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50 #include <sys/types.h>
52 #include "gromacs/awh/read-params.h"
53 #include "gromacs/commandline/pargs.h"
54 #include "gromacs/ewald/ewald-utils.h"
55 #include "gromacs/ewald/pme.h"
56 #include "gromacs/fft/calcgrid.h"
57 #include "gromacs/fileio/confio.h"
58 #include "gromacs/fileio/enxio.h"
59 #include "gromacs/fileio/tpxio.h"
60 #include "gromacs/fileio/trxio.h"
61 #include "gromacs/fileio/warninp.h"
62 #include "gromacs/gmxpreprocess/add_par.h"
63 #include "gromacs/gmxpreprocess/convparm.h"
64 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
65 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
66 #include "gromacs/gmxpreprocess/grompp-impl.h"
67 #include "gromacs/gmxpreprocess/notset.h"
68 #include "gromacs/gmxpreprocess/readir.h"
69 #include "gromacs/gmxpreprocess/tomorse.h"
70 #include "gromacs/gmxpreprocess/topio.h"
71 #include "gromacs/gmxpreprocess/toputil.h"
72 #include "gromacs/gmxpreprocess/vsite_parm.h"
73 #include "gromacs/imd/imd.h"
74 #include "gromacs/math/functions.h"
75 #include "gromacs/math/invertmatrix.h"
76 #include "gromacs/math/units.h"
77 #include "gromacs/math/vec.h"
78 #include "gromacs/mdlib/calc_verletbuf.h"
79 #include "gromacs/mdlib/compute_io.h"
80 #include "gromacs/mdlib/constr.h"
81 #include "gromacs/mdlib/perf_est.h"
82 #include "gromacs/mdlib/qmmm.h"
83 #include "gromacs/mdlib/sim_util.h"
84 #include "gromacs/mdrunutility/mdmodules.h"
85 #include "gromacs/mdtypes/inputrec.h"
86 #include "gromacs/mdtypes/md_enums.h"
87 #include "gromacs/mdtypes/nblist.h"
88 #include "gromacs/mdtypes/state.h"
89 #include "gromacs/pbcutil/boxutilities.h"
90 #include "gromacs/pbcutil/pbc.h"
91 #include "gromacs/pulling/pull.h"
92 #include "gromacs/random/seed.h"
93 #include "gromacs/topology/ifunc.h"
94 #include "gromacs/topology/mtop_util.h"
95 #include "gromacs/topology/symtab.h"
96 #include "gromacs/topology/topology.h"
97 #include "gromacs/trajectory/trajectoryframe.h"
98 #include "gromacs/utility/arraysize.h"
99 #include "gromacs/utility/cstringutil.h"
100 #include "gromacs/utility/exceptions.h"
101 #include "gromacs/utility/fatalerror.h"
102 #include "gromacs/utility/futil.h"
103 #include "gromacs/utility/gmxassert.h"
104 #include "gromacs/utility/smalloc.h"
105 #include "gromacs/utility/snprintf.h"
107 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
112 /* For all the molecule types */
113 for (i = 0; i < nrmols; i++)
115 n += mols[i].plist[ifunc].nr;
116 mols[i].plist[ifunc].nr = 0;
121 static int check_atom_names(const char *fn1, const char *fn2,
122 gmx_mtop_t *mtop, const t_atoms *at)
124 int m, i, j, nmismatch;
126 #define MAXMISMATCH 20
128 if (mtop->natoms != at->nr)
130 gmx_incons("comparing atom names");
135 for (const gmx_molblock_t &molb : mtop->molblock)
137 tat = &mtop->moltype[molb.type].atoms;
138 for (m = 0; m < molb.nmol; m++)
140 for (j = 0; j < tat->nr; j++)
142 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
144 if (nmismatch < MAXMISMATCH)
147 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
148 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
150 else if (nmismatch == MAXMISMATCH)
152 fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
164 static void check_eg_vs_cg(gmx_mtop_t *mtop)
166 int astart, m, cg, j, firstj;
167 unsigned char firsteg, eg;
170 /* Go through all the charge groups and make sure all their
171 * atoms are in the same energy group.
175 for (const gmx_molblock_t &molb : mtop->molblock)
177 molt = &mtop->moltype[molb.type];
178 for (m = 0; m < molb.nmol; m++)
180 for (cg = 0; cg < molt->cgs.nr; cg++)
182 /* Get the energy group of the first atom in this charge group */
183 firstj = astart + molt->cgs.index[cg];
184 firsteg = getGroupType(mtop->groups, egcENER, firstj);
185 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
187 eg = getGroupType(mtop->groups, egcENER, astart+j);
190 gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
191 firstj+1, astart+j+1, cg+1, *molt->name);
195 astart += molt->atoms.nr;
200 static void check_cg_sizes(const char *topfn, const t_block *cgs, warninp *wi)
203 char warn_buf[STRLEN];
206 for (cg = 0; cg < cgs->nr; cg++)
208 maxsize = std::max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
211 if (maxsize > MAX_CHARGEGROUP_SIZE)
213 gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
215 else if (maxsize > 10)
217 set_warning_line(wi, topfn, -1);
219 "The largest charge group contains %d atoms.\n"
220 "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"
221 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
222 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
224 warning_note(wi, warn_buf);
228 static void check_bonds_timestep(const gmx_mtop_t *mtop, double dt, warninp *wi)
230 /* This check is not intended to ensure accurate integration,
231 * rather it is to signal mistakes in the mdp settings.
232 * A common mistake is to forget to turn on constraints
233 * for MD after energy minimization with flexible bonds.
234 * This check can also detect too large time steps for flexible water
235 * models, but such errors will often be masked by the constraints
236 * mdp options, which turns flexible water into water with bond constraints,
237 * but without an angle constraint. Unfortunately such incorrect use
238 * of water models can not easily be detected without checking
239 * for specific model names.
241 * The stability limit of leap-frog or velocity verlet is 4.44 steps
242 * per oscillational period.
243 * But accurate bonds distributions are lost far before that limit.
244 * To allow relatively common schemes (although not common with Gromacs)
245 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
246 * we set the note limit to 10.
248 int min_steps_warn = 5;
249 int min_steps_note = 10;
251 int i, a1, a2, w_a1, w_a2, j;
252 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
253 bool bFound, bWater, bWarn;
254 char warn_buf[STRLEN];
256 /* Get the interaction parameters */
257 gmx::ArrayRef<const t_iparams> ip = mtop->ffparams.iparams;
259 twopi2 = gmx::square(2*M_PI);
261 limit2 = gmx::square(min_steps_note*dt);
266 const gmx_moltype_t *w_moltype = nullptr;
267 for (const gmx_moltype_t &moltype : mtop->moltype)
269 const t_atom *atom = moltype.atoms.atom;
270 const InteractionLists &ilist = moltype.ilist;
271 const InteractionList &ilc = ilist[F_CONSTR];
272 const InteractionList &ils = ilist[F_SETTLE];
273 for (ftype = 0; ftype < F_NRE; ftype++)
275 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
280 const InteractionList &ilb = ilist[ftype];
281 for (i = 0; i < ilb.size(); i += 3)
283 fc = ip[ilb.iatoms[i]].harmonic.krA;
284 re = ip[ilb.iatoms[i]].harmonic.rA;
285 if (ftype == F_G96BONDS)
287 /* Convert squared sqaure fc to harmonic fc */
290 a1 = ilb.iatoms[i+1];
291 a2 = ilb.iatoms[i+2];
294 if (fc > 0 && m1 > 0 && m2 > 0)
296 period2 = twopi2*m1*m2/((m1 + m2)*fc);
300 period2 = GMX_FLOAT_MAX;
304 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
305 fc, m1, m2, std::sqrt(period2));
307 if (period2 < limit2)
310 for (j = 0; j < ilc.size(); j += 3)
312 if ((ilc.iatoms[j+1] == a1 && ilc.iatoms[j+2] == a2) ||
313 (ilc.iatoms[j+1] == a2 && ilc.iatoms[j+2] == a1))
318 for (j = 0; j < ils.size(); j += 4)
320 if ((a1 == ils.iatoms[j+1] || a1 == ils.iatoms[j+2] || a1 == ils.iatoms[j+3]) &&
321 (a2 == ils.iatoms[j+1] || a2 == ils.iatoms[j+2] || a2 == ils.iatoms[j+3]))
327 (w_moltype == nullptr || period2 < w_period2))
329 w_moltype = &moltype;
339 if (w_moltype != nullptr)
341 bWarn = (w_period2 < gmx::square(min_steps_warn*dt));
342 /* A check that would recognize most water models */
343 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
344 w_moltype->atoms.nr <= 5);
345 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"
348 w_a1+1, *w_moltype->atoms.atomname[w_a1],
349 w_a2+1, *w_moltype->atoms.atomname[w_a2],
350 std::sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
352 "Maybe you asked for fexible water." :
353 "Maybe you forgot to change the constraints mdp option.");
356 warning(wi, warn_buf);
360 warning_note(wi, warn_buf);
365 static void check_vel(gmx_mtop_t *mtop, rvec v[])
367 for (const AtomProxy atomP : AtomRange(*mtop))
369 const t_atom &local = atomP.atom();
370 int i = atomP.globalAtomNumber();
371 if (local.ptype == eptShell ||
372 local.ptype == eptBond ||
373 local.ptype == eptVSite)
380 static void check_shells_inputrec(gmx_mtop_t *mtop,
385 char warn_buf[STRLEN];
387 for (const AtomProxy atomP : AtomRange(*mtop))
389 const t_atom &local = atomP.atom();
390 if (local.ptype == eptShell ||
391 local.ptype == eptBond)
396 if ((nshells > 0) && (ir->nstcalcenergy != 1))
398 set_warning_line(wi, "unknown", -1);
399 snprintf(warn_buf, STRLEN,
400 "There are %d shells, changing nstcalcenergy from %d to 1",
401 nshells, ir->nstcalcenergy);
402 ir->nstcalcenergy = 1;
403 warning(wi, warn_buf);
407 /* TODO Decide whether this function can be consolidated with
408 * gmx_mtop_ftype_count */
409 static int nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
412 for (const gmx_molblock_t &molb : mtop->molblock)
414 nint += molb.nmol*mi[molb.type].plist[ftype].nr;
420 /* This routine reorders the molecule type array
421 * in the order of use in the molblocks,
422 * unused molecule types are deleted.
424 static void renumber_moltypes(gmx_mtop_t *sys,
425 int *nmolinfo, t_molinfo **molinfo)
430 snew(order, *nmolinfo);
432 for (gmx_molblock_t &molblock : sys->molblock)
435 for (i = 0; i < norder; i++)
437 if (order[i] == molblock.type)
444 /* This type did not occur yet, add it */
445 order[norder] = molblock.type;
446 /* Renumber the moltype in the topology */
452 /* We still need to reorder the molinfo structs */
454 for (int mi = 0; mi < *nmolinfo; mi++)
457 for (i = 0; i < norder; i++)
466 done_mi(&(*molinfo)[mi]);
470 minew[i] = (*molinfo)[mi];
480 static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
482 mtop->moltype.resize(nmi);
483 for (int m = 0; m < nmi; m++)
485 gmx_moltype_t &molt = mtop->moltype[m];
486 molt.name = mi[m].name;
487 molt.atoms = mi[m].atoms;
488 /* ilists are copied later */
489 molt.cgs = mi[m].cgs;
490 molt.excls = mi[m].excls;
495 new_status(const char *topfile, const char *topppfile, const char *confin,
496 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
497 bool bGenVel, bool bVerbose, t_state *state,
498 gpp_atomtype *atype, gmx_mtop_t *sys,
499 int *nmi, t_molinfo **mi, t_molinfo **intermolecular_interactions,
501 int *comb, double *reppow, real *fudgeQQ,
505 t_molinfo *molinfo = nullptr;
506 std::vector<gmx_molblock_t> molblock;
507 int i, nrmols, nmismatch;
508 bool ffParametrizedWithHBondConstraints;
510 char warn_buf[STRLEN];
512 /* TOPOLOGY processing */
513 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
514 plist, comb, reppow, fudgeQQ,
515 atype, &nrmols, &molinfo, intermolecular_interactions,
518 &ffParametrizedWithHBondConstraints,
521 sys->molblock.clear();
524 for (const gmx_molblock_t &molb : molblock)
526 if (!sys->molblock.empty() &&
527 molb.type == sys->molblock.back().type)
529 /* Merge consecutive blocks with the same molecule type */
530 sys->molblock.back().nmol += molb.nmol;
532 else if (molb.nmol > 0)
534 /* Add a new molblock to the topology */
535 sys->molblock.push_back(molb);
537 sys->natoms += molb.nmol*molinfo[sys->molblock.back().type].atoms.nr;
539 if (sys->molblock.empty())
541 gmx_fatal(FARGS, "No molecules were defined in the system");
544 renumber_moltypes(sys, &nrmols, &molinfo);
548 convert_harmonics(nrmols, molinfo, atype);
551 if (ir->eDisre == edrNone)
553 i = rm_interactions(F_DISRES, nrmols, molinfo);
556 set_warning_line(wi, "unknown", -1);
557 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
558 warning_note(wi, warn_buf);
563 i = rm_interactions(F_ORIRES, nrmols, molinfo);
566 set_warning_line(wi, "unknown", -1);
567 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
568 warning_note(wi, warn_buf);
572 /* Copy structures from msys to sys */
573 molinfo2mtop(nrmols, molinfo, sys);
575 gmx_mtop_finalize(sys);
577 /* Discourage using the, previously common, setup of applying constraints
578 * to all bonds with force fields that have been parametrized with H-bond
579 * constraints only. Do not print note with large timesteps or vsites.
581 if (opts->nshake == eshALLBONDS &&
582 ffParametrizedWithHBondConstraints &&
583 ir->delta_t < 0.0026 &&
584 gmx_mtop_ftype_count(sys, F_VSITE3FD) == 0)
586 set_warning_line(wi, "unknown", -1);
587 warning_note(wi, "You are using constraints on all bonds, whereas the forcefield "
588 "has been parametrized only with constraints involving hydrogen atoms. "
589 "We suggest using constraints = h-bonds instead, this will also improve performance.");
592 /* COORDINATE file processing */
595 fprintf(stderr, "processing coordinates...\n");
602 read_tps_conf(confin, conftop, nullptr, &x, &v, state->box, FALSE);
603 state->natoms = conftop->atoms.nr;
604 if (state->natoms != sys->natoms)
606 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
607 " does not match topology (%s, %d)",
608 confin, state->natoms, topfile, sys->natoms);
610 /* It would be nice to get rid of the copies below, but we don't know
611 * a priori if the number of atoms in confin matches what we expect.
613 state->flags |= (1 << estX);
616 state->flags |= (1 << estV);
618 state_change_natoms(state, state->natoms);
619 std::copy(x, x+state->natoms, state->x.data());
623 std::copy(v, v+state->natoms, state->v.data());
626 /* This call fixes the box shape for runs with pressure scaling */
627 set_box_rel(ir, state);
629 nmismatch = check_atom_names(topfile, confin, sys, &conftop->atoms);
635 sprintf(buf, "%d non-matching atom name%s\n"
636 "atom names from %s will be used\n"
637 "atom names from %s will be ignored\n",
638 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
642 /* If using the group scheme, make sure charge groups are made whole to avoid errors
643 * in calculating charge group size later on
645 if (ir->cutoff_scheme == ecutsGROUP && ir->ePBC != epbcNONE)
647 // Need temporary rvec for coordinates
648 do_pbc_first_mtop(nullptr, ir->ePBC, state->box, sys, state->x.rvec_array());
651 /* Do more checks, mostly related to constraints */
654 fprintf(stderr, "double-checking input for internal consistency...\n");
657 bool bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
658 nint_ftype(sys, molinfo, F_CONSTRNC));
659 bool bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
660 double_check(ir, state->box,
661 bHasNormalConstraints,
670 snew(mass, state->natoms);
671 for (const AtomProxy atomP : AtomRange(*sys))
673 const t_atom &local = atomP.atom();
674 int i = atomP.globalAtomNumber();
678 if (opts->seed == -1)
680 opts->seed = static_cast<int>(gmx::makeRandomSeed());
681 fprintf(stderr, "Setting gen_seed to %d\n", opts->seed);
683 state->flags |= (1 << estV);
684 maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array());
686 stop_cm(stdout, state->natoms, mass, state->x.rvec_array(), state->v.rvec_array());
694 static void copy_state(const char *slog, t_trxframe *fr,
695 bool bReadVel, t_state *state,
698 if (fr->not_ok & FRAME_NOT_OK)
700 gmx_fatal(FARGS, "Can not start from an incomplete frame");
704 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
708 std::copy(fr->x, fr->x+state->natoms, state->x.data());
713 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
715 std::copy(fr->v, fr->v+state->natoms, state->v.data());
719 copy_mat(fr->box, state->box);
722 *use_time = fr->time;
725 static void cont_status(const char *slog, const char *ener,
726 bool bNeedVel, bool bGenVel, real fr_time,
727 t_inputrec *ir, t_state *state,
729 const gmx_output_env_t *oenv)
730 /* If fr_time == -1 read the last frame available which is complete */
737 bReadVel = (bNeedVel && !bGenVel);
740 "Reading Coordinates%s and Box size from old trajectory\n",
741 bReadVel ? ", Velocities" : "");
744 fprintf(stderr, "Will read whole trajectory\n");
748 fprintf(stderr, "Will read till time %g\n", fr_time);
754 fprintf(stderr, "Velocities generated: "
755 "ignoring velocities in input trajectory\n");
757 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
761 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
767 "WARNING: Did not find a frame with velocities in file %s,\n"
768 " all velocities will be set to zero!\n\n", slog);
769 for (auto &vi : makeArrayRef(state->v))
774 /* Search for a frame without velocities */
776 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
780 state->natoms = fr.natoms;
782 if (sys->natoms != state->natoms)
784 gmx_fatal(FARGS, "Number of atoms in Topology "
785 "is not the same as in Trajectory");
787 copy_state(slog, &fr, bReadVel, state, &use_time);
789 /* Find the appropriate frame */
790 while ((fr_time == -1 || fr.time < fr_time) &&
791 read_next_frame(oenv, fp, &fr))
793 copy_state(slog, &fr, bReadVel, state, &use_time);
798 /* Set the relative box lengths for preserving the box shape.
799 * Note that this call can lead to differences in the last bit
800 * with respect to using gmx convert-tpr to create a [REF].tpx[ref] file.
802 set_box_rel(ir, state);
804 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
805 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
807 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
809 get_enx_state(ener, use_time, &sys->groups, ir, state);
810 preserve_box_shape(ir, state->box_rel, state->boxv);
814 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
816 int rc_scaling, int ePBC,
826 int natoms, npbcdim = 0;
827 char warn_buf[STRLEN];
828 int a, i, ai, j, k, nat_molb;
833 read_tps_conf(fn, top, nullptr, &x, &v, box, FALSE);
834 natoms = top->atoms.nr;
837 if (natoms != mtop->natoms)
839 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, std::min(mtop->natoms, natoms), fn);
840 warning(wi, warn_buf);
843 npbcdim = ePBC2npbcdim(ePBC);
845 if (rc_scaling != erscNO)
847 copy_mat(box, invbox);
848 for (j = npbcdim; j < DIM; j++)
850 clear_rvec(invbox[j]);
853 gmx::invertBoxMatrix(invbox, invbox);
856 /* Copy the reference coordinates to mtop */
860 snew(hadAtom, natoms);
861 for (gmx_molblock_t &molb : mtop->molblock)
863 nat_molb = molb.nmol*mtop->moltype[molb.type].atoms.nr;
864 pr = &(molinfo[molb.type].plist[F_POSRES]);
865 prfb = &(molinfo[molb.type].plist[F_FBPOSRES]);
866 if (pr->nr > 0 || prfb->nr > 0)
868 atom = mtop->moltype[molb.type].atoms.atom;
869 for (i = 0; (i < pr->nr); i++)
871 ai = pr->param[i].ai();
874 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
875 ai+1, *molinfo[molb.type].name, fn, natoms);
878 if (rc_scaling == erscCOM)
880 /* Determine the center of mass of the posres reference coordinates */
881 for (j = 0; j < npbcdim; j++)
883 sum[j] += atom[ai].m*x[a+ai][j];
885 totmass += atom[ai].m;
888 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
889 for (i = 0; (i < prfb->nr); i++)
891 ai = prfb->param[i].ai();
894 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
895 ai+1, *molinfo[molb.type].name, fn, natoms);
897 if (rc_scaling == erscCOM && !hadAtom[ai])
899 /* Determine the center of mass of the posres reference coordinates */
900 for (j = 0; j < npbcdim; j++)
902 sum[j] += atom[ai].m*x[a+ai][j];
904 totmass += atom[ai].m;
909 molb.posres_xA.resize(nat_molb);
910 for (i = 0; i < nat_molb; i++)
912 copy_rvec(x[a+i], molb.posres_xA[i]);
917 molb.posres_xB.resize(nat_molb);
918 for (i = 0; i < nat_molb; i++)
920 copy_rvec(x[a+i], molb.posres_xB[i]);
926 if (rc_scaling == erscCOM)
930 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
932 for (j = 0; j < npbcdim; j++)
934 com[j] = sum[j]/totmass;
936 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]);
939 if (rc_scaling != erscNO)
941 GMX_ASSERT(npbcdim <= DIM, "Only DIM dimensions can have PBC");
943 for (gmx_molblock_t &molb : mtop->molblock)
945 nat_molb = molb.nmol*mtop->moltype[molb.type].atoms.nr;
946 if (!molb.posres_xA.empty() || !molb.posres_xB.empty())
948 std::vector<gmx::RVec> &xp = (!bTopB ? molb.posres_xA : molb.posres_xB);
949 for (i = 0; i < nat_molb; i++)
951 for (j = 0; j < npbcdim; j++)
953 if (rc_scaling == erscALL)
955 /* Convert from Cartesian to crystal coordinates */
956 xp[i][j] *= invbox[j][j];
957 for (k = j+1; k < npbcdim; k++)
959 xp[i][j] += invbox[k][j]*xp[i][k];
962 else if (rc_scaling == erscCOM)
964 /* Subtract the center of mass */
972 if (rc_scaling == erscCOM)
974 /* Convert the COM from Cartesian to crystal coordinates */
975 for (j = 0; j < npbcdim; j++)
977 com[j] *= invbox[j][j];
978 for (k = j+1; k < npbcdim; k++)
980 com[j] += invbox[k][j]*com[k];
991 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
992 const char *fnA, const char *fnB,
993 int rc_scaling, int ePBC,
997 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
998 /* It is safer to simply read the b-state posres rather than trying
999 * to be smart and copy the positions.
1001 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
1004 static void set_wall_atomtype(gpp_atomtype *at, t_gromppopts *opts,
1005 t_inputrec *ir, warninp *wi)
1008 char warn_buf[STRLEN];
1012 fprintf(stderr, "Searching the wall atom type(s)\n");
1014 for (i = 0; i < ir->nwall; i++)
1016 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
1017 if (ir->wall_atomtype[i] == NOTSET)
1019 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
1020 warning_error(wi, warn_buf);
1025 static int nrdf_internal(t_atoms *atoms)
1030 for (i = 0; i < atoms->nr; i++)
1032 /* Vsite ptype might not be set here yet, so also check the mass */
1033 if ((atoms->atom[i].ptype == eptAtom ||
1034 atoms->atom[i].ptype == eptNucleus)
1035 && atoms->atom[i].m > 0)
1042 case 0: nrdf = 0; break;
1043 case 1: nrdf = 0; break;
1044 case 2: nrdf = 1; break;
1045 default: nrdf = nmass*3 - 6; break;
1052 spline1d( double dx,
1064 for (i = 1; i < n-1; i++)
1066 p = 0.5*y2[i-1]+2.0;
1068 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1069 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1074 for (i = n-2; i >= 0; i--)
1076 y2[i] = y2[i]*y2[i+1]+u[i];
1082 interpolate1d( double xmin,
1093 ix = static_cast<int>((x-xmin)/dx);
1095 a = (xmin+(ix+1)*dx-x)/dx;
1096 b = (x-xmin-ix*dx)/dx;
1098 *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;
1099 *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];
1104 setup_cmap (int grid_spacing,
1107 gmx_cmap_t * cmap_grid)
1109 int i, j, k, ii, jj, kk, idx;
1111 double dx, xmin, v, v1, v2, v12;
1114 std::vector<double> tmp_u(2*grid_spacing, 0.0);
1115 std::vector<double> tmp_u2(2*grid_spacing, 0.0);
1116 std::vector<double> tmp_yy(2*grid_spacing, 0.0);
1117 std::vector<double> tmp_y1(2*grid_spacing, 0.0);
1118 std::vector<double> tmp_t2(2*grid_spacing*2*grid_spacing, 0.0);
1119 std::vector<double> tmp_grid(2*grid_spacing*2*grid_spacing, 0.0);
1121 dx = 360.0/grid_spacing;
1122 xmin = -180.0-dx*grid_spacing/2;
1124 for (kk = 0; kk < nc; kk++)
1126 /* Compute an offset depending on which cmap we are using
1127 * Offset will be the map number multiplied with the
1128 * grid_spacing * grid_spacing * 2
1130 offset = kk * grid_spacing * grid_spacing * 2;
1132 for (i = 0; i < 2*grid_spacing; i++)
1134 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1136 for (j = 0; j < 2*grid_spacing; j++)
1138 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1139 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1143 for (i = 0; i < 2*grid_spacing; i++)
1145 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u.data(), &(tmp_t2[2*grid_spacing*i]));
1148 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1150 ii = i-grid_spacing/2;
1153 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1155 jj = j-grid_spacing/2;
1158 for (k = 0; k < 2*grid_spacing; k++)
1160 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1161 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1164 spline1d(dx, tmp_yy.data(), 2*grid_spacing, tmp_u.data(), tmp_u2.data());
1165 interpolate1d(xmin, dx, tmp_yy.data(), tmp_u2.data(), phi, &v, &v1);
1166 spline1d(dx, tmp_y1.data(), 2*grid_spacing, tmp_u.data(), tmp_u2.data());
1167 interpolate1d(xmin, dx, tmp_y1.data(), tmp_u2.data(), phi, &v2, &v12);
1169 idx = ii*grid_spacing+jj;
1170 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1171 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1172 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1173 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1179 static void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1183 cmap_grid->grid_spacing = grid_spacing;
1184 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1186 cmap_grid->cmapdata.resize(ngrid);
1188 for (i = 0; i < ngrid; i++)
1190 cmap_grid->cmapdata[i].cmap.resize(4*nelem);
1195 static int count_constraints(const gmx_mtop_t *mtop, t_molinfo *mi, warninp *wi)
1197 int count, count_mol, i;
1202 for (const gmx_molblock_t &molb : mtop->molblock)
1205 plist = mi[molb.type].plist;
1207 for (i = 0; i < F_NRE; i++)
1211 count_mol += 3*plist[i].nr;
1213 else if (interaction_function[i].flags & IF_CONSTRAINT)
1215 count_mol += plist[i].nr;
1219 if (count_mol > nrdf_internal(&mi[molb.type].atoms))
1222 "Molecule type '%s' has %d constraints.\n"
1223 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1224 *mi[molb.type].name, count_mol,
1225 nrdf_internal(&mi[molb.type].atoms));
1228 count += molb.nmol*count_mol;
1234 static real calc_temp(const gmx_mtop_t *mtop,
1235 const t_inputrec *ir,
1239 for (const AtomProxy atomP : AtomRange(*mtop))
1241 const t_atom &local = atomP.atom();
1242 int i = atomP.globalAtomNumber();
1243 sum_mv2 += local.m*norm2(v[i]);
1247 for (int g = 0; g < ir->opts.ngtc; g++)
1249 nrdf += ir->opts.nrdf[g];
1252 return sum_mv2/(nrdf*BOLTZ);
1255 static real get_max_reference_temp(const t_inputrec *ir,
1264 for (i = 0; i < ir->opts.ngtc; i++)
1266 if (ir->opts.tau_t[i] < 0)
1272 ref_t = std::max(ref_t, ir->opts.ref_t[i]);
1280 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.",
1288 /* Checks if there are unbound atoms in moleculetype molt.
1289 * Prints a note for each unbound atoms and a warning if any is present.
1291 static void checkForUnboundAtoms(const gmx_moltype_t *molt,
1295 const t_atoms *atoms = &molt->atoms;
1299 /* Only one atom, there can't be unbound atoms */
1303 std::vector<int> count(atoms->nr, 0);
1305 for (int ftype = 0; ftype < F_NRE; ftype++)
1307 if (((interaction_function[ftype].flags & IF_BOND) && ftype != F_CONNBONDS) ||
1308 (interaction_function[ftype].flags & IF_CONSTRAINT) ||
1311 const InteractionList &il = molt->ilist[ftype];
1312 const int nral = NRAL(ftype);
1314 for (int i = 0; i < il.size(); i += 1 + nral)
1316 for (int j = 0; j < nral; j++)
1318 count[il.iatoms[i + 1 + j]]++;
1324 int numDanglingAtoms = 0;
1325 for (int a = 0; a < atoms->nr; a++)
1327 if (atoms->atom[a].ptype != eptVSite &&
1332 fprintf(stderr, "\nAtom %d '%s' in moleculetype '%s' is not bound by a potential or constraint to any other atom in the same moleculetype.\n",
1333 a + 1, *atoms->atomname[a], *molt->name);
1339 if (numDanglingAtoms > 0)
1342 sprintf(buf, "In moleculetype '%s' %d atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.",
1343 *molt->name, numDanglingAtoms);
1344 warning_note(wi, buf);
1348 /* Checks all moleculetypes for unbound atoms */
1349 static void checkForUnboundAtoms(const gmx_mtop_t *mtop,
1353 for (const gmx_moltype_t &molt : mtop->moltype)
1355 checkForUnboundAtoms(&molt, bVerbose, wi);
1359 /*! \brief Checks if there are decoupled modes in moleculetype \p molt.
1361 * The specific decoupled modes this routine check for are angle modes
1362 * where the two bonds are constrained and the atoms a both ends are only
1363 * involved in a single constraint; the mass of the two atoms needs to
1364 * differ by more than \p massFactorThreshold.
1366 static bool haveDecoupledModeInMol(const gmx_moltype_t &molt,
1367 gmx::ArrayRef<const t_iparams> iparams,
1368 real massFactorThreshold)
1370 if (molt.ilist[F_CONSTR].size() == 0 &&
1371 molt.ilist[F_CONSTRNC].size() == 0)
1376 const t_atom * atom = molt.atoms.atom;
1378 t_blocka atomToConstraints =
1379 gmx::make_at2con(molt, iparams,
1380 gmx::FlexibleConstraintTreatment::Exclude);
1382 bool haveDecoupledMode = false;
1383 for (int ftype = 0; ftype < F_NRE; ftype++)
1385 if (interaction_function[ftype].flags & IF_ATYPE)
1387 const int nral = NRAL(ftype);
1388 const InteractionList &il = molt.ilist[ftype];
1389 for (int i = 0; i < il.size(); i += 1 + nral)
1391 /* Here we check for the mass difference between the atoms
1392 * at both ends of the angle, that the atoms at the ends have
1393 * 1 contraint and the atom in the middle at least 3; we check
1394 * that the 3 atoms are linked by constraints below.
1395 * We check for at least three constraints for the middle atom,
1396 * since with only the two bonds in the angle, we have 3-atom
1397 * molecule, which has much more thermal exhange in this single
1398 * angle mode than molecules with more atoms.
1399 * Note that this check also catches molecules where more atoms
1400 * are connected to one or more atoms in the angle, but by
1401 * bond potentials instead of angles. But such cases will not
1402 * occur in "normal" molecules and it doesn't hurt running
1403 * those with higher accuracy settings as well.
1405 int a0 = il.iatoms[1 + i];
1406 int a1 = il.iatoms[1 + i + 1];
1407 int a2 = il.iatoms[1 + i + 2];
1408 if ((atom[a0].m > atom[a2].m*massFactorThreshold ||
1409 atom[a2].m > atom[a0].m*massFactorThreshold) &&
1410 atomToConstraints.index[a0 + 1] - atomToConstraints.index[a0] == 1 &&
1411 atomToConstraints.index[a2 + 1] - atomToConstraints.index[a2] == 1 &&
1412 atomToConstraints.index[a1 + 1] - atomToConstraints.index[a1] >= 3)
1414 int constraint0 = atomToConstraints.a[atomToConstraints.index[a0]];
1415 int constraint2 = atomToConstraints.a[atomToConstraints.index[a2]];
1417 bool foundAtom0 = false;
1418 bool foundAtom2 = false;
1419 for (int conIndex = atomToConstraints.index[a1]; conIndex < atomToConstraints.index[a1 + 1]; conIndex++)
1421 if (atomToConstraints.a[conIndex] == constraint0)
1425 if (atomToConstraints.a[conIndex] == constraint2)
1430 if (foundAtom0 && foundAtom2)
1432 haveDecoupledMode = true;
1439 done_blocka(&atomToConstraints);
1441 return haveDecoupledMode;
1444 /*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.
1446 * When decoupled modes are present and the accuray in insufficient,
1447 * this routine issues a warning if the accuracy is insufficient.
1449 static void checkDecoupledModeAccuracy(const gmx_mtop_t *mtop,
1450 const t_inputrec *ir,
1453 /* We only have issues with decoupled modes with normal MD.
1454 * With stochastic dynamics equipartitioning is enforced strongly.
1461 /* When atoms of very different mass are involved in an angle potential
1462 * and both bonds in the angle are constrained, the dynamic modes in such
1463 * angles have very different periods and significant energy exchange
1464 * takes several nanoseconds. Thus even a small amount of error in
1465 * different algorithms can lead to violation of equipartitioning.
1466 * The parameters below are mainly based on an all-atom chloroform model
1467 * with all bonds constrained. Equipartitioning is off by more than 1%
1468 * (need to run 5-10 ns) when the difference in mass between H and Cl
1469 * is more than a factor 13 and the accuracy is less than the thresholds
1470 * given below. This has been verified on some other molecules.
1472 * Note that the buffer and shake parameters have unit length and
1473 * energy/time, respectively, so they will "only" work correctly
1474 * for atomistic force fields using MD units.
1476 const real massFactorThreshold = 13.0;
1477 const real bufferToleranceThreshold = 1e-4;
1478 const int lincsIterationThreshold = 2;
1479 const int lincsOrderThreshold = 4;
1480 const real shakeToleranceThreshold = 0.005*ir->delta_t;
1482 bool lincsWithSufficientTolerance = (ir->eConstrAlg == econtLINCS && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
1483 bool shakeWithSufficientTolerance = (ir->eConstrAlg == econtSHAKE && ir->shake_tol <= 1.1*shakeToleranceThreshold);
1484 if (ir->cutoff_scheme == ecutsVERLET &&
1485 ir->verletbuf_tol <= 1.1*bufferToleranceThreshold &&
1486 (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
1491 bool haveDecoupledMode = false;
1492 for (const gmx_moltype_t &molt : mtop->moltype)
1494 if (haveDecoupledModeInMol(molt, mtop->ffparams.iparams,
1495 massFactorThreshold))
1497 haveDecoupledMode = true;
1501 if (haveDecoupledMode)
1503 std::string message = gmx::formatString(
1504 "There are atoms at both ends of an angle, connected by constraints "
1505 "and with masses that differ by more than a factor of %g. This means "
1506 "that there are likely dynamic modes that are only very weakly coupled.",
1507 massFactorThreshold);
1508 if (ir->cutoff_scheme == ecutsVERLET)
1510 message += gmx::formatString(
1511 " To ensure good equipartitioning, you need to either not use "
1512 "constraints on all bonds (but, if possible, only on bonds involving "
1513 "hydrogens) or use integrator = %s or decrease one or more tolerances: "
1514 "verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
1515 ">= %d or SHAKE tolerance <= %g",
1517 bufferToleranceThreshold,
1518 lincsIterationThreshold, lincsOrderThreshold,
1519 shakeToleranceThreshold);
1523 message += gmx::formatString(
1524 " To ensure good equipartitioning, we suggest to switch to the %s "
1525 "cutoff-scheme, since that allows for better control over the Verlet "
1526 "buffer size and thus over the energy drift.",
1527 ecutscheme_names[ecutsVERLET]);
1529 warning(wi, message);
1533 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1541 char warn_buf[STRLEN];
1543 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1545 /* Calculate the buffer size for simple atom vs atoms list */
1546 VerletbufListSetup listSetup1x1;
1547 listSetup1x1.cluster_size_i = 1;
1548 listSetup1x1.cluster_size_j = 1;
1549 calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
1550 buffer_temp, &listSetup1x1,
1551 &n_nonlin_vsite, &rlist_1x1);
1553 /* Set the pair-list buffer size in ir */
1554 VerletbufListSetup listSetup4x4 =
1555 verletbufGetSafeListSetup(ListSetupType::CpuNoSimd);
1556 calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
1557 buffer_temp, &listSetup4x4,
1558 &n_nonlin_vsite, &ir->rlist);
1560 if (n_nonlin_vsite > 0)
1562 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);
1563 warning_note(wi, warn_buf);
1566 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1567 1, 1, rlist_1x1, rlist_1x1-std::max(ir->rvdw, ir->rcoulomb));
1569 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1570 listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j,
1571 ir->rlist, ir->rlist-std::max(ir->rvdw, ir->rcoulomb));
1573 printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
1575 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
1577 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->rlist, std::sqrt(max_cutoff2(ir->ePBC, box)));
1581 int gmx_grompp(int argc, char *argv[])
1583 const char *desc[] = {
1584 "[THISMODULE] (the gromacs preprocessor)",
1585 "reads a molecular topology file, checks the validity of the",
1586 "file, expands the topology from a molecular description to an atomic",
1587 "description. The topology file contains information about",
1588 "molecule types and the number of molecules, the preprocessor",
1589 "copies each molecule as needed. ",
1590 "There is no limitation on the number of molecule types. ",
1591 "Bonds and bond-angles can be converted into constraints, separately",
1592 "for hydrogens and heavy atoms.",
1593 "Then a coordinate file is read and velocities can be generated",
1594 "from a Maxwellian distribution if requested.",
1595 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1596 "(eg. number of MD steps, time step, cut-off), and others such as",
1597 "NEMD parameters, which are corrected so that the net acceleration",
1599 "Eventually a binary file is produced that can serve as the sole input",
1600 "file for the MD program.[PAR]",
1602 "[THISMODULE] uses the atom names from the topology file. The atom names",
1603 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1604 "warnings when they do not match the atom names in the topology.",
1605 "Note that the atom names are irrelevant for the simulation as",
1606 "only the atom types are used for generating interaction parameters.[PAR]",
1608 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1609 "etc. The preprocessor supports the following keywords::",
1612 " #ifndef VARIABLE",
1615 " #define VARIABLE",
1617 " #include \"filename\"",
1618 " #include <filename>",
1620 "The functioning of these statements in your topology may be modulated by",
1621 "using the following two flags in your [REF].mdp[ref] file::",
1623 " define = -DVARIABLE1 -DVARIABLE2",
1624 " include = -I/home/john/doe",
1626 "For further information a C-programming textbook may help you out.",
1627 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1628 "topology file written out so that you can verify its contents.[PAR]",
1630 "When using position restraints, a file with restraint coordinates",
1631 "must be supplied with [TT]-r[tt] (can be the same file as supplied",
1632 "for [TT]-c[tt]). For free energy calculations, separate reference",
1633 "coordinates for the B topology can be supplied with [TT]-rb[tt],",
1634 "otherwise they will be equal to those of the A topology.[PAR]",
1636 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1637 "The last frame with coordinates and velocities will be read,",
1638 "unless the [TT]-time[tt] option is used. Only if this information",
1639 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1640 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1641 "in your [REF].mdp[ref] file. An energy file can be supplied with",
1642 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1645 "[THISMODULE] can be used to restart simulations (preserving",
1646 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1647 "However, for simply changing the number of run steps to extend",
1648 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1649 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1650 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1651 "like output frequency, then supplying the checkpoint file to",
1652 "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
1653 "with [TT]-f[tt] is the recommended procedure. Actually preserving",
1654 "the ensemble (if possible) still requires passing the checkpoint",
1655 "file to [gmx-mdrun] [TT]-cpi[tt].[PAR]",
1657 "By default, all bonded interactions which have constant energy due to",
1658 "virtual site constructions will be removed. If this constant energy is",
1659 "not zero, this will result in a shift in the total energy. All bonded",
1660 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1661 "all constraints for distances which will be constant anyway because",
1662 "of virtual site constructions will be removed. If any constraints remain",
1663 "which involve virtual sites, a fatal error will result.[PAR]",
1665 "To verify your run input file, please take note of all warnings",
1666 "on the screen, and correct where necessary. Do also look at the contents",
1667 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1668 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1669 "with the [TT]-debug[tt] option which will give you more information",
1670 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1671 "can see the contents of the run input file with the [gmx-dump]",
1672 "program. [gmx-check] can be used to compare the contents of two",
1673 "run input files.[PAR]",
1675 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1676 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1677 "harmless, but usually they are not. The user is advised to carefully",
1678 "interpret the output messages before attempting to bypass them with",
1683 t_molinfo *mi, *intermolecular_interactions;
1684 gpp_atomtype *atype;
1689 const char *mdparin;
1691 bool bNeedVel, bGenVel;
1692 gmx_bool have_atomnumber;
1693 gmx_output_env_t *oenv;
1694 gmx_bool bVerbose = FALSE;
1696 char warn_buf[STRLEN];
1699 { efMDP, nullptr, nullptr, ffREAD },
1700 { efMDP, "-po", "mdout", ffWRITE },
1701 { efSTX, "-c", nullptr, ffREAD },
1702 { efSTX, "-r", "restraint", ffOPTRD },
1703 { efSTX, "-rb", "restraint", ffOPTRD },
1704 { efNDX, nullptr, nullptr, ffOPTRD },
1705 { efTOP, nullptr, nullptr, ffREAD },
1706 { efTOP, "-pp", "processed", ffOPTWR },
1707 { efTPR, "-o", nullptr, ffWRITE },
1708 { efTRN, "-t", nullptr, ffOPTRD },
1709 { efEDR, "-e", nullptr, ffOPTRD },
1710 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1711 { efGRO, "-imd", "imdgroup", ffOPTWR },
1712 { efTRN, "-ref", "rotref", ffOPTRW }
1714 #define NFILE asize(fnm)
1716 /* Command line options */
1717 gmx_bool bRenum = TRUE;
1718 gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1722 { "-v", FALSE, etBOOL, {&bVerbose},
1723 "Be loud and noisy" },
1724 { "-time", FALSE, etREAL, {&fr_time},
1725 "Take frame at or first after this time." },
1726 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1727 "Remove constant bonded interactions with virtual sites" },
1728 { "-maxwarn", FALSE, etINT, {&maxwarn},
1729 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1730 { "-zero", FALSE, etBOOL, {&bZero},
1731 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1732 { "-renum", FALSE, etBOOL, {&bRenum},
1733 "Renumber atomtypes and minimize number of atomtypes" }
1736 /* Parse the command line */
1737 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1738 asize(desc), desc, 0, nullptr, &oenv))
1743 /* Initiate some variables */
1744 gmx::MDModules mdModules;
1745 t_inputrec irInstance;
1746 t_inputrec *ir = &irInstance;
1748 snew(opts->include, STRLEN);
1749 snew(opts->define, STRLEN);
1751 wi = init_warning(TRUE, maxwarn);
1753 /* PARAMETER file processing */
1754 mdparin = opt2fn("-f", NFILE, fnm);
1755 set_warning_line(wi, mdparin, -1);
1758 get_ir(mdparin, opt2fn("-po", NFILE, fnm), &mdModules, ir, opts, WriteMdpHeader::yes, wi);
1760 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1764 fprintf(stderr, "checking input for internal consistency...\n");
1766 check_ir(mdparin, ir, opts, wi);
1768 if (ir->ld_seed == -1)
1770 ir->ld_seed = static_cast<int>(gmx::makeRandomSeed());
1771 fprintf(stderr, "Setting the LD random seed to %" PRId64 "\n", ir->ld_seed);
1774 if (ir->expandedvals->lmc_seed == -1)
1776 ir->expandedvals->lmc_seed = static_cast<int>(gmx::makeRandomSeed());
1777 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1780 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1781 bGenVel = (bNeedVel && opts->bGenVel);
1782 if (bGenVel && ir->bContinuation)
1785 "Generating velocities is inconsistent with attempting "
1786 "to continue a previous run. Choose only one of "
1787 "gen-vel = yes and continuation = yes.");
1788 warning_error(wi, warn_buf);
1794 atype = init_atomtype();
1797 pr_symtab(debug, 0, "Just opened", &sys.symtab);
1800 const char *fn = ftp2fn(efTOP, NFILE, fnm);
1801 if (!gmx_fexist(fn))
1803 gmx_fatal(FARGS, "%s does not exist", fn);
1807 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1808 opts, ir, bZero, bGenVel, bVerbose, &state,
1809 atype, &sys, &nmi, &mi, &intermolecular_interactions,
1810 plist, &comb, &reppow, &fudgeQQ,
1816 pr_symtab(debug, 0, "After new_status", &sys.symtab);
1820 /* set parameters for virtual site construction (not for vsiten) */
1821 for (size_t mt = 0; mt < sys.moltype.size(); mt++)
1824 set_vsites(bVerbose, &sys.moltype[mt].atoms, atype, mi[mt].plist);
1826 /* now throw away all obsolete bonds, angles and dihedrals: */
1827 /* note: constraints are ALWAYS removed */
1830 for (size_t mt = 0; mt < sys.moltype.size(); mt++)
1832 clean_vsite_bondeds(mi[mt].plist, sys.moltype[mt].atoms.nr, bRmVSBds);
1836 if (ir->cutoff_scheme == ecutsVERLET)
1838 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1839 ecutscheme_names[ir->cutoff_scheme]);
1841 /* Remove all charge groups */
1842 gmx_mtop_remove_chargegroups(&sys);
1845 if (count_constraints(&sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1847 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1849 sprintf(warn_buf, "Can not do %s with %s, use %s",
1850 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1851 warning_error(wi, warn_buf);
1853 if (ir->bPeriodicMols)
1855 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1856 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1857 warning_error(wi, warn_buf);
1861 if (EI_SD (ir->eI) && ir->etc != etcNO)
1863 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1866 /* If we are doing QM/MM, check that we got the atom numbers */
1867 have_atomnumber = TRUE;
1868 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1870 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1872 if (!have_atomnumber && ir->bQMMM)
1876 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1877 "field you are using does not contain atom numbers fields. This is an\n"
1878 "optional field (introduced in GROMACS 3.3) for general runs, but mandatory\n"
1879 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1880 "an integer just before the mass column in ffXXXnb.itp.\n"
1881 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1884 /* Check for errors in the input now, since they might cause problems
1885 * during processing further down.
1887 check_warning_error(wi, FARGS);
1889 if (nint_ftype(&sys, mi, F_POSRES) > 0 ||
1890 nint_ftype(&sys, mi, F_FBPOSRES) > 0)
1892 if (ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
1894 sprintf(warn_buf, "You are combining position restraints with %s pressure coupling, which can lead to instabilities. If you really want to combine position restraints with pressure coupling, we suggest to use %s pressure coupling instead.",
1895 EPCOUPLTYPE(ir->epc), EPCOUPLTYPE(epcBERENDSEN));
1896 warning_note(wi, warn_buf);
1899 const char *fn = opt2fn("-r", NFILE, fnm);
1902 if (!gmx_fexist(fn))
1905 "Cannot find position restraint file %s (option -r).\n"
1906 "From GROMACS-2018, you need to specify the position restraint "
1907 "coordinate files explicitly to avoid mistakes, although you can "
1908 "still use the same file as you specify for the -c option.", fn);
1911 if (opt2bSet("-rb", NFILE, fnm))
1913 fnB = opt2fn("-rb", NFILE, fnm);
1914 if (!gmx_fexist(fnB))
1917 "Cannot find B-state position restraint file %s (option -rb).\n"
1918 "From GROMACS-2018, you need to specify the position restraint "
1919 "coordinate files explicitly to avoid mistakes, although you can "
1920 "still use the same file as you specify for the -c option.", fn);
1930 fprintf(stderr, "Reading position restraint coords from %s", fn);
1931 if (strcmp(fn, fnB) == 0)
1933 fprintf(stderr, "\n");
1937 fprintf(stderr, " and %s\n", fnB);
1940 gen_posres(&sys, mi, fn, fnB,
1941 ir->refcoord_scaling, ir->ePBC,
1942 ir->posres_com, ir->posres_comB,
1946 /* If we are using CMAP, setup the pre-interpolation grid */
1947 if (plist[F_CMAP].ncmap > 0)
1949 init_cmap_grid(&sys.ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
1950 setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys.ffparams.cmap_grid);
1953 set_wall_atomtype(atype, opts, ir, wi);
1956 renum_atype(plist, &sys, ir->wall_atomtype, atype, bVerbose);
1957 get_atomtype_ntypes(atype);
1960 if (ir->implicit_solvent)
1962 gmx_fatal(FARGS, "Implicit solvation is no longer supported");
1965 /* PELA: Copy the atomtype data to the topology atomtype list */
1966 copy_atomtype_atomtypes(atype, &(sys.atomtypes));
1970 pr_symtab(debug, 0, "After renum_atype", &sys.symtab);
1975 fprintf(stderr, "converting bonded parameters...\n");
1978 ntype = get_atomtype_ntypes(atype);
1979 convert_params(ntype, plist, mi, intermolecular_interactions,
1980 comb, reppow, fudgeQQ, &sys);
1984 pr_symtab(debug, 0, "After convert_params", &sys.symtab);
1987 /* set ptype to VSite for virtual sites */
1988 for (gmx_moltype_t &moltype : sys.moltype)
1990 set_vsites_ptype(FALSE, &moltype);
1994 pr_symtab(debug, 0, "After virtual sites", &sys.symtab);
1996 /* Check velocity for virtual sites and shells */
1999 check_vel(&sys, state.v.rvec_array());
2002 /* check for shells and inpurecs */
2003 check_shells_inputrec(&sys, ir, wi);
2006 check_mol(&sys, wi);
2008 checkForUnboundAtoms(&sys, bVerbose, wi);
2010 for (const gmx_moltype_t &moltype : sys.moltype)
2012 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &moltype.cgs, wi);
2015 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
2017 check_bonds_timestep(&sys, ir->delta_t, wi);
2020 checkDecoupledModeAccuracy(&sys, ir, wi);
2022 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
2024 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.");
2027 check_warning_error(wi, FARGS);
2031 fprintf(stderr, "initialising group options...\n");
2033 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
2037 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0)
2039 if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
2043 if (EI_MD(ir->eI) && ir->etc == etcNO)
2047 buffer_temp = opts->tempi;
2051 buffer_temp = calc_temp(&sys, ir, state.v.rvec_array());
2053 if (buffer_temp > 0)
2055 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
2056 warning_note(wi, warn_buf);
2060 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
2061 gmx::roundToInt(verlet_buffer_ratio_NVE_T0*100));
2062 warning_note(wi, warn_buf);
2067 buffer_temp = get_max_reference_temp(ir, wi);
2070 if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
2072 /* NVE with initial T=0: we add a fixed ratio to rlist.
2073 * Since we don't actually use verletbuf_tol, we set it to -1
2074 * so it can't be misused later.
2076 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
2077 ir->verletbuf_tol = -1;
2081 /* We warn for NVE simulations with a drift tolerance that
2082 * might result in a 1(.1)% drift over the total run-time.
2083 * Note that we can't warn when nsteps=0, since we don't
2084 * know how many steps the user intends to run.
2086 if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
2089 const real driftTolerance = 0.01;
2090 /* We use 2 DOF per atom = 2kT pot+kin energy,
2091 * to be on the safe side with constraints.
2093 const real totalEnergyDriftPerAtomPerPicosecond = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
2095 if (ir->verletbuf_tol > 1.1*driftTolerance*totalEnergyDriftPerAtomPerPicosecond)
2097 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%% when using constraints, you might need to set verlet-buffer-tolerance to %.1e.",
2098 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
2099 gmx::roundToInt(ir->verletbuf_tol/totalEnergyDriftPerAtomPerPicosecond*100),
2100 gmx::roundToInt(100*driftTolerance),
2101 driftTolerance*totalEnergyDriftPerAtomPerPicosecond);
2102 warning_note(wi, warn_buf);
2106 set_verlet_buffer(&sys, ir, buffer_temp, state.box, wi);
2111 /* Init the temperature coupling state */
2112 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
2116 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
2118 check_eg_vs_cg(&sys);
2122 pr_symtab(debug, 0, "After index", &sys.symtab);
2125 triple_check(mdparin, ir, &sys, wi);
2126 close_symtab(&sys.symtab);
2129 pr_symtab(debug, 0, "After close", &sys.symtab);
2132 /* make exclusions between QM atoms and remove charges if needed */
2135 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
2137 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
2141 generate_qmexcl(&sys, ir, wi, GmxQmmmMode::GMX_QMMM_ORIGINAL);
2143 if (ir->QMMMscheme != eQMMMschemeoniom)
2145 std::vector<int> qmmmAtoms = qmmmAtomIndices(*ir, sys);
2146 removeQmmmAtomCharges(&sys, qmmmAtoms);
2150 if (ir->eI == eiMimic)
2152 generate_qmexcl(&sys, ir, wi, GmxQmmmMode::GMX_QMMM_MIMIC);
2155 if (ftp2bSet(efTRN, NFILE, fnm))
2159 fprintf(stderr, "getting data from old trajectory ...\n");
2161 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
2162 bNeedVel, bGenVel, fr_time, ir, &state, &sys, oenv);
2165 if (ir->ePBC == epbcXY && ir->nwall != 2)
2167 clear_rvec(state.box[ZZ]);
2170 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
2172 set_warning_line(wi, mdparin, -1);
2173 check_chargegroup_radii(&sys, ir, state.x.rvec_array(), wi);
2176 if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
2178 /* Calculate the optimal grid dimensions */
2180 EwaldBoxZScaler boxScaler(*ir);
2181 boxScaler.scaleBox(state.box, scaledBox);
2183 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
2185 /* Mark fourier_spacing as not used */
2186 ir->fourier_spacing = 0;
2188 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
2190 set_warning_line(wi, mdparin, -1);
2191 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
2193 const int minGridSize = minimalPmeGridSize(ir->pme_order);
2194 calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize,
2195 &(ir->nkx), &(ir->nky), &(ir->nkz));
2196 if (ir->nkx < minGridSize ||
2197 ir->nky < minGridSize ||
2198 ir->nkz < minGridSize)
2200 warning_error(wi, "The PME grid size should be >= 2*(pme-order - 1); either manually increase the grid size or decrease pme-order");
2204 /* MRS: eventually figure out better logic for initializing the fep
2205 values that makes declaring the lambda and declaring the state not
2206 potentially conflict if not handled correctly. */
2207 if (ir->efep != efepNO)
2209 state.fep_state = ir->fepvals->init_fep_state;
2210 for (i = 0; i < efptNR; i++)
2212 /* init_lambda trumps state definitions*/
2213 if (ir->fepvals->init_lambda >= 0)
2215 state.lambda[i] = ir->fepvals->init_lambda;
2219 if (ir->fepvals->all_lambda[i] == nullptr)
2221 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
2225 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
2231 pull_t *pull = nullptr;
2235 pull = set_pull_init(ir, &sys, state.x.rvec_array(), state.box, state.lambda[efptMASS], wi);
2238 /* Modules that supply external potential for pull coordinates
2239 * should register those potentials here. finish_pull() will check
2240 * that providers have been registerd for all external potentials.
2245 setStateDependentAwhParams(ir->awhParams, ir->pull, pull,
2246 state.box, ir->ePBC, &ir->opts, wi);
2256 set_reference_positions(ir->rot, state.x.rvec_array(), state.box,
2257 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
2261 /* reset_multinr(sys); */
2263 if (EEL_PME(ir->coulombtype))
2265 float ratio = pme_load_estimate(&sys, ir, state.box);
2266 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2267 /* With free energy we might need to do PME both for the A and B state
2268 * charges. This will double the cost, but the optimal performance will
2269 * then probably be at a slightly larger cut-off and grid spacing.
2271 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2272 (ir->efep != efepNO && ratio > 2.0/3.0))
2275 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2276 "and for highly parallel simulations between 0.25 and 0.33,\n"
2277 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2278 if (ir->efep != efepNO)
2281 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2287 char warn_buf[STRLEN];
2288 double cio = compute_io(ir, sys.natoms, &sys.groups, F_NRE, 1);
2289 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2292 set_warning_line(wi, mdparin, -1);
2293 warning_note(wi, warn_buf);
2297 printf("%s\n", warn_buf);
2303 fprintf(stderr, "writing run input file...\n");
2306 done_warning(wi, FARGS);
2307 write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, &sys);
2309 /* Output IMD group, if bIMD is TRUE */
2310 write_IMDgroup_to_file(ir->bIMD, ir, &state, &sys, NFILE, fnm);
2312 sfree(opts->define);
2313 sfree(opts->include);
2317 for (int i = 0; i < nmi; i++)
2319 // Some of the contents of molinfo have been stolen, so
2320 // done_mi can't be called.
2321 done_block(&mi[i].mols);
2322 done_plist(mi[i].plist);
2325 done_atomtype(atype);
2326 done_inputrec_strings();
2327 output_env_done(oenv);