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49 #include "gromacs/awh/read_params.h"
50 #include "gromacs/fileio/readinp.h"
51 #include "gromacs/fileio/warninp.h"
52 #include "gromacs/gmxlib/chargegroup.h"
53 #include "gromacs/gmxlib/network.h"
54 #include "gromacs/gmxpreprocess/keyvaluetreemdpwriter.h"
55 #include "gromacs/gmxpreprocess/toputil.h"
56 #include "gromacs/math/functions.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/mdlib/calc_verletbuf.h"
60 #include "gromacs/mdrunutility/mdmodules.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/mdtypes/pull_params.h"
64 #include "gromacs/options/options.h"
65 #include "gromacs/options/treesupport.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/index.h"
70 #include "gromacs/topology/mtop_util.h"
71 #include "gromacs/topology/symtab.h"
72 #include "gromacs/topology/topology.h"
73 #include "gromacs/utility/cstringutil.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/filestream.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/ikeyvaluetreeerror.h"
79 #include "gromacs/utility/keyvaluetree.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreetransform.h"
82 #include "gromacs/utility/smalloc.h"
83 #include "gromacs/utility/strconvert.h"
84 #include "gromacs/utility/stringcompare.h"
85 #include "gromacs/utility/stringutil.h"
86 #include "gromacs/utility/textwriter.h"
91 /* Resource parameters
92 * Do not change any of these until you read the instruction
93 * in readinp.h. Some cpp's do not take spaces after the backslash
94 * (like the c-shell), which will give you a very weird compiler
98 typedef struct t_inputrec_strings
100 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
101 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
102 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
103 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
104 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
106 char fep_lambda[efptNR][STRLEN];
107 char lambda_weights[STRLEN];
110 char anneal[STRLEN], anneal_npoints[STRLEN],
111 anneal_time[STRLEN], anneal_temp[STRLEN];
112 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
113 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
114 SAoff[STRLEN], SAsteps[STRLEN];
116 } gmx_inputrec_strings;
118 static gmx_inputrec_strings *is = nullptr;
120 void init_inputrec_strings()
124 gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
129 void done_inputrec_strings()
137 egrptpALL, /* All particles have to be a member of a group. */
138 egrptpALL_GENREST, /* A rest group with name is generated for particles *
139 * that are not part of any group. */
140 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
141 * for the rest group. */
142 egrptpONE /* Merge all selected groups into one group, *
143 * make a rest group for the remaining particles. */
146 static const char *constraints[eshNR+1] = {
147 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", nullptr
150 static const char *couple_lam[ecouplamNR+1] = {
151 "vdw-q", "vdw", "q", "none", nullptr
154 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
159 for (i = 0; i < ntemps; i++)
161 /* simple linear scaling -- allows more control */
162 if (simtemp->eSimTempScale == esimtempLINEAR)
164 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
166 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
168 simtemp->temperatures[i] = simtemp->simtemp_low * std::pow(simtemp->simtemp_high/simtemp->simtemp_low, static_cast<real>((1.0*i)/(ntemps-1)));
170 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
172 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(std::expm1(temperature_lambdas[i])/std::expm1(1.0));
177 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
178 gmx_fatal(FARGS, "%s", errorstr);
185 static void _low_check(bool b, const char *s, warninp_t wi)
189 warning_error(wi, s);
193 static void check_nst(const char *desc_nst, int nst,
194 const char *desc_p, int *p,
199 if (*p > 0 && *p % nst != 0)
201 /* Round up to the next multiple of nst */
202 *p = ((*p)/nst + 1)*nst;
203 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
204 desc_p, desc_nst, desc_p, *p);
209 static bool ir_NVE(const t_inputrec *ir)
211 return (EI_MD(ir->eI) && ir->etc == etcNO);
214 static int lcd(int n1, int n2)
219 for (i = 2; (i <= n1 && i <= n2); i++)
221 if (n1 % i == 0 && n2 % i == 0)
230 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
232 if (*eintmod == eintmodPOTSHIFT_VERLET)
234 if (ir->cutoff_scheme == ecutsVERLET)
236 *eintmod = eintmodPOTSHIFT;
240 *eintmod = eintmodNONE;
245 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
247 /* Check internal consistency.
248 * NOTE: index groups are not set here yet, don't check things
249 * like temperature coupling group options here, but in triple_check
252 /* Strange macro: first one fills the err_buf, and then one can check
253 * the condition, which will print the message and increase the error
256 #define CHECK(b) _low_check(b, err_buf, wi)
257 char err_buf[256], warn_buf[STRLEN];
260 t_lambda *fep = ir->fepvals;
261 t_expanded *expand = ir->expandedvals;
263 set_warning_line(wi, mdparin, -1);
265 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
267 sprintf(warn_buf, "%s electrostatics is no longer supported",
268 eel_names[eelRF_NEC_UNSUPPORTED]);
269 warning_error(wi, warn_buf);
272 /* BASIC CUT-OFF STUFF */
273 if (ir->rcoulomb < 0)
275 warning_error(wi, "rcoulomb should be >= 0");
279 warning_error(wi, "rvdw should be >= 0");
282 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
284 warning_error(wi, "rlist should be >= 0");
286 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
287 CHECK(ir->nstlist < 0);
289 process_interaction_modifier(ir, &ir->coulomb_modifier);
290 process_interaction_modifier(ir, &ir->vdw_modifier);
292 if (ir->cutoff_scheme == ecutsGROUP)
295 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
296 "release when all interaction forms are supported for the verlet scheme. The verlet "
297 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
299 if (ir->rlist > 0 && ir->rlist < ir->rcoulomb)
301 gmx_fatal(FARGS, "rcoulomb must not be greater than rlist (twin-range schemes are not supported)");
303 if (ir->rlist > 0 && ir->rlist < ir->rvdw)
305 gmx_fatal(FARGS, "rvdw must not be greater than rlist (twin-range schemes are not supported)");
308 if (ir->rlist == 0 && ir->ePBC != epbcNONE)
310 warning_error(wi, "Can not have an infinite cut-off with PBC");
314 if (ir->cutoff_scheme == ecutsVERLET)
318 /* Normal Verlet type neighbor-list, currently only limited feature support */
319 if (inputrec2nboundeddim(ir) < 3)
321 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
324 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
325 if (ir->rcoulomb != ir->rvdw)
327 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
328 // for PME load balancing, we can support this exception.
329 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) &&
330 ir->vdwtype == evdwCUT &&
331 ir->rcoulomb > ir->rvdw);
332 if (!bUsesPmeTwinRangeKernel)
334 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported (except for rcoulomb>rvdw with PME electrostatics)");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) ||
362 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
364 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
366 if (!(ir->coulomb_modifier == eintmodNONE ||
367 ir->coulomb_modifier == eintmodPOTSHIFT))
369 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
370 warning_error(wi, warn_buf);
373 if (EEL_USER(ir->coulombtype))
375 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme", eel_names[ir->coulombtype]);
376 warning_error(wi, warn_buf);
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
389 rc_max = std::max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
410 if (ir->rlist > rc_max)
412 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
440 /* GENERAL INTEGRATOR STUFF */
443 if (ir->etc != etcNO)
445 if (EI_RANDOM(ir->eI))
447 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling implicitly. See the documentation for more information on which parameters affect temperature for %s.", etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
451 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
453 warning_note(wi, warn_buf);
457 if (ir->eI == eiVVAK)
459 sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
460 warning_note(wi, warn_buf);
462 if (!EI_DYNAMICS(ir->eI))
464 if (ir->epc != epcNO)
466 sprintf(warn_buf, "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.", epcoupl_names[ir->epc], ei_names[ir->eI]);
467 warning_note(wi, warn_buf);
471 if (EI_DYNAMICS(ir->eI))
473 if (ir->nstcalcenergy < 0)
475 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
476 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
478 /* nstcalcenergy larger than nstener does not make sense.
479 * We ideally want nstcalcenergy=nstener.
483 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
487 ir->nstcalcenergy = ir->nstenergy;
491 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
492 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
493 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
496 const char *nsten = "nstenergy";
497 const char *nstdh = "nstdhdl";
498 const char *min_name = nsten;
499 int min_nst = ir->nstenergy;
501 /* find the smallest of ( nstenergy, nstdhdl ) */
502 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
503 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
505 min_nst = ir->fepvals->nstdhdl;
508 /* If the user sets nstenergy small, we should respect that */
510 "Setting nstcalcenergy (%d) equal to %s (%d)",
511 ir->nstcalcenergy, min_name, min_nst);
512 warning_note(wi, warn_buf);
513 ir->nstcalcenergy = min_nst;
516 if (ir->epc != epcNO)
518 if (ir->nstpcouple < 0)
520 ir->nstpcouple = ir_optimal_nstpcouple(ir);
524 if (ir->nstcalcenergy > 0)
526 if (ir->efep != efepNO)
528 /* nstdhdl should be a multiple of nstcalcenergy */
529 check_nst("nstcalcenergy", ir->nstcalcenergy,
530 "nstdhdl", &ir->fepvals->nstdhdl, wi);
534 /* nstexpanded should be a multiple of nstcalcenergy */
535 check_nst("nstcalcenergy", ir->nstcalcenergy,
536 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
538 /* for storing exact averages nstenergy should be
539 * a multiple of nstcalcenergy
541 check_nst("nstcalcenergy", ir->nstcalcenergy,
542 "nstenergy", &ir->nstenergy, wi);
546 if (ir->nsteps == 0 && !ir->bContinuation)
548 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
552 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
553 ir->bContinuation && ir->ld_seed != -1)
555 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
561 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
562 CHECK(ir->ePBC != epbcXYZ);
563 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
564 CHECK(ir->ns_type != ensGRID);
565 sprintf(err_buf, "with TPI nstlist should be larger than zero");
566 CHECK(ir->nstlist <= 0);
567 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
568 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
569 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
570 CHECK(ir->cutoff_scheme == ecutsVERLET);
574 if ( (opts->nshake > 0) && (opts->bMorse) )
577 "Using morse bond-potentials while constraining bonds is useless");
578 warning(wi, warn_buf);
581 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
582 ir->bContinuation && ir->ld_seed != -1)
584 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
586 /* verify simulated tempering options */
590 bool bAllTempZero = TRUE;
591 for (i = 0; i < fep->n_lambda; i++)
593 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
594 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
595 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
597 bAllTempZero = FALSE;
600 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
601 CHECK(bAllTempZero == TRUE);
603 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
604 CHECK(ir->eI != eiVV);
606 /* check compatability of the temperature coupling with simulated tempering */
608 if (ir->etc == etcNOSEHOOVER)
610 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
611 warning_note(wi, warn_buf);
614 /* check that the temperatures make sense */
616 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
617 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
619 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
620 CHECK(ir->simtempvals->simtemp_high <= 0);
622 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
623 CHECK(ir->simtempvals->simtemp_low <= 0);
626 /* verify free energy options */
628 if (ir->efep != efepNO)
631 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
633 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
635 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
636 static_cast<int>(fep->sc_r_power));
637 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
639 sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
640 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
642 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
643 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
645 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
646 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
648 sprintf(err_buf, "Free-energy not implemented for Ewald");
649 CHECK(ir->coulombtype == eelEWALD);
651 /* check validty of lambda inputs */
652 if (fep->n_lambda == 0)
654 /* Clear output in case of no states:*/
655 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
656 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
660 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
661 CHECK((fep->init_fep_state >= fep->n_lambda));
664 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
665 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
667 sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
668 fep->init_lambda, fep->init_fep_state);
669 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
673 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
677 for (i = 0; i < efptNR; i++)
679 if (fep->separate_dvdl[i])
684 if (n_lambda_terms > 1)
686 sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
687 warning(wi, warn_buf);
690 if (n_lambda_terms < 2 && fep->n_lambda > 0)
693 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
697 for (j = 0; j < efptNR; j++)
699 for (i = 0; i < fep->n_lambda; i++)
701 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
702 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
706 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
708 for (i = 0; i < fep->n_lambda; i++)
710 sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
711 fep->all_lambda[efptCOUL][i]);
712 CHECK((fep->sc_alpha > 0) &&
713 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
714 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
715 ((fep->all_lambda[efptVDW][i] > 0.0) &&
716 (fep->all_lambda[efptVDW][i] < 1.0))));
720 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
722 real sigma, lambda, r_sc;
725 /* Maximum estimate for A and B charges equal with lambda power 1 */
727 r_sc = std::pow(lambda*fep->sc_alpha*std::pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
728 sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
730 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
731 warning_note(wi, warn_buf);
734 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
735 be treated differently, but that's the next step */
737 for (i = 0; i < efptNR; i++)
739 for (j = 0; j < fep->n_lambda; j++)
741 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
742 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
747 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
751 /* checking equilibration of weights inputs for validity */
753 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
754 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
755 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
757 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
758 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
759 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
761 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
762 expand->equil_steps, elmceq_names[elmceqSTEPS]);
763 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
765 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
766 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
767 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
769 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_ratio, elmceq_names[elmceqRATIO]);
771 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
773 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
774 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
775 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
777 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
778 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
779 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
781 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
782 expand->equil_steps, elmceq_names[elmceqSTEPS]);
783 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
785 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
786 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
787 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
789 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
790 expand->equil_ratio, elmceq_names[elmceqRATIO]);
791 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
793 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
794 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
795 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
797 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
798 CHECK((expand->lmc_repeats <= 0));
799 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
800 CHECK((expand->minvarmin <= 0));
801 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
802 CHECK((expand->c_range < 0));
803 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
804 fep->init_fep_state, expand->lmc_forced_nstart);
805 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
806 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
807 CHECK((expand->lmc_forced_nstart < 0));
808 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
809 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
811 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
812 CHECK((expand->init_wl_delta < 0));
813 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
814 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
815 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
816 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
818 /* if there is no temperature control, we need to specify an MC temperature */
819 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO) && (expand->mc_temp <= 0.0))
821 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set to a positive number");
822 warning_error(wi, err_buf);
824 if (expand->nstTij > 0)
826 sprintf(err_buf, "nstlog must be non-zero");
827 CHECK(ir->nstlog == 0);
828 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
829 expand->nstTij, ir->nstlog);
830 CHECK((expand->nstTij % ir->nstlog) != 0);
835 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
836 CHECK(ir->nwall && ir->ePBC != epbcXY);
839 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
841 if (ir->ePBC == epbcNONE)
843 if (ir->epc != epcNO)
845 warning(wi, "Turning off pressure coupling for vacuum system");
851 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
852 epbc_names[ir->ePBC]);
853 CHECK(ir->epc != epcNO);
855 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
856 CHECK(EEL_FULL(ir->coulombtype));
858 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
859 epbc_names[ir->ePBC]);
860 CHECK(ir->eDispCorr != edispcNO);
863 if (ir->rlist == 0.0)
865 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
866 "with coulombtype = %s or coulombtype = %s\n"
867 "without periodic boundary conditions (pbc = %s) and\n"
868 "rcoulomb and rvdw set to zero",
869 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
870 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
871 (ir->ePBC != epbcNONE) ||
872 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
876 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
881 if (ir->nstcomm == 0)
883 ir->comm_mode = ecmNO;
885 if (ir->comm_mode != ecmNO)
889 warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
890 ir->nstcomm = abs(ir->nstcomm);
893 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
895 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
896 ir->nstcomm = ir->nstcalcenergy;
899 if (ir->comm_mode == ecmANGULAR)
901 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
902 CHECK(ir->bPeriodicMols);
903 if (ir->ePBC != epbcNONE)
905 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
910 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
912 sprintf(warn_buf, "Tumbling and flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR or use integrator = %s.", ei_names[eiSD1]);
913 warning_note(wi, warn_buf);
916 /* TEMPERATURE COUPLING */
917 if (ir->etc == etcYES)
919 ir->etc = etcBERENDSEN;
920 warning_note(wi, "Old option for temperature coupling given: "
921 "changing \"yes\" to \"Berendsen\"\n");
924 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
926 if (ir->opts.nhchainlength < 1)
928 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
929 ir->opts.nhchainlength = 1;
930 warning(wi, warn_buf);
933 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
935 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
936 ir->opts.nhchainlength = 1;
941 ir->opts.nhchainlength = 0;
944 if (ir->eI == eiVVAK)
946 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
948 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
951 if (ETC_ANDERSEN(ir->etc))
953 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
954 CHECK(!(EI_VV(ir->eI)));
956 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
958 sprintf(warn_buf, "Center of mass removal not necessary for %s. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
959 warning_note(wi, warn_buf);
962 sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
963 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
966 if (ir->etc == etcBERENDSEN)
968 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
969 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
970 warning_note(wi, warn_buf);
973 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
974 && ir->epc == epcBERENDSEN)
976 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
977 "true ensemble for the thermostat");
978 warning(wi, warn_buf);
981 /* PRESSURE COUPLING */
982 if (ir->epc == epcISOTROPIC)
984 ir->epc = epcBERENDSEN;
985 warning_note(wi, "Old option for pressure coupling given: "
986 "changing \"Isotropic\" to \"Berendsen\"\n");
989 if (ir->epc != epcNO)
991 dt_pcoupl = ir->nstpcouple*ir->delta_t;
993 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
994 CHECK(ir->tau_p <= 0);
996 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
998 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
999 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1000 warning(wi, warn_buf);
1003 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1004 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1005 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1006 ir->compress[ZZ][ZZ] < 0 ||
1007 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1008 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1010 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1013 "You are generating velocities so I am assuming you "
1014 "are equilibrating a system. You are using "
1015 "%s pressure coupling, but this can be "
1016 "unstable for equilibration. If your system crashes, try "
1017 "equilibrating first with Berendsen pressure coupling. If "
1018 "you are not equilibrating the system, you can probably "
1019 "ignore this warning.",
1020 epcoupl_names[ir->epc]);
1021 warning(wi, warn_buf);
1027 if (ir->epc > epcNO)
1029 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1031 warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
1037 if (ir->epc == epcMTTK)
1039 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1043 /* ELECTROSTATICS */
1044 /* More checks are in triple check (grompp.c) */
1046 if (ir->coulombtype == eelSWITCH)
1048 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1049 "artifacts, advice: use coulombtype = %s",
1050 eel_names[ir->coulombtype],
1051 eel_names[eelRF_ZERO]);
1052 warning(wi, warn_buf);
1055 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1057 sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
1058 warning(wi, warn_buf);
1059 ir->epsilon_rf = ir->epsilon_r;
1060 ir->epsilon_r = 1.0;
1063 if (ir->epsilon_r == 0)
1066 "It is pointless to use long-range electrostatics with infinite relative permittivity."
1067 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1068 CHECK(EEL_FULL(ir->coulombtype));
1071 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1073 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1074 CHECK(ir->epsilon_r < 0);
1077 if (EEL_RF(ir->coulombtype))
1079 /* reaction field (at the cut-off) */
1081 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1083 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1084 eel_names[ir->coulombtype]);
1085 warning(wi, warn_buf);
1086 ir->epsilon_rf = 0.0;
1089 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1090 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1091 (ir->epsilon_r == 0));
1092 if (ir->epsilon_rf == ir->epsilon_r)
1094 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1095 eel_names[ir->coulombtype]);
1096 warning(wi, warn_buf);
1099 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1100 * means the interaction is zero outside rcoulomb, but it helps to
1101 * provide accurate energy conservation.
1103 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1105 if (ir_coulomb_switched(ir))
1108 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1109 eel_names[ir->coulombtype]);
1110 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1113 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1115 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1117 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1118 eel_names[ir->coulombtype]);
1119 CHECK(ir->rlist > ir->rcoulomb);
1123 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1126 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1127 CHECK( ir->coulomb_modifier != eintmodNONE);
1129 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1132 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1133 CHECK( ir->vdw_modifier != eintmodNONE);
1136 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1137 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1140 "The switch/shift interaction settings are just for compatibility; you will get better "
1141 "performance from applying potential modifiers to your interactions!\n");
1142 warning_note(wi, warn_buf);
1145 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1147 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1149 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1150 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1151 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1152 warning(wi, warn_buf);
1156 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1158 if (ir->rvdw_switch == 0)
1160 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1161 warning(wi, warn_buf);
1165 if (EEL_FULL(ir->coulombtype))
1167 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1168 ir->coulombtype == eelPMEUSERSWITCH)
1170 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1171 eel_names[ir->coulombtype]);
1172 CHECK(ir->rcoulomb > ir->rlist);
1174 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1176 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1179 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1180 "For optimal energy conservation,consider using\n"
1181 "a potential modifier.", eel_names[ir->coulombtype]);
1182 CHECK(ir->rcoulomb != ir->rlist);
1187 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1189 // TODO: Move these checks into the ewald module with the options class
1191 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1193 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1195 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
1196 warning_error(wi, warn_buf);
1200 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1202 if (ir->ewald_geometry == eewg3D)
1204 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1205 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1206 warning(wi, warn_buf);
1208 /* This check avoids extra pbc coding for exclusion corrections */
1209 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1210 CHECK(ir->wall_ewald_zfac < 2);
1212 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1213 EEL_FULL(ir->coulombtype))
1215 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1216 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1217 warning(wi, warn_buf);
1219 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1221 if (ir->cutoff_scheme == ecutsVERLET)
1223 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1224 eel_names[ir->coulombtype]);
1225 warning(wi, warn_buf);
1229 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1230 eel_names[ir->coulombtype]);
1231 warning_note(wi, warn_buf);
1235 if (ir_vdw_switched(ir))
1237 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1238 CHECK(ir->rvdw_switch >= ir->rvdw);
1240 if (ir->rvdw_switch < 0.5*ir->rvdw)
1242 sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
1243 ir->rvdw_switch, ir->rvdw);
1244 warning_note(wi, warn_buf);
1247 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1249 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1251 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1252 CHECK(ir->rlist > ir->rvdw);
1256 if (ir->vdwtype == evdwPME)
1258 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1260 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1261 evdw_names[ir->vdwtype],
1262 eintmod_names[eintmodPOTSHIFT],
1263 eintmod_names[eintmodNONE]);
1264 warning_error(wi, err_buf);
1268 if (ir->cutoff_scheme == ecutsGROUP)
1270 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1271 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1273 warning_note(wi, "With exact cut-offs, rlist should be "
1274 "larger than rcoulomb and rvdw, so that there "
1275 "is a buffer region for particle motion "
1276 "between neighborsearch steps");
1279 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1281 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1282 warning_note(wi, warn_buf);
1284 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1286 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1287 warning_note(wi, warn_buf);
1291 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1293 warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
1296 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1299 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1302 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1304 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1307 /* ENERGY CONSERVATION */
1308 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1310 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1312 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1313 evdw_names[evdwSHIFT]);
1314 warning_note(wi, warn_buf);
1316 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1318 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1319 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1320 warning_note(wi, warn_buf);
1324 /* IMPLICIT SOLVENT */
1325 if (ir->coulombtype == eelGB_NOTUSED)
1327 sprintf(warn_buf, "Invalid option %s for coulombtype",
1328 eel_names[ir->coulombtype]);
1329 warning_error(wi, warn_buf);
1334 if (ir->cutoff_scheme != ecutsGROUP)
1336 warning_error(wi, "QMMM is currently only supported with cutoff-scheme=group");
1338 if (!EI_DYNAMICS(ir->eI))
1341 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1342 warning_error(wi, buf);
1348 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1352 /* interpret a number of doubles from a string and put them in an array,
1353 after allocating space for them.
1354 str = the input string
1355 n = the (pre-allocated) number of doubles read
1356 r = the output array of doubles. */
1357 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1359 auto values = gmx::splitString(str);
1363 for (int i = 0; i < *n; i++)
1367 (*r)[i] = gmx::fromString<real>(values[i]);
1369 catch (gmx::GromacsException &)
1371 warning_error(wi, "Invalid value " + values[i] + " in string in mdp file. Expected a real number.");
1377 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1380 int i, j, max_n_lambda, nweights, nfep[efptNR];
1381 t_lambda *fep = ir->fepvals;
1382 t_expanded *expand = ir->expandedvals;
1383 real **count_fep_lambdas;
1384 bool bOneLambda = TRUE;
1386 snew(count_fep_lambdas, efptNR);
1388 /* FEP input processing */
1389 /* first, identify the number of lambda values for each type.
1390 All that are nonzero must have the same number */
1392 for (i = 0; i < efptNR; i++)
1394 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1397 /* now, determine the number of components. All must be either zero, or equal. */
1400 for (i = 0; i < efptNR; i++)
1402 if (nfep[i] > max_n_lambda)
1404 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1405 must have the same number if its not zero.*/
1410 for (i = 0; i < efptNR; i++)
1414 ir->fepvals->separate_dvdl[i] = FALSE;
1416 else if (nfep[i] == max_n_lambda)
1418 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1419 respect to the temperature currently */
1421 ir->fepvals->separate_dvdl[i] = TRUE;
1426 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1427 nfep[i], efpt_names[i], max_n_lambda);
1430 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1431 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1433 /* the number of lambdas is the number we've read in, which is either zero
1434 or the same for all */
1435 fep->n_lambda = max_n_lambda;
1437 /* allocate space for the array of lambda values */
1438 snew(fep->all_lambda, efptNR);
1439 /* if init_lambda is defined, we need to set lambda */
1440 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1442 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1444 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1445 for (i = 0; i < efptNR; i++)
1447 snew(fep->all_lambda[i], fep->n_lambda);
1448 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1451 for (j = 0; j < fep->n_lambda; j++)
1453 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1455 sfree(count_fep_lambdas[i]);
1458 sfree(count_fep_lambdas);
1460 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1461 bookkeeping -- for now, init_lambda */
1463 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1465 for (i = 0; i < fep->n_lambda; i++)
1467 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1471 /* check to see if only a single component lambda is defined, and soft core is defined.
1472 In this case, turn on coulomb soft core */
1474 if (max_n_lambda == 0)
1480 for (i = 0; i < efptNR; i++)
1482 if ((nfep[i] != 0) && (i != efptFEP))
1488 if ((bOneLambda) && (fep->sc_alpha > 0))
1490 fep->bScCoul = TRUE;
1493 /* Fill in the others with the efptFEP if they are not explicitly
1494 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1495 they are all zero. */
1497 for (i = 0; i < efptNR; i++)
1499 if ((nfep[i] == 0) && (i != efptFEP))
1501 for (j = 0; j < fep->n_lambda; j++)
1503 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1509 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1510 if (fep->sc_r_power == 48)
1512 if (fep->sc_alpha > 0.1)
1514 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1518 /* now read in the weights */
1519 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1522 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1524 else if (nweights != fep->n_lambda)
1526 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1527 nweights, fep->n_lambda);
1529 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1531 expand->nstexpanded = fep->nstdhdl;
1532 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1537 static void do_simtemp_params(t_inputrec *ir)
1540 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1541 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1545 convertYesNos(warninp_t /*wi*/, gmx::ArrayRef<const std::string> inputs, const char * /*name*/, gmx_bool *outputs)
1548 for (const auto &input : inputs)
1550 outputs[i] = (gmx_strncasecmp(input.c_str(), "Y", 1) == 0);
1555 template <typename T> void
1556 convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, T *outputs)
1559 for (const auto &input : inputs)
1563 outputs[i] = gmx::fromStdString<T>(input);
1565 catch (gmx::GromacsException &)
1567 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of integers separated by spaces.",
1569 warning_error(wi, message);
1576 convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, real *outputs)
1579 for (const auto &input : inputs)
1583 outputs[i] = gmx::fromString<real>(input);
1585 catch (gmx::GromacsException &)
1587 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of real numbers separated by spaces.",
1589 warning_error(wi, message);
1596 convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, rvec *outputs)
1599 for (const auto &input : inputs)
1603 outputs[i][d] = gmx::fromString<real>(input);
1605 catch (gmx::GromacsException &)
1607 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of real numbers separated by spaces.",
1609 warning_error(wi, message);
1620 static void do_wall_params(t_inputrec *ir,
1621 char *wall_atomtype, char *wall_density,
1625 opts->wall_atomtype[0] = nullptr;
1626 opts->wall_atomtype[1] = nullptr;
1628 ir->wall_atomtype[0] = -1;
1629 ir->wall_atomtype[1] = -1;
1630 ir->wall_density[0] = 0;
1631 ir->wall_density[1] = 0;
1635 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1636 if (wallAtomTypes.size() != size_t(ir->nwall))
1638 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu",
1639 ir->nwall, wallAtomTypes.size());
1641 for (int i = 0; i < ir->nwall; i++)
1643 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1646 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1648 auto wallDensity = gmx::splitString(wall_density);
1649 if (wallDensity.size() != size_t(ir->nwall))
1651 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall, wallDensity.size());
1653 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1654 for (int i = 0; i < ir->nwall; i++)
1656 if (ir->wall_density[i] <= 0)
1658 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1665 static void add_wall_energrps(SimulationGroups *groups, int nwall, t_symtab *symtab)
1669 t_grps *grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1670 srenew(grps->nm_ind, grps->nr+nwall);
1671 for (int i = 0; i < nwall; i++)
1673 groups->groupNames.emplace_back(
1676 gmx::formatString("wall%d", i).c_str()));
1677 grps->nm_ind[grps->nr++] = groups->groupNames.size() - 1;
1682 static void read_expandedparams(std::vector<t_inpfile> *inp,
1683 t_expanded *expand, warninp_t wi)
1685 /* read expanded ensemble parameters */
1686 printStringNewline(inp, "expanded ensemble variables");
1687 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1688 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1689 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1690 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1691 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1692 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1693 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1694 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1695 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1696 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1697 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1698 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1699 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1700 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1701 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1702 expand->bSymmetrizedTMatrix = (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1703 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1704 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1705 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1706 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1707 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1708 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1709 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1712 /*! \brief Return whether an end state with the given coupling-lambda
1713 * value describes fully-interacting VDW.
1715 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1716 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1718 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1720 return (couple_lambda_value == ecouplamVDW ||
1721 couple_lambda_value == ecouplamVDWQ);
1727 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1730 explicit MdpErrorHandler(warninp_t wi)
1731 : wi_(wi), mapping_(nullptr)
1735 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1737 mapping_ = &mapping;
1740 bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context) override
1742 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1743 getOptionName(context).c_str()));
1744 std::string message = gmx::formatExceptionMessageToString(*ex);
1745 warning_error(wi_, message.c_str());
1750 std::string getOptionName(const gmx::KeyValueTreePath &context)
1752 if (mapping_ != nullptr)
1754 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1755 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1758 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1763 const gmx::IKeyValueTreeBackMapping *mapping_;
1768 void get_ir(const char *mdparin, const char *mdparout,
1769 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1770 WriteMdpHeader writeMdpHeader, warninp_t wi)
1773 double dumdub[2][6];
1775 char warn_buf[STRLEN];
1776 t_lambda *fep = ir->fepvals;
1777 t_expanded *expand = ir->expandedvals;
1779 const char *no_names[] = { "no", nullptr };
1781 init_inputrec_strings();
1782 gmx::TextInputFile stream(mdparin);
1783 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1785 snew(dumstr[0], STRLEN);
1786 snew(dumstr[1], STRLEN);
1788 if (-1 == search_einp(inp, "cutoff-scheme"))
1791 "%s did not specify a value for the .mdp option "
1792 "\"cutoff-scheme\". Probably it was first intended for use "
1793 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1794 "introduced, but the group scheme was still the default. "
1795 "The default is now the Verlet scheme, so you will observe "
1796 "different behaviour.", mdparin);
1797 warning_note(wi, warn_buf);
1800 /* ignore the following deprecated commands */
1801 replace_inp_entry(inp, "title", nullptr);
1802 replace_inp_entry(inp, "cpp", nullptr);
1803 replace_inp_entry(inp, "domain-decomposition", nullptr);
1804 replace_inp_entry(inp, "andersen-seed", nullptr);
1805 replace_inp_entry(inp, "dihre", nullptr);
1806 replace_inp_entry(inp, "dihre-fc", nullptr);
1807 replace_inp_entry(inp, "dihre-tau", nullptr);
1808 replace_inp_entry(inp, "nstdihreout", nullptr);
1809 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1810 replace_inp_entry(inp, "optimize-fft", nullptr);
1811 replace_inp_entry(inp, "adress_type", nullptr);
1812 replace_inp_entry(inp, "adress_const_wf", nullptr);
1813 replace_inp_entry(inp, "adress_ex_width", nullptr);
1814 replace_inp_entry(inp, "adress_hy_width", nullptr);
1815 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1816 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1817 replace_inp_entry(inp, "adress_site", nullptr);
1818 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1819 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1820 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1821 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1822 replace_inp_entry(inp, "rlistlong", nullptr);
1823 replace_inp_entry(inp, "nstcalclr", nullptr);
1824 replace_inp_entry(inp, "pull-print-com2", nullptr);
1825 replace_inp_entry(inp, "gb-algorithm", nullptr);
1826 replace_inp_entry(inp, "nstgbradii", nullptr);
1827 replace_inp_entry(inp, "rgbradii", nullptr);
1828 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1829 replace_inp_entry(inp, "gb-saltconc", nullptr);
1830 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1831 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1832 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1833 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1834 replace_inp_entry(inp, "sa-algorithm", nullptr);
1835 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1837 /* replace the following commands with the clearer new versions*/
1838 replace_inp_entry(inp, "unconstrained-start", "continuation");
1839 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1840 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1841 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1842 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1843 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1844 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1846 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1847 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1848 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1849 setStringEntry(&inp, "include", opts->include, nullptr);
1850 printStringNoNewline(&inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1851 setStringEntry(&inp, "define", opts->define, nullptr);
1853 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1854 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1855 printStringNoNewline(&inp, "Start time and timestep in ps");
1856 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1857 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1858 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1859 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1860 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1861 printStringNoNewline(&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1862 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1863 printStringNoNewline(&inp, "mode for center of mass motion removal");
1864 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1865 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1866 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1867 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1868 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1870 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1871 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1872 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1873 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1876 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1877 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1878 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1879 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1880 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1881 ir->niter = get_eint(&inp, "niter", 20, wi);
1882 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1883 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1884 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1885 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1886 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1888 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1889 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1891 /* Output options */
1892 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1893 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1894 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1895 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1896 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1897 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1898 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1899 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1900 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1901 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1902 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1903 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1904 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1905 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1906 printStringNoNewline(&inp, "default, all atoms will be written.");
1907 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1908 printStringNoNewline(&inp, "Selection of energy groups");
1909 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1911 /* Neighbor searching */
1912 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1913 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1914 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1915 printStringNoNewline(&inp, "nblist update frequency");
1916 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1917 printStringNoNewline(&inp, "ns algorithm (simple or grid)");
1918 ir->ns_type = get_eeenum(&inp, "ns-type", ens_names, wi);
1919 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1920 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1921 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1922 printStringNoNewline(&inp, "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1923 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1924 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1925 printStringNoNewline(&inp, "nblist cut-off");
1926 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1927 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1929 /* Electrostatics */
1930 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1931 printStringNoNewline(&inp, "Method for doing electrostatics");
1932 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1933 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1934 printStringNoNewline(&inp, "cut-off lengths");
1935 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1936 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1937 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
1938 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1939 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1940 printStringNoNewline(&inp, "Method for doing Van der Waals");
1941 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1942 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1943 printStringNoNewline(&inp, "cut-off lengths");
1944 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1945 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1946 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1947 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1948 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1949 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1950 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1951 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1952 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1953 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1954 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1955 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1956 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1957 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1958 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1959 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1960 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1961 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1962 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1963 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1964 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1966 /* Implicit solvation is no longer supported, but we need grompp
1967 to be able to refuse old .mdp files that would have built a tpr
1968 to run it. Thus, only "no" is accepted. */
1969 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
1971 /* Coupling stuff */
1972 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
1973 printStringNoNewline(&inp, "Temperature coupling");
1974 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
1975 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
1976 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
1977 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
1978 printStringNoNewline(&inp, "Groups to couple separately");
1979 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
1980 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
1981 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
1982 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
1983 printStringNoNewline(&inp, "pressure coupling");
1984 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
1985 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
1986 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
1987 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
1988 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
1989 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
1990 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
1991 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
1992 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
1995 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
1996 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
1997 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
1998 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
1999 printStringNoNewline(&inp, "QM method");
2000 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2001 printStringNoNewline(&inp, "QMMM scheme");
2002 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2003 printStringNoNewline(&inp, "QM basisset");
2004 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2005 printStringNoNewline(&inp, "QM charge");
2006 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2007 printStringNoNewline(&inp, "QM multiplicity");
2008 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2009 printStringNoNewline(&inp, "Surface Hopping");
2010 setStringEntry(&inp, "SH", is->bSH, nullptr);
2011 printStringNoNewline(&inp, "CAS space options");
2012 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2013 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2014 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2015 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2016 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2017 printStringNoNewline(&inp, "Scale factor for MM charges");
2018 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2020 /* Simulated annealing */
2021 printStringNewline(&inp, "SIMULATED ANNEALING");
2022 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2023 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2024 printStringNoNewline(&inp, "Number of time points to use for specifying annealing in each group");
2025 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2026 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2027 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2028 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2029 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2032 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2033 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2034 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2035 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2038 printStringNewline(&inp, "OPTIONS FOR BONDS");
2039 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2040 printStringNoNewline(&inp, "Type of constraint algorithm");
2041 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2042 printStringNoNewline(&inp, "Do not constrain the start configuration");
2043 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2044 printStringNoNewline(&inp, "Use successive overrelaxation to reduce the number of shake iterations");
2045 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2046 printStringNoNewline(&inp, "Relative tolerance of shake");
2047 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2048 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2049 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2050 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2051 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2052 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2053 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2054 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2055 printStringNoNewline(&inp, "rotates over more degrees than");
2056 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2057 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2058 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2060 /* Energy group exclusions */
2061 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2062 printStringNoNewline(&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2063 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2066 printStringNewline(&inp, "WALLS");
2067 printStringNoNewline(&inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2068 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2069 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2070 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2071 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2072 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2073 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2076 printStringNewline(&inp, "COM PULLING");
2077 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2081 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2085 NOTE: needs COM pulling input */
2086 printStringNewline(&inp, "AWH biasing");
2087 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2092 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2096 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2100 /* Enforced rotation */
2101 printStringNewline(&inp, "ENFORCED ROTATION");
2102 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2103 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2107 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2110 /* Interactive MD */
2112 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2113 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2114 if (is->imd_grp[0] != '\0')
2121 printStringNewline(&inp, "NMR refinement stuff");
2122 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2123 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2124 printStringNoNewline(&inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2125 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2126 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2127 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2128 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2129 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2130 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2131 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2132 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2133 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2134 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2135 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2136 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2137 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2138 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2139 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2141 /* free energy variables */
2142 printStringNewline(&inp, "Free energy variables");
2143 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2144 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2145 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2146 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2147 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2149 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2151 it was not entered */
2152 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2153 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2154 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2155 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2156 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2157 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2158 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2159 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2160 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2161 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2162 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2163 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2164 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2165 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2166 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2167 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2168 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2169 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2170 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2171 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2172 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2173 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2174 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2175 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2177 /* Non-equilibrium MD stuff */
2178 printStringNewline(&inp, "Non-equilibrium MD stuff");
2179 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2180 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2181 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2182 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2183 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2184 setStringEntry(&inp, "deform", is->deform, nullptr);
2186 /* simulated tempering variables */
2187 printStringNewline(&inp, "simulated tempering variables");
2188 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2189 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2190 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2191 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2193 /* expanded ensemble variables */
2194 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2196 read_expandedparams(&inp, expand, wi);
2199 /* Electric fields */
2201 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2202 gmx::KeyValueTreeTransformer transform;
2203 transform.rules()->addRule()
2204 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2205 mdModules->initMdpTransform(transform.rules());
2206 for (const auto &path : transform.mappedPaths())
2208 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2209 mark_einp_set(inp, path[0].c_str());
2211 MdpErrorHandler errorHandler(wi);
2213 = transform.transform(convertedValues, &errorHandler);
2214 ir->params = new gmx::KeyValueTreeObject(result.object());
2215 mdModules->adjustInputrecBasedOnModules(ir);
2216 errorHandler.setBackMapping(result.backMapping());
2217 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2220 /* Ion/water position swapping ("computational electrophysiology") */
2221 printStringNewline(&inp, "Ion/water position swapping for computational electrophysiology setups");
2222 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2223 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2224 if (ir->eSwapCoords != eswapNO)
2231 printStringNoNewline(&inp, "Swap attempt frequency");
2232 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2233 printStringNoNewline(&inp, "Number of ion types to be controlled");
2234 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2237 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2239 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2240 snew(ir->swap->grp, ir->swap->ngrp);
2241 for (i = 0; i < ir->swap->ngrp; i++)
2243 snew(ir->swap->grp[i].molname, STRLEN);
2245 printStringNoNewline(&inp, "Two index groups that contain the compartment-partitioning atoms");
2246 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2247 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2248 printStringNoNewline(&inp, "Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2249 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2250 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2252 printStringNoNewline(&inp, "Name of solvent molecules");
2253 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2255 printStringNoNewline(&inp, "Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2256 printStringNoNewline(&inp, "Note that the split cylinder settings do not have an influence on the swapping protocol,");
2257 printStringNoNewline(&inp, "however, if correctly defined, the permeation events are recorded per channel");
2258 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2259 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2260 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2261 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2262 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2263 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2265 printStringNoNewline(&inp, "Average the number of ions per compartment over these many swap attempt steps");
2266 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2268 printStringNoNewline(&inp, "Names of the ion types that can be exchanged with solvent molecules,");
2269 printStringNoNewline(&inp, "and the requested number of ions of this type in compartments A and B");
2270 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2271 for (i = 0; i < nIonTypes; i++)
2273 int ig = eSwapFixedGrpNR + i;
2275 sprintf(buf, "iontype%d-name", i);
2276 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2277 sprintf(buf, "iontype%d-in-A", i);
2278 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2279 sprintf(buf, "iontype%d-in-B", i);
2280 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2283 printStringNoNewline(&inp, "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2284 printStringNoNewline(&inp, "at maximum distance (= bulk concentration) to the split group layers. However,");
2285 printStringNoNewline(&inp, "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2286 printStringNoNewline(&inp, "towards one of the compartment-partitioning layers (at +/- 1.0).");
2287 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2288 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2289 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2290 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2292 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2295 printStringNoNewline(&inp, "Start to swap ions if threshold difference to requested count is reached");
2296 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2299 /* AdResS is no longer supported, but we need grompp to be able to
2300 refuse to process old .mdp files that used it. */
2301 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2303 /* User defined thingies */
2304 printStringNewline(&inp, "User defined thingies");
2305 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2306 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2307 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2308 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2309 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2310 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2311 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2312 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2313 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2314 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2318 gmx::TextOutputFile stream(mdparout);
2319 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2321 // Transform module data into a flat key-value tree for output.
2322 gmx::KeyValueTreeBuilder builder;
2323 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2324 mdModules->buildMdpOutput(&builderObject);
2326 gmx::TextWriter writer(&stream);
2327 writeKeyValueTreeAsMdp(&writer, builder.build());
2332 /* Process options if necessary */
2333 for (m = 0; m < 2; m++)
2335 for (i = 0; i < 2*DIM; i++)
2344 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2346 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2348 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2350 case epctSEMIISOTROPIC:
2351 case epctSURFACETENSION:
2352 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2354 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2356 dumdub[m][YY] = dumdub[m][XX];
2358 case epctANISOTROPIC:
2359 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2360 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2361 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2363 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2367 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2368 epcoupltype_names[ir->epct]);
2372 clear_mat(ir->ref_p);
2373 clear_mat(ir->compress);
2374 for (i = 0; i < DIM; i++)
2376 ir->ref_p[i][i] = dumdub[1][i];
2377 ir->compress[i][i] = dumdub[0][i];
2379 if (ir->epct == epctANISOTROPIC)
2381 ir->ref_p[XX][YY] = dumdub[1][3];
2382 ir->ref_p[XX][ZZ] = dumdub[1][4];
2383 ir->ref_p[YY][ZZ] = dumdub[1][5];
2384 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2386 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2388 ir->compress[XX][YY] = dumdub[0][3];
2389 ir->compress[XX][ZZ] = dumdub[0][4];
2390 ir->compress[YY][ZZ] = dumdub[0][5];
2391 for (i = 0; i < DIM; i++)
2393 for (m = 0; m < i; m++)
2395 ir->ref_p[i][m] = ir->ref_p[m][i];
2396 ir->compress[i][m] = ir->compress[m][i];
2401 if (ir->comm_mode == ecmNO)
2406 opts->couple_moltype = nullptr;
2407 if (strlen(is->couple_moltype) > 0)
2409 if (ir->efep != efepNO)
2411 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2412 if (opts->couple_lam0 == opts->couple_lam1)
2414 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2416 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2417 opts->couple_lam1 == ecouplamNONE))
2419 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2424 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2427 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2428 if (ir->efep != efepNO)
2430 if (fep->delta_lambda > 0)
2432 ir->efep = efepSLOWGROWTH;
2436 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2438 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2439 warning_note(wi, "Old option for dhdl-print-energy given: "
2440 "changing \"yes\" to \"total\"\n");
2443 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2445 /* always print out the energy to dhdl if we are doing
2446 expanded ensemble, since we need the total energy for
2447 analysis if the temperature is changing. In some
2448 conditions one may only want the potential energy, so
2449 we will allow that if the appropriate mdp setting has
2450 been enabled. Otherwise, total it is:
2452 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2455 if ((ir->efep != efepNO) || ir->bSimTemp)
2457 ir->bExpanded = FALSE;
2458 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2460 ir->bExpanded = TRUE;
2462 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2463 if (ir->bSimTemp) /* done after fep params */
2465 do_simtemp_params(ir);
2468 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2469 * setup and not on the old way of specifying the free-energy setup,
2470 * we should check for using soft-core when not needed, since that
2471 * can complicate the sampling significantly.
2472 * Note that we only check for the automated coupling setup.
2473 * If the (advanced) user does FEP through manual topology changes,
2474 * this check will not be triggered.
2476 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2477 ir->fepvals->sc_alpha != 0 &&
2478 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2479 couple_lambda_has_vdw_on(opts->couple_lam1)))
2481 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2486 ir->fepvals->n_lambda = 0;
2489 /* WALL PARAMETERS */
2491 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2493 /* ORIENTATION RESTRAINT PARAMETERS */
2495 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2497 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2500 /* DEFORMATION PARAMETERS */
2502 clear_mat(ir->deform);
2503 for (i = 0; i < 6; i++)
2508 double gmx_unused canary;
2509 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2510 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2511 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2513 if (strlen(is->deform) > 0 && ndeform != 6)
2515 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2517 for (i = 0; i < 3; i++)
2519 ir->deform[i][i] = dumdub[0][i];
2521 ir->deform[YY][XX] = dumdub[0][3];
2522 ir->deform[ZZ][XX] = dumdub[0][4];
2523 ir->deform[ZZ][YY] = dumdub[0][5];
2524 if (ir->epc != epcNO)
2526 for (i = 0; i < 3; i++)
2528 for (j = 0; j <= i; j++)
2530 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2532 warning_error(wi, "A box element has deform set and compressibility > 0");
2536 for (i = 0; i < 3; i++)
2538 for (j = 0; j < i; j++)
2540 if (ir->deform[i][j] != 0)
2542 for (m = j; m < DIM; m++)
2544 if (ir->compress[m][j] != 0)
2546 sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
2547 warning(wi, warn_buf);
2555 /* Ion/water position swapping checks */
2556 if (ir->eSwapCoords != eswapNO)
2558 if (ir->swap->nstswap < 1)
2560 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2562 if (ir->swap->nAverage < 1)
2564 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2566 if (ir->swap->threshold < 1.0)
2568 warning_error(wi, "Ion count threshold must be at least 1.\n");
2576 static int search_QMstring(const char *s, int ng, const char *gn[])
2578 /* same as normal search_string, but this one searches QM strings */
2581 for (i = 0; (i < ng); i++)
2583 if (gmx_strcasecmp(s, gn[i]) == 0)
2589 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2590 } /* search_QMstring */
2592 /* We would like gn to be const as well, but C doesn't allow this */
2593 /* TODO this is utility functionality (search for the index of a
2594 string in a collection), so should be refactored and located more
2596 int search_string(const char *s, int ng, char *gn[])
2600 for (i = 0; (i < ng); i++)
2602 if (gmx_strcasecmp(s, gn[i]) == 0)
2609 "Group %s referenced in the .mdp file was not found in the index file.\n"
2610 "Group names must match either [moleculetype] names or custom index group\n"
2611 "names, in which case you must supply an index file to the '-n' option\n"
2616 static bool do_numbering(int natoms, SimulationGroups *groups,
2617 gmx::ArrayRef<std::string> groupsFromMdpFile,
2618 t_blocka *block, char *gnames[],
2619 SimulationAtomGroupType gtype, int restnm,
2620 int grptp, bool bVerbose,
2623 unsigned short *cbuf;
2624 t_grps *grps = &(groups->groups[gtype]);
2625 int j, gid, aj, ognr, ntot = 0;
2628 char warn_buf[STRLEN];
2630 title = shortName(gtype);
2633 /* Mark all id's as not set */
2634 for (int i = 0; (i < natoms); i++)
2639 snew(grps->nm_ind, groupsFromMdpFile.size()+1); /* +1 for possible rest group */
2640 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2642 /* Lookup the group name in the block structure */
2643 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2644 if ((grptp != egrptpONE) || (i == 0))
2646 grps->nm_ind[grps->nr++] = gid;
2649 /* Now go over the atoms in the group */
2650 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2655 /* Range checking */
2656 if ((aj < 0) || (aj >= natoms))
2658 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2660 /* Lookup up the old group number */
2664 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2665 aj+1, title, ognr+1, i+1);
2669 /* Store the group number in buffer */
2670 if (grptp == egrptpONE)
2683 /* Now check whether we have done all atoms */
2687 if (grptp == egrptpALL)
2689 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2690 natoms-ntot, title);
2692 else if (grptp == egrptpPART)
2694 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2695 natoms-ntot, title);
2696 warning_note(wi, warn_buf);
2698 /* Assign all atoms currently unassigned to a rest group */
2699 for (j = 0; (j < natoms); j++)
2701 if (cbuf[j] == NOGID)
2707 if (grptp != egrptpPART)
2712 "Making dummy/rest group for %s containing %d elements\n",
2713 title, natoms-ntot);
2715 /* Add group name "rest" */
2716 grps->nm_ind[grps->nr] = restnm;
2718 /* Assign the rest name to all atoms not currently assigned to a group */
2719 for (j = 0; (j < natoms); j++)
2721 if (cbuf[j] == NOGID)
2730 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2732 /* All atoms are part of one (or no) group, no index required */
2733 groups->groupNumbers[gtype].clear();
2737 for (int j = 0; (j < natoms); j++)
2739 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2745 return (bRest && grptp == egrptpPART);
2748 static void calc_nrdf(const gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2751 pull_params_t *pull;
2752 int natoms, imin, jmin;
2753 int *nrdf2, *na_vcm, na_tot;
2754 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2759 * First calc 3xnr-atoms for each group
2760 * then subtract half a degree of freedom for each constraint
2762 * Only atoms and nuclei contribute to the degrees of freedom...
2767 const SimulationGroups &groups = mtop->groups;
2768 natoms = mtop->natoms;
2770 /* Allocate one more for a possible rest group */
2771 /* We need to sum degrees of freedom into doubles,
2772 * since floats give too low nrdf's above 3 million atoms.
2774 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr+1);
2775 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1);
2776 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1);
2777 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1);
2778 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1);
2780 for (int i = 0; i < groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr; i++)
2784 for (int i = 0; i < groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1; i++)
2787 clear_ivec(dof_vcm[i]);
2789 nrdf_vcm_sub[i] = 0;
2791 snew(nrdf2, natoms);
2792 for (const AtomProxy atomP : AtomRange(*mtop))
2794 const t_atom &local = atomP.atom();
2795 int i = atomP.globalAtomNumber();
2797 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2799 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2800 for (int d = 0; d < DIM; d++)
2802 if (opts->nFreeze[g][d] == 0)
2804 /* Add one DOF for particle i (counted as 2*1) */
2806 /* VCM group i has dim d as a DOF */
2807 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] = 1;
2810 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] += 0.5*nrdf2[i];
2811 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] += 0.5*nrdf2[i];
2816 for (const gmx_molblock_t &molb : mtop->molblock)
2818 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2819 const t_atom *atom = molt.atoms.atom;
2820 for (int mol = 0; mol < molb.nmol; mol++)
2822 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2824 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2825 for (int i = 0; i < molt.ilist[ftype].size(); )
2827 /* Subtract degrees of freedom for the constraints,
2828 * if the particles still have degrees of freedom left.
2829 * If one of the particles is a vsite or a shell, then all
2830 * constraint motion will go there, but since they do not
2831 * contribute to the constraints the degrees of freedom do not
2834 int ai = as + ia[i + 1];
2835 int aj = as + ia[i + 2];
2836 if (((atom[ia[i + 1]].ptype == eptNucleus) ||
2837 (atom[ia[i + 1]].ptype == eptAtom)) &&
2838 ((atom[ia[i + 2]].ptype == eptNucleus) ||
2839 (atom[ia[i + 2]].ptype == eptAtom)))
2857 imin = std::min(imin, nrdf2[ai]);
2858 jmin = std::min(jmin, nrdf2[aj]);
2861 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2862 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -= 0.5*jmin;
2863 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2864 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -= 0.5*jmin;
2866 i += interaction_function[ftype].nratoms+1;
2869 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2870 for (int i = 0; i < molt.ilist[F_SETTLE].size(); )
2872 /* Subtract 1 dof from every atom in the SETTLE */
2873 for (int j = 0; j < 3; j++)
2875 int ai = as + ia[i + 1 + j];
2876 imin = std::min(2, nrdf2[ai]);
2878 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2879 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2883 as += molt.atoms.nr;
2889 /* Correct nrdf for the COM constraints.
2890 * We correct using the TC and VCM group of the first atom
2891 * in the reference and pull group. If atoms in one pull group
2892 * belong to different TC or VCM groups it is anyhow difficult
2893 * to determine the optimal nrdf assignment.
2897 for (int i = 0; i < pull->ncoord; i++)
2899 if (pull->coord[i].eType != epullCONSTRAINT)
2906 for (int j = 0; j < 2; j++)
2908 const t_pull_group *pgrp;
2910 pgrp = &pull->group[pull->coord[i].group[j]];
2914 /* Subtract 1/2 dof from each group */
2915 int ai = pgrp->ind[0];
2916 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2917 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2918 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
2920 gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
2925 /* We need to subtract the whole DOF from group j=1 */
2932 if (ir->nstcomm != 0)
2936 /* We remove COM motion up to dim ndof_com() */
2937 ndim_rm_vcm = ndof_com(ir);
2939 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
2940 * the number of degrees of freedom in each vcm group when COM
2941 * translation is removed and 6 when rotation is removed as well.
2943 for (int j = 0; j < groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1; j++)
2945 switch (ir->comm_mode)
2948 case ecmLINEAR_ACCELERATION_CORRECTION:
2949 nrdf_vcm_sub[j] = 0;
2950 for (int d = 0; d < ndim_rm_vcm; d++)
2959 nrdf_vcm_sub[j] = 6;
2962 gmx_incons("Checking comm_mode");
2966 for (int i = 0; i < groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr; i++)
2968 /* Count the number of atoms of TC group i for every VCM group */
2969 for (int j = 0; j < groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1; j++)
2974 for (int ai = 0; ai < natoms; ai++)
2976 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
2978 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
2982 /* Correct for VCM removal according to the fraction of each VCM
2983 * group present in this TC group.
2985 nrdf_uc = nrdf_tc[i];
2987 for (int j = 0; j < groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].nr+1; j++)
2989 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
2991 nrdf_tc[i] += nrdf_uc*(static_cast<double>(na_vcm[j])/static_cast<double>(na_tot))*
2992 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
2997 for (int i = 0; (i < groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr); i++)
2999 opts->nrdf[i] = nrdf_tc[i];
3000 if (opts->nrdf[i] < 0)
3005 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3006 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[i]], opts->nrdf[i]);
3014 sfree(nrdf_vcm_sub);
3017 static bool do_egp_flag(t_inputrec *ir, SimulationGroups *groups,
3018 const char *option, const char *val, int flag)
3020 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3021 * But since this is much larger than STRLEN, such a line can not be parsed.
3022 * The real maximum is the number of names that fit in a string: STRLEN/2.
3024 #define EGP_MAX (STRLEN/2)
3028 auto names = gmx::splitString(val);
3029 if (names.size() % 2 != 0)
3031 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3033 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].nr;
3035 for (size_t i = 0; i < names.size() / 2; i++)
3037 // TODO this needs to be replaced by a solution using std::find_if
3040 gmx_strcasecmp(names[2*i].c_str(), *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[j]])))
3046 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3047 names[2*i].c_str(), option);
3051 gmx_strcasecmp(names[2*i+1].c_str(), *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[k]])))
3057 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3058 names[2*i+1].c_str(), option);
3060 if ((j < nr) && (k < nr))
3062 ir->opts.egp_flags[nr*j+k] |= flag;
3063 ir->opts.egp_flags[nr*k+j] |= flag;
3072 static void make_swap_groups(
3077 int ig = -1, i = 0, gind;
3081 /* Just a quick check here, more thorough checks are in mdrun */
3082 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3084 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3087 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3088 for (ig = 0; ig < swap->ngrp; ig++)
3090 swapg = &swap->grp[ig];
3091 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3092 swapg->nat = grps->index[gind+1] - grps->index[gind];
3096 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3097 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3098 swap->grp[ig].molname, swapg->nat);
3099 snew(swapg->ind, swapg->nat);
3100 for (i = 0; i < swapg->nat; i++)
3102 swapg->ind[i] = grps->a[grps->index[gind]+i];
3107 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3113 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3118 ig = search_string(IMDgname, grps->nr, gnames);
3119 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3121 if (IMDgroup->nat > 0)
3123 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3124 IMDgname, IMDgroup->nat);
3125 snew(IMDgroup->ind, IMDgroup->nat);
3126 for (i = 0; i < IMDgroup->nat; i++)
3128 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3133 void do_index(const char* mdparin, const char *ndx,
3139 t_blocka *defaultIndexGroups;
3143 char warnbuf[STRLEN], **gnames;
3147 int i, j, k, restnm;
3148 bool bExcl, bTable, bAnneal, bRest;
3149 char warn_buf[STRLEN];
3153 fprintf(stderr, "processing index file...\n");
3157 snew(defaultIndexGroups, 1);
3158 snew(defaultIndexGroups->index, 1);
3160 atoms_all = gmx_mtop_global_atoms(mtop);
3161 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3162 done_atom(&atoms_all);
3166 defaultIndexGroups = init_index(ndx, &gnames);
3169 SimulationGroups *groups = &mtop->groups;
3170 natoms = mtop->natoms;
3171 symtab = &mtop->symtab;
3173 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3175 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3177 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3178 restnm = groups->groupNames.size() - 1;
3179 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3180 srenew(gnames, defaultIndexGroups->nr+1);
3181 gnames[restnm] = *(groups->groupNames.back());
3183 set_warning_line(wi, mdparin, -1);
3185 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3186 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3187 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3188 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size() ||
3189 temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3191 gmx_fatal(FARGS, "Invalid T coupling input: %zu groups, %zu ref-t values and "
3193 temperatureCouplingGroupNames.size(),
3194 temperatureCouplingReferenceValues.size(),
3195 temperatureCouplingTauValues.size());
3198 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3199 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3200 SimulationAtomGroupType::TemperatureCoupling,
3201 restnm, useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3202 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].nr;
3204 snew(ir->opts.nrdf, nr);
3205 snew(ir->opts.tau_t, nr);
3206 snew(ir->opts.ref_t, nr);
3207 if (ir->eI == eiBD && ir->bd_fric == 0)
3209 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3212 if (useReferenceTemperature)
3214 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3216 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3220 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3221 for (i = 0; (i < nr); i++)
3223 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3225 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3226 warning_error(wi, warn_buf);
3229 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3231 warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3234 if (ir->opts.tau_t[i] >= 0)
3236 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3239 if (ir->etc != etcNO && ir->nsttcouple == -1)
3241 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3246 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3248 gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
3250 if (ir->epc == epcMTTK)
3252 if (ir->etc != etcNOSEHOOVER)
3254 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3258 if (ir->nstpcouple != ir->nsttcouple)
3260 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3261 ir->nstpcouple = ir->nsttcouple = mincouple;
3262 sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
3263 warning_note(wi, warn_buf);
3268 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3269 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3271 if (ETC_ANDERSEN(ir->etc))
3273 if (ir->nsttcouple != 1)
3276 sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
3277 warning_note(wi, warn_buf);
3280 nstcmin = tcouple_min_integration_steps(ir->etc);
3283 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3285 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3286 ETCOUPLTYPE(ir->etc),
3288 ir->nsttcouple*ir->delta_t);
3289 warning(wi, warn_buf);
3292 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3293 for (i = 0; (i < nr); i++)
3295 if (ir->opts.ref_t[i] < 0)
3297 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3300 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3301 if we are in this conditional) if mc_temp is negative */
3302 if (ir->expandedvals->mc_temp < 0)
3304 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3308 /* Simulated annealing for each group. There are nr groups */
3309 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3310 if (simulatedAnnealingGroupNames.size() == 1 &&
3311 gmx_strncasecmp(simulatedAnnealingGroupNames[0].c_str(), "N", 1) == 0)
3313 simulatedAnnealingGroupNames.resize(0);
3315 if (!simulatedAnnealingGroupNames.empty() &&
3316 gmx::ssize(simulatedAnnealingGroupNames) != nr)
3318 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3319 simulatedAnnealingGroupNames.size(), nr);
3323 snew(ir->opts.annealing, nr);
3324 snew(ir->opts.anneal_npoints, nr);
3325 snew(ir->opts.anneal_time, nr);
3326 snew(ir->opts.anneal_temp, nr);
3327 for (i = 0; i < nr; i++)
3329 ir->opts.annealing[i] = eannNO;
3330 ir->opts.anneal_npoints[i] = 0;
3331 ir->opts.anneal_time[i] = nullptr;
3332 ir->opts.anneal_temp[i] = nullptr;
3334 if (!simulatedAnnealingGroupNames.empty())
3337 for (i = 0; i < nr; i++)
3339 if (gmx_strncasecmp(simulatedAnnealingGroupNames[i].c_str(), "N", 1) == 0)
3341 ir->opts.annealing[i] = eannNO;
3343 else if (gmx_strncasecmp(simulatedAnnealingGroupNames[i].c_str(), "S", 1) == 0)
3345 ir->opts.annealing[i] = eannSINGLE;
3348 else if (gmx_strncasecmp(simulatedAnnealingGroupNames[i].c_str(), "P", 1) == 0)
3350 ir->opts.annealing[i] = eannPERIODIC;
3356 /* Read the other fields too */
3357 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3358 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3360 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3361 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3363 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3364 size_t numSimulatedAnnealingFields = 0;
3365 for (i = 0; i < nr; i++)
3367 if (ir->opts.anneal_npoints[i] == 1)
3369 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3371 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3372 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3373 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3376 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3378 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3380 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3381 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3383 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3384 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3386 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3387 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3390 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3391 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3392 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3393 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp", allSimulatedAnnealingTemperatures.data());
3394 for (i = 0, k = 0; i < nr; i++)
3396 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3398 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3399 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3402 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3404 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3410 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3412 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3413 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3416 if (ir->opts.anneal_temp[i][j] < 0)
3418 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3423 /* Print out some summary information, to make sure we got it right */
3424 for (i = 0; i < nr; i++)
3426 if (ir->opts.annealing[i] != eannNO)
3428 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[i];
3429 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3430 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3431 ir->opts.anneal_npoints[i]);
3432 fprintf(stderr, "Time (ps) Temperature (K)\n");
3433 /* All terms except the last one */
3434 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3436 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3439 /* Finally the last one */
3440 j = ir->opts.anneal_npoints[i]-1;
3441 if (ir->opts.annealing[i] == eannSINGLE)
3443 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3447 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3448 if (std::fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3450 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3461 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3463 make_pull_coords(ir->pull);
3468 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3471 if (ir->eSwapCoords != eswapNO)
3473 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3476 /* Make indices for IMD session */
3479 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3482 auto accelerations = gmx::splitString(is->acc);
3483 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3484 if (accelerationGroupNames.size() * DIM != accelerations.size())
3486 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3487 accelerationGroupNames.size(), accelerations.size());
3489 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3490 SimulationAtomGroupType::Acceleration,
3491 restnm, egrptpALL_GENREST, bVerbose, wi);
3492 nr = groups->groups[SimulationAtomGroupType::Acceleration].nr;
3493 snew(ir->opts.acc, nr);
3494 ir->opts.ngacc = nr;
3496 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3498 auto freezeDims = gmx::splitString(is->frdim);
3499 auto freezeGroupNames = gmx::splitString(is->freeze);
3500 if (freezeDims.size() != DIM * freezeGroupNames.size())
3502 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3503 freezeGroupNames.size(), freezeDims.size());
3505 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3506 SimulationAtomGroupType::Freeze,
3507 restnm, egrptpALL_GENREST, bVerbose, wi);
3508 nr = groups->groups[SimulationAtomGroupType::Freeze].nr;
3509 ir->opts.ngfrz = nr;
3510 snew(ir->opts.nFreeze, nr);
3511 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3513 for (j = 0; (j < DIM); j++, k++)
3515 ir->opts.nFreeze[i][j] = static_cast<int>(gmx_strncasecmp(freezeDims[k].c_str(), "Y", 1) == 0);
3516 if (!ir->opts.nFreeze[i][j])
3518 if (gmx_strncasecmp(freezeDims[k].c_str(), "N", 1) != 0)
3520 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3521 "(not %s)", freezeDims[k].c_str());
3522 warning(wi, warn_buf);
3527 for (; (i < nr); i++)
3529 for (j = 0; (j < DIM); j++)
3531 ir->opts.nFreeze[i][j] = 0;
3535 auto energyGroupNames = gmx::splitString(is->energy);
3536 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3537 SimulationAtomGroupType::EnergyOutput,
3538 restnm, egrptpALL_GENREST, bVerbose, wi);
3539 add_wall_energrps(groups, ir->nwall, symtab);
3540 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].nr;
3541 auto vcmGroupNames = gmx::splitString(is->vcm);
3543 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3544 SimulationAtomGroupType::MassCenterVelocityRemoval,
3545 restnm, vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3548 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3549 "This may lead to artifacts.\n"
3550 "In most cases one should use one group for the whole system.");
3553 /* Now we have filled the freeze struct, so we can calculate NRDF */
3554 calc_nrdf(mtop, ir, gnames);
3556 auto user1GroupNames = gmx::splitString(is->user1);
3557 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3558 SimulationAtomGroupType::User1,
3559 restnm, egrptpALL_GENREST, bVerbose, wi);
3560 auto user2GroupNames = gmx::splitString(is->user2);
3561 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3562 SimulationAtomGroupType::User2,
3563 restnm, egrptpALL_GENREST, bVerbose, wi);
3564 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3565 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3566 SimulationAtomGroupType::CompressedPositionOutput,
3567 restnm, egrptpONE, bVerbose, wi);
3568 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3569 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3570 SimulationAtomGroupType::OrientationRestraintsFit,
3571 restnm, egrptpALL_GENREST, bVerbose, wi);
3573 /* QMMM input processing */
3574 auto qmGroupNames = gmx::splitString(is->QMMM);
3575 auto qmMethods = gmx::splitString(is->QMmethod);
3576 auto qmBasisSets = gmx::splitString(is->QMbasis);
3577 if (ir->eI != eiMimic)
3579 if (qmMethods.size() != qmGroupNames.size() ||
3580 qmBasisSets.size() != qmGroupNames.size())
3582 gmx_fatal(FARGS, "Invalid QMMM input: %zu groups %zu basissets"
3583 " and %zu methods\n", qmGroupNames.size(),
3584 qmBasisSets.size(), qmMethods.size());
3586 /* group rest, if any, is always MM! */
3587 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3588 SimulationAtomGroupType::QuantumMechanics,
3589 restnm, egrptpALL_GENREST, bVerbose, wi);
3590 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3591 ir->opts.ngQM = qmGroupNames.size();
3592 snew(ir->opts.QMmethod, nr);
3593 snew(ir->opts.QMbasis, nr);
3594 for (i = 0; i < nr; i++)
3596 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3597 * converted to the corresponding enum in names.c
3599 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(),
3602 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(),
3607 auto qmMultiplicities = gmx::splitString(is->QMmult);
3608 auto qmCharges = gmx::splitString(is->QMcharge);
3609 auto qmbSH = gmx::splitString(is->bSH);
3610 snew(ir->opts.QMmult, nr);
3611 snew(ir->opts.QMcharge, nr);
3612 snew(ir->opts.bSH, nr);
3613 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3614 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3615 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3617 auto CASelectrons = gmx::splitString(is->CASelectrons);
3618 auto CASorbitals = gmx::splitString(is->CASorbitals);
3619 snew(ir->opts.CASelectrons, nr);
3620 snew(ir->opts.CASorbitals, nr);
3621 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3622 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3624 auto SAon = gmx::splitString(is->SAon);
3625 auto SAoff = gmx::splitString(is->SAoff);
3626 auto SAsteps = gmx::splitString(is->SAsteps);
3627 snew(ir->opts.SAon, nr);
3628 snew(ir->opts.SAoff, nr);
3629 snew(ir->opts.SAsteps, nr);
3630 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3631 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3632 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3637 if (qmGroupNames.size() > 1)
3639 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3641 /* group rest, if any, is always MM! */
3642 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3643 SimulationAtomGroupType::QuantumMechanics,
3644 restnm, egrptpALL_GENREST, bVerbose, wi);
3646 ir->opts.ngQM = qmGroupNames.size();
3649 /* end of QMMM input */
3653 for (auto group : gmx::keysOf(groups->groups))
3655 fprintf(stderr, "%-16s has %d element(s):", shortName(group), groups->groups[group].nr);
3656 for (int j = 0; (j < groups->groups[group].nr); j++)
3658 fprintf(stderr, " %s", *(groups->groupNames[groups->groups[group].nm_ind[j]]));
3660 fprintf(stderr, "\n");
3664 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].nr;
3665 snew(ir->opts.egp_flags, nr*nr);
3667 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3668 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3670 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3672 if (bExcl && EEL_FULL(ir->coulombtype))
3674 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3677 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3678 if (bTable && !(ir->vdwtype == evdwUSER) &&
3679 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3680 !(ir->coulombtype == eelPMEUSERSWITCH))
3682 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3685 /* final check before going out of scope if simulated tempering variables
3686 * need to be set to default values.
3688 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3690 ir->expandedvals->nstexpanded = 2*static_cast<int>(ir->opts.tau_t[0]/ir->delta_t);
3691 warning(wi, gmx::formatString("the value for nstexpanded was not specified for "
3692 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3693 "by default, but it is recommended to set it to an explicit value!",
3694 ir->expandedvals->nstexpanded));
3696 for (i = 0; (i < defaultIndexGroups->nr); i++)
3701 done_blocka(defaultIndexGroups);
3702 sfree(defaultIndexGroups);
3708 static void check_disre(const gmx_mtop_t *mtop)
3710 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3712 const gmx_ffparams_t &ffparams = mtop->ffparams;
3715 for (int i = 0; i < ffparams.numTypes(); i++)
3717 int ftype = ffparams.functype[i];
3718 if (ftype == F_DISRES)
3720 int label = ffparams.iparams[i].disres.label;
3721 if (label == old_label)
3723 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3731 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3732 "probably the parameters for multiple pairs in one restraint "
3733 "are not identical\n", ndouble);
3738 static bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3743 gmx_mtop_ilistloop_t iloop;
3752 for (d = 0; d < DIM; d++)
3754 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3756 /* Check for freeze groups */
3757 for (g = 0; g < ir->opts.ngfrz; g++)
3759 for (d = 0; d < DIM; d++)
3761 if (ir->opts.nFreeze[g][d] != 0)
3769 /* Check for position restraints */
3770 iloop = gmx_mtop_ilistloop_init(sys);
3771 while (const InteractionLists *ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3774 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3776 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3778 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3779 for (d = 0; d < DIM; d++)
3781 if (pr->posres.fcA[d] != 0)
3787 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3789 /* Check for flat-bottom posres */
3790 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3791 if (pr->fbposres.k != 0)
3793 switch (pr->fbposres.geom)
3795 case efbposresSPHERE:
3796 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3798 case efbposresCYLINDERX:
3799 AbsRef[YY] = AbsRef[ZZ] = 1;
3801 case efbposresCYLINDERY:
3802 AbsRef[XX] = AbsRef[ZZ] = 1;
3804 case efbposresCYLINDER:
3805 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3806 case efbposresCYLINDERZ:
3807 AbsRef[XX] = AbsRef[YY] = 1;
3809 case efbposresX: /* d=XX */
3810 case efbposresY: /* d=YY */
3811 case efbposresZ: /* d=ZZ */
3812 d = pr->fbposres.geom - efbposresX;
3816 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3817 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3825 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3829 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3830 bool *bC6ParametersWorkWithGeometricRules,
3831 bool *bC6ParametersWorkWithLBRules,
3832 bool *bLBRulesPossible)
3834 int ntypes, tpi, tpj;
3837 double c6i, c6j, c12i, c12j;
3838 double c6, c6_geometric, c6_LB;
3839 double sigmai, sigmaj, epsi, epsj;
3840 bool bCanDoLBRules, bCanDoGeometricRules;
3843 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3844 * force-field floating point parameters.
3847 ptr = getenv("GMX_LJCOMB_TOL");
3851 double gmx_unused canary;
3853 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3855 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3860 *bC6ParametersWorkWithLBRules = TRUE;
3861 *bC6ParametersWorkWithGeometricRules = TRUE;
3862 bCanDoLBRules = TRUE;
3863 ntypes = mtop->ffparams.atnr;
3864 snew(typecount, ntypes);
3865 gmx_mtop_count_atomtypes(mtop, state, typecount);
3866 *bLBRulesPossible = TRUE;
3867 for (tpi = 0; tpi < ntypes; ++tpi)
3869 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3870 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3871 for (tpj = tpi; tpj < ntypes; ++tpj)
3873 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3874 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3875 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3876 c6_geometric = std::sqrt(c6i * c6j);
3877 if (!gmx_numzero(c6_geometric))
3879 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3881 sigmai = gmx::sixthroot(c12i / c6i);
3882 sigmaj = gmx::sixthroot(c12j / c6j);
3883 epsi = c6i * c6i /(4.0 * c12i);
3884 epsj = c6j * c6j /(4.0 * c12j);
3885 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3889 *bLBRulesPossible = FALSE;
3890 c6_LB = c6_geometric;
3892 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3897 *bC6ParametersWorkWithLBRules = FALSE;
3900 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3902 if (!bCanDoGeometricRules)
3904 *bC6ParametersWorkWithGeometricRules = FALSE;
3912 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3915 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3917 check_combination_rule_differences(mtop, 0,
3918 &bC6ParametersWorkWithGeometricRules,
3919 &bC6ParametersWorkWithLBRules,
3921 if (ir->ljpme_combination_rule == eljpmeLB)
3923 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
3925 warning(wi, "You are using arithmetic-geometric combination rules "
3926 "in LJ-PME, but your non-bonded C6 parameters do not "
3927 "follow these rules.");
3932 if (!bC6ParametersWorkWithGeometricRules)
3934 if (ir->eDispCorr != edispcNO)
3936 warning_note(wi, "You are using geometric combination rules in "
3937 "LJ-PME, but your non-bonded C6 parameters do "
3938 "not follow these rules. "
3939 "This will introduce very small errors in the forces and energies in "
3940 "your simulations. Dispersion correction will correct total energy "
3941 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3945 warning_note(wi, "You are using geometric combination rules in "
3946 "LJ-PME, but your non-bonded C6 parameters do "
3947 "not follow these rules. "
3948 "This will introduce very small errors in the forces and energies in "
3949 "your simulations. If your system is homogeneous, consider using dispersion correction "
3950 "for the total energy and pressure.");
3956 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3959 char err_buf[STRLEN];
3964 gmx_mtop_atomloop_block_t aloopb;
3966 char warn_buf[STRLEN];
3968 set_warning_line(wi, mdparin, -1);
3970 if (ir->cutoff_scheme == ecutsVERLET &&
3971 ir->verletbuf_tol > 0 &&
3973 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3974 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3976 /* Check if a too small Verlet buffer might potentially
3977 * cause more drift than the thermostat can couple off.
3979 /* Temperature error fraction for warning and suggestion */
3980 const real T_error_warn = 0.002;
3981 const real T_error_suggest = 0.001;
3982 /* For safety: 2 DOF per atom (typical with constraints) */
3983 const real nrdf_at = 2;
3984 real T, tau, max_T_error;
3989 for (i = 0; i < ir->opts.ngtc; i++)
3991 T = std::max(T, ir->opts.ref_t[i]);
3992 tau = std::max(tau, ir->opts.tau_t[i]);
3996 /* This is a worst case estimate of the temperature error,
3997 * assuming perfect buffer estimation and no cancelation
3998 * of errors. The factor 0.5 is because energy distributes
3999 * equally over Ekin and Epot.
4001 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4002 if (max_T_error > T_error_warn)
4004 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4005 ir->verletbuf_tol, T, tau,
4007 100*T_error_suggest,
4008 ir->verletbuf_tol*T_error_suggest/max_T_error);
4009 warning(wi, warn_buf);
4014 if (ETC_ANDERSEN(ir->etc))
4018 for (i = 0; i < ir->opts.ngtc; i++)
4020 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4021 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4022 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4023 i, ir->opts.tau_t[i]);
4024 CHECK(ir->opts.tau_t[i] < 0);
4027 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4029 for (i = 0; i < ir->opts.ngtc; i++)
4031 int nsteps = gmx::roundToInt(ir->opts.tau_t[i]/ir->delta_t);
4032 sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4033 CHECK(nsteps % ir->nstcomm != 0);
4038 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4039 ir->comm_mode == ecmNO &&
4040 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4041 !ETC_ANDERSEN(ir->etc))
4043 warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
4046 if (ir->epc == epcPARRINELLORAHMAN &&
4047 ir->etc == etcNOSEHOOVER)
4050 for (int g = 0; g < ir->opts.ngtc; g++)
4052 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4054 if (ir->tau_p < 1.9*tau_t_max)
4056 std::string message =
4057 gmx::formatString("With %s T-coupling and %s p-coupling, "
4058 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4059 etcoupl_names[ir->etc],
4060 epcoupl_names[ir->epc],
4062 "tau-t", tau_t_max);
4063 warning(wi, message.c_str());
4067 /* Check for pressure coupling with absolute position restraints */
4068 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4070 absolute_reference(ir, sys, TRUE, AbsRef);
4072 for (m = 0; m < DIM; m++)
4074 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4076 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4084 aloopb = gmx_mtop_atomloop_block_init(sys);
4086 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4088 if (atom->q != 0 || atom->qB != 0)
4096 if (EEL_FULL(ir->coulombtype))
4099 "You are using full electrostatics treatment %s for a system without charges.\n"
4100 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4101 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4102 warning(wi, err_buf);
4107 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4110 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4111 "You might want to consider using %s electrostatics.\n",
4113 warning_note(wi, err_buf);
4117 /* Check if combination rules used in LJ-PME are the same as in the force field */
4118 if (EVDW_PME(ir->vdwtype))
4120 check_combination_rules(ir, sys, wi);
4123 /* Generalized reaction field */
4124 if (ir->opts.ngtc == 0)
4126 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4128 CHECK(ir->coulombtype == eelGRF);
4132 sprintf(err_buf, "When using coulombtype = %s"
4133 " ref-t for temperature coupling should be > 0",
4135 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4139 for (int i = 0; (i < sys->groups.groups[SimulationAtomGroupType::Acceleration].nr); i++)
4141 for (m = 0; (m < DIM); m++)
4143 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4152 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].nr);
4153 for (const AtomProxy atomP : AtomRange(*sys))
4155 const t_atom &local = atomP.atom();
4156 int i = atomP.globalAtomNumber();
4157 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4160 for (i = 0; (i < sys->groups.groups[SimulationAtomGroupType::Acceleration].nr); i++)
4162 for (m = 0; (m < DIM); m++)
4164 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4168 for (m = 0; (m < DIM); m++)
4170 if (fabs(acc[m]) > 1e-6)
4172 const char *dim[DIM] = { "X", "Y", "Z" };
4174 "Net Acceleration in %s direction, will %s be corrected\n",
4175 dim[m], ir->nstcomm != 0 ? "" : "not");
4176 if (ir->nstcomm != 0 && m < ndof_com(ir))
4179 for (i = 0; (i < sys->groups.groups[SimulationAtomGroupType::Acceleration].nr); i++)
4181 ir->opts.acc[i][m] -= acc[m];
4189 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4190 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4192 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4200 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4202 if (ir->pull->coord[i].group[0] == 0 ||
4203 ir->pull->coord[i].group[1] == 0)
4205 absolute_reference(ir, sys, FALSE, AbsRef);
4206 for (m = 0; m < DIM; m++)
4208 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4210 warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
4218 for (i = 0; i < 3; i++)
4220 for (m = 0; m <= i; m++)
4222 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4223 ir->deform[i][m] != 0)
4225 for (c = 0; c < ir->pull->ncoord; c++)
4227 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4228 ir->pull->coord[c].vec[m] != 0)
4230 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4241 void double_check(t_inputrec *ir, matrix box,
4242 bool bHasNormalConstraints,
4243 bool bHasAnyConstraints,
4247 char warn_buf[STRLEN];
4250 ptr = check_box(ir->ePBC, box);
4253 warning_error(wi, ptr);
4256 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4258 if (ir->shake_tol <= 0.0)
4260 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4262 warning_error(wi, warn_buf);
4266 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4268 /* If we have Lincs constraints: */
4269 if (ir->eI == eiMD && ir->etc == etcNO &&
4270 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4272 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4273 warning_note(wi, warn_buf);
4276 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4278 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4279 warning_note(wi, warn_buf);
4281 if (ir->epc == epcMTTK)
4283 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4287 if (bHasAnyConstraints && ir->epc == epcMTTK)
4289 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4292 if (ir->LincsWarnAngle > 90.0)
4294 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4295 warning(wi, warn_buf);
4296 ir->LincsWarnAngle = 90.0;
4299 if (ir->ePBC != epbcNONE)
4301 if (ir->nstlist == 0)
4303 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4305 if (ir->ns_type == ensGRID)
4307 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4309 sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.\n");
4310 warning_error(wi, warn_buf);
4315 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4316 if (2*ir->rlist >= min_size)
4318 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4319 warning_error(wi, warn_buf);
4322 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4329 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4333 real rvdw1, rvdw2, rcoul1, rcoul2;
4334 char warn_buf[STRLEN];
4336 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4340 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4345 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4351 if (rvdw1 + rvdw2 > ir->rlist ||
4352 rcoul1 + rcoul2 > ir->rlist)
4355 "The sum of the two largest charge group radii (%f) "
4356 "is larger than rlist (%f)\n",
4357 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4358 warning(wi, warn_buf);
4362 /* Here we do not use the zero at cut-off macro,
4363 * since user defined interactions might purposely
4364 * not be zero at the cut-off.
4366 if (ir_vdw_is_zero_at_cutoff(ir) &&
4367 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4369 sprintf(warn_buf, "The sum of the two largest charge group "
4370 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4371 "With exact cut-offs, better performance can be "
4372 "obtained with cutoff-scheme = %s, because it "
4373 "does not use charge groups at all.",
4375 ir->rlist, ir->rvdw,
4376 ecutscheme_names[ecutsVERLET]);
4379 warning(wi, warn_buf);
4383 warning_note(wi, warn_buf);
4386 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4387 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4389 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4390 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4392 ir->rlist, ir->rcoulomb,
4393 ecutscheme_names[ecutsVERLET]);
4396 warning(wi, warn_buf);
4400 warning_note(wi, warn_buf);