond-angles can be converted into constraints, separately",
1309 "for hydrogens and heavy atoms.",
1310 "Then a coordinate file is read and velocities can be generated",
1311 "from a Maxwellian distribution if requested.",
1312 "[TT]grompp[tt] also reads parameters for the [TT]mdrun[tt] ",
1313 "(eg. number of MD steps, time step, cut-off), and others such as",
1314 "NEMD parameters, which are corrected so that the net acceleration",
1316 "Eventually a binary file is produced that can serve as the sole input",
1317 "file for the MD program.[PAR]",
1319 "[TT]grompp[tt] uses the atom names from the topology file. The atom names",
1320 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1321 "warnings when they do not match the atom names in the topology.",
1322 "Note that the atom names are irrelevant for the simulation as",
1323 "only the atom types are used for generating interaction parameters.[PAR]",
1325 "[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros, ",
1326 "etc. The preprocessor supports the following keywords:[PAR]",
1327 "#ifdef VARIABLE[BR]",
1328 "#ifndef VARIABLE[BR]",
1331 "#define VARIABLE[BR]",
1332 "#undef VARIABLE[BR]"
1333 "#include \"filename\"[BR]",
1334 "#include <filename>[PAR]",
1335 "The functioning of these statements in your topology may be modulated by",
1336 "using the following two flags in your [TT].mdp[tt] file:[PAR]",
1337 "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
1338 "include = -I/home/john/doe[tt][BR]",
1339 "For further information a C-programming textbook may help you out.",
1340 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1341 "topology file written out so that you can verify its contents.[PAR]",
1343 /* cpp has been unnecessary for some time, hasn't it?
1344 "If your system does not have a C-preprocessor, you can still",
1345 "use [TT]grompp[tt], but you do not have access to the features ",
1346 "from the cpp. Command line options to the C-preprocessor can be given",
1347 "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
1350 "When using position restraints a file with restraint coordinates",
1351 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1352 "with respect to the conformation from the [TT]-c[tt] option.",
1353 "For free energy calculation the the coordinates for the B topology",
1354 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1355 "those of the A topology.[PAR]",
1357 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1358 "The last frame with coordinates and velocities will be read,",
1359 "unless the [TT]-time[tt] option is used. Only if this information",
1360 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1361 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1362 "in your [TT].mdp[tt] file. An energy file can be supplied with",
1363 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1366 "[TT]grompp[tt] can be used to restart simulations (preserving",
1367 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1368 "However, for simply changing the number of run steps to extend",
1369 "a run, using [TT]tpbconv[tt] is more convenient than [TT]grompp[tt].",
1370 "You then supply the old checkpoint file directly to [TT]mdrun[tt]",
1371 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1372 "like output frequency, then supplying the checkpoint file to",
1373 "[TT]grompp[tt] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
1374 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1376 "By default, all bonded interactions which have constant energy due to",
1377 "virtual site constructions will be removed. If this constant energy is",
1378 "not zero, this will result in a shift in the total energy. All bonded",
1379 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1380 "all constraints for distances which will be constant anyway because",
1381 "of virtual site constructions will be removed. If any constraints remain",
1382 "which involve virtual sites, a fatal error will result.[PAR]"
1384 "To verify your run input file, please take note of all warnings",
1385 "on the screen, and correct where necessary. Do also look at the contents",
1386 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1387 "the input that [TT]grompp[tt] has read. If in doubt, you can start [TT]grompp[tt]",
1388 "with the [TT]-debug[tt] option which will give you more information",
1389 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1390 "can see the contents of the run input file with the [TT]gmxdump[tt]",
1391 "program. [TT]gmxcheck[tt] can be used to compare the contents of two",
1392 "run input files.[PAR]"
1394 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1395 "by [TT]grompp[tt] that otherwise halt output. In some cases, warnings are",
1396 "harmless, but usually they are not. The user is advised to carefully",
1397 "interpret the output messages before attempting to bypass them with",
1404 gpp_atomtype_t atype;
1406 int natoms, nvsite, comb, mt;
1410 real max_spacing, fudgeQQ;
1412 char fn[STRLEN], fnB[STRLEN];
1413 const char *mdparin;
1415 gmx_bool bNeedVel, bGenVel;
1416 gmx_bool have_atomnumber;
1418 t_params *gb_plist = NULL;
1419 gmx_genborn_t *born = NULL;
1421 gmx_bool bVerbose = FALSE;
1423 char warn_buf[STRLEN];
1426 { efMDP, NULL, NULL, ffREAD },
1427 { efMDP, "-po", "mdout", ffWRITE },
1428 { efSTX, "-c", NULL, ffREAD },
1429 { efSTX, "-r", NULL, ffOPTRD },
1430 { efSTX, "-rb", NULL, ffOPTRD },
1431 { efNDX, NULL, NULL, ffOPTRD },
1432 { efTOP, NULL, NULL, ffREAD },
1433 { efTOP, "-pp", "processed", ffOPTWR },
1434 { efTPX, "-o", NULL, ffWRITE },
1435 { efTRN, "-t", NULL, ffOPTRD },
1436 { efEDR, "-e", NULL, ffOPTRD },
1437 { efTRN, "-ref", "rotref", ffOPTRW }
1439 #define NFILE asize(fnm)
1441 /* Command line options */
1442 static gmx_bool bRenum = TRUE;
1443 static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1444 static int i, maxwarn = 0;
1445 static real fr_time = -1;
1447 { "-v", FALSE, etBOOL, {&bVerbose},
1448 "Be loud and noisy" },
1449 { "-time", FALSE, etREAL, {&fr_time},
1450 "Take frame at or first after this time." },
1451 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1452 "Remove constant bonded interactions with virtual sites" },
1453 { "-maxwarn", FALSE, etINT, {&maxwarn},
1454 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1455 { "-zero", FALSE, etBOOL, {&bZero},
1456 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1457 { "-renum", FALSE, etBOOL, {&bRenum},
1458 "Renumber atomtypes and minimize number of atomtypes" }
1461 CopyRight(stderr, argv[0]);
1463 /* Initiate some variables */
1468 /* Parse the command line */
1469 parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1470 asize(desc), desc, 0, NULL, &oenv);
1472 wi = init_warning(TRUE, maxwarn);
1474 /* PARAMETER file processing */
1475 mdparin = opt2fn("-f", NFILE, fnm);
1476 set_warning_line(wi, mdparin, -1);
1477 get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
1481 fprintf(stderr, "checking input for internal consistency...\n");
1483 check_ir(mdparin, ir, opts, wi);
1485 if (ir->ld_seed == -1)
1487 ir->ld_seed = make_seed();
1488 fprintf(stderr, "Setting the LD random seed to %d\n", ir->ld_seed);
1491 if (ir->expandedvals->lmc_seed == -1)
1493 ir->expandedvals->lmc_seed = make_seed();
1494 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1497 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1498 bGenVel = (bNeedVel && opts->bGenVel);
1499 if (bGenVel && ir->bContinuation)
1502 "Generating velocities is inconsistent with attempting "
1503 "to continue a previous run. Choose only one of "
1504 "gen-vel = yes and continuation = yes.");
1505 warning_error(wi, warn_buf);
1511 atype = init_atomtype();
1514 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1517 strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
1518 if (!gmx_fexist(fn))
1520 gmx_fatal(FARGS, "%s does not exist", fn);
1522 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1523 opts, ir, bZero, bGenVel, bVerbose, &state,
1524 atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
1530 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1534 /* set parameters for virtual site construction (not for vsiten) */
1535 for (mt = 0; mt < sys->nmoltype; mt++)
1538 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1540 /* now throw away all obsolete bonds, angles and dihedrals: */
1541 /* note: constraints are ALWAYS removed */
1544 for (mt = 0; mt < sys->nmoltype; mt++)
1546 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1550 if (ir->cutoff_scheme == ecutsVERLET)
1552 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1553 ecutscheme_names[ir->cutoff_scheme]);
1555 /* Remove all charge groups */
1556 gmx_mtop_remove_chargegroups(sys);
1559 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1561 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1563 sprintf(warn_buf, "Can not do %s with %s, use %s",
1564 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1565 warning_error(wi, warn_buf);
1567 if (ir->bPeriodicMols)
1569 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1570 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1571 warning_error(wi, warn_buf);
1575 if (EI_SD (ir->eI) && ir->etc != etcNO)
1577 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1580 /* If we are doing QM/MM, check that we got the atom numbers */
1581 have_atomnumber = TRUE;
1582 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1584 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1586 if (!have_atomnumber && ir->bQMMM)
1590 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1591 "field you are using does not contain atom numbers fields. This is an\n"
1592 "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
1593 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1594 "an integer just before the mass column in ffXXXnb.itp.\n"
1595 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1600 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1602 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1604 /** \TODO check size of ex+hy width against box size */
1607 /* Check for errors in the input now, since they might cause problems
1608 * during processing further down.
1610 check_warning_error(wi, FARGS);
1612 if (opt2bSet("-r", NFILE, fnm))
1614 sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
1618 sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
1620 if (opt2bSet("-rb", NFILE, fnm))
1622 sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
1629 if (nint_ftype(sys, mi, F_POSRES) > 0)
1633 fprintf(stderr, "Reading position restraint coords from %s", fn);
1634 if (strcmp(fn, fnB) == 0)
1636 fprintf(stderr, "\n");
1640 fprintf(stderr, " and %s\n", fnB);
1643 gen_posres(sys, mi, fn, fnB,
1644 ir->refcoord_scaling, ir->ePBC,
1645 ir->posres_com, ir->posres_comB,
1649 /* If we are using CMAP, setup the pre-interpolation grid */
1650 if (plist->ncmap > 0)
1652 init_cmap_grid(&sys->ffparams.cmap_grid, plist->nc, plist->grid_spacing);
1653 setup_cmap(plist->grid_spacing, plist->nc, plist->cmap, &sys->ffparams.cmap_grid);
1656 set_wall_atomtype(atype, opts, ir, wi);
1659 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1660 ntype = get_atomtype_ntypes(atype);
1663 if (ir->implicit_solvent != eisNO)
1665 /* Now we have renumbered the atom types, we can check the GBSA params */
1666 check_gbsa_params(ir, atype);
1668 /* Check that all atoms that have charge and/or LJ-parameters also have
1669 * sensible GB-parameters
1671 check_gbsa_params_charged(sys, atype);
1674 /* PELA: Copy the atomtype data to the topology atomtype list */
1675 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1679 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1684 fprintf(stderr, "converting bonded parameters...\n");
1687 ntype = get_atomtype_ntypes(atype);
1688 convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
1692 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1695 /* set ptype to VSite for virtual sites */
1696 for (mt = 0; mt < sys->nmoltype; mt++)
1698 set_vsites_ptype(FALSE, &sys->moltype[mt]);
1702 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1704 /* Check velocity for virtual sites and shells */
1707 check_vel(sys, state.v);
1713 for (i = 0; i < sys->nmoltype; i++)
1715 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
1718 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
1720 check_bonds_timestep(sys, ir->delta_t, wi);
1723 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
1725 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.");
1728 check_warning_error(wi, FARGS);
1732 fprintf(stderr, "initialising group options...\n");
1734 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
1736 bGenVel ? state.v : NULL,
1739 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_drift > 0 &&
1742 if (EI_DYNAMICS(ir->eI) &&
1743 !(EI_MD(ir->eI) && ir->etc == etcNO) &&
1744 inputrec2nboundeddim(ir) == 3)
1746 set_verlet_buffer(sys, ir, state.box, ir->verletbuf_drift, wi);
1750 /* Init the temperature coupling state */
1751 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1755 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
1757 check_eg_vs_cg(sys);
1761 pr_symtab(debug, 0, "After index", &sys->symtab);
1763 triple_check(mdparin, ir, sys, wi);
1764 close_symtab(&sys->symtab);
1767 pr_symtab(debug, 0, "After close", &sys->symtab);
1770 /* make exclusions between QM atoms */
1773 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1775 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1779 generate_qmexcl(sys, ir, wi);
1783 if (ftp2bSet(efTRN, NFILE, fnm))
1787 fprintf(stderr, "getting data from old trajectory ...\n");
1789 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
1790 bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
1793 if (ir->ePBC == epbcXY && ir->nwall != 2)
1795 clear_rvec(state.box[ZZ]);
1798 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1800 set_warning_line(wi, mdparin, -1);
1801 check_chargegroup_radii(sys, ir, state.x, wi);
1804 if (EEL_FULL(ir->coulombtype))
1806 /* Calculate the optimal grid dimensions */
1807 copy_mat(state.box, box);
1808 if (ir->ePBC == epbcXY && ir->nwall == 2)
1810 svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
1812 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
1814 /* Mark fourier_spacing as not used */
1815 ir->fourier_spacing = 0;
1817 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
1819 set_warning_line(wi, mdparin, -1);
1820 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
1822 max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
1823 &(ir->nkx), &(ir->nky), &(ir->nkz));
1826 /* MRS: eventually figure out better logic for initializing the fep
1827 values that makes declaring the lambda and declaring the state not
1828 potentially conflict if not handled correctly. */
1829 if (ir->efep != efepNO)
1831 state.fep_state = ir->fepvals->init_fep_state;
1832 for (i = 0; i < efptNR; i++)
1834 /* init_lambda trumps state definitions*/
1835 if (ir->fepvals->init_lambda >= 0)
1837 state.lambda[i] = ir->fepvals->init_lambda;
1841 if (ir->fepvals->all_lambda[i] == NULL)
1843 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
1847 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
1853 if (ir->ePull != epullNO)
1855 set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
1860 set_reference_positions(ir->rot, sys, state.x, state.box,
1861 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
1865 /* reset_multinr(sys); */
1867 if (EEL_PME(ir->coulombtype))
1869 float ratio = pme_load_estimate(sys, ir, state.box);
1870 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
1871 /* With free energy we might need to do PME both for the A and B state
1872 * charges. This will double the cost, but the optimal performance will
1873 * then probably be at a slightly larger cut-off and grid spacing.
1875 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
1876 (ir->efep != efepNO && ratio > 2.0/3.0))
1879 "The optimal PME mesh load for parallel simulations is below 0.5\n"
1880 "and for highly parallel simulations between 0.25 and 0.33,\n"
1881 "for higher performance, increase the cut-off and the PME grid spacing.\n");
1882 if (ir->efep != efepNO)
1885 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
1891 char warn_buf[STRLEN];
1892 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
1893 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
1896 set_warning_line(wi, mdparin, -1);
1897 warning_note(wi, warn_buf);
1901 printf("%s\n", warn_buf);
1907 fprintf(stderr, "writing run input file...\n");
1910 done_warning(wi, FARGS);
1912 write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);