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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/mdrun/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 // TODO Change this behaviour. There should be exactly one way
884 // to turn off an algorithm.
885 ir->comm_mode = ecmNO;
887 if (ir->comm_mode != ecmNO)
891 // TODO Such input was once valid. Now that we've been
892 // helpful for a few years, we should reject such input,
893 // lest we have to support every historical decision
895 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");
896 ir->nstcomm = abs(ir->nstcomm);
899 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
901 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
902 ir->nstcomm = ir->nstcalcenergy;
905 if (ir->comm_mode == ecmANGULAR)
907 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
908 CHECK(ir->bPeriodicMols);
909 if (ir->ePBC != epbcNONE)
911 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.");
916 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
918 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]);
919 warning_note(wi, warn_buf);
922 /* TEMPERATURE COUPLING */
923 if (ir->etc == etcYES)
925 ir->etc = etcBERENDSEN;
926 warning_note(wi, "Old option for temperature coupling given: "
927 "changing \"yes\" to \"Berendsen\"\n");
930 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
932 if (ir->opts.nhchainlength < 1)
934 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
935 ir->opts.nhchainlength = 1;
936 warning(wi, warn_buf);
939 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
941 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
942 ir->opts.nhchainlength = 1;
947 ir->opts.nhchainlength = 0;
950 if (ir->eI == eiVVAK)
952 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
954 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
957 if (ETC_ANDERSEN(ir->etc))
959 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
960 CHECK(!(EI_VV(ir->eI)));
962 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
964 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]);
965 warning_note(wi, warn_buf);
968 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]);
969 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
972 if (ir->etc == etcBERENDSEN)
974 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
975 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
976 warning_note(wi, warn_buf);
979 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
980 && ir->epc == epcBERENDSEN)
982 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
983 "true ensemble for the thermostat");
984 warning(wi, warn_buf);
987 /* PRESSURE COUPLING */
988 if (ir->epc == epcISOTROPIC)
990 ir->epc = epcBERENDSEN;
991 warning_note(wi, "Old option for pressure coupling given: "
992 "changing \"Isotropic\" to \"Berendsen\"\n");
995 if (ir->epc != epcNO)
997 dt_pcoupl = ir->nstpcouple*ir->delta_t;
999 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1000 CHECK(ir->tau_p <= 0);
1002 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1004 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1005 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1006 warning(wi, warn_buf);
1009 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1010 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1011 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1012 ir->compress[ZZ][ZZ] < 0 ||
1013 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1014 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1016 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1019 "You are generating velocities so I am assuming you "
1020 "are equilibrating a system. You are using "
1021 "%s pressure coupling, but this can be "
1022 "unstable for equilibration. If your system crashes, try "
1023 "equilibrating first with Berendsen pressure coupling. If "
1024 "you are not equilibrating the system, you can probably "
1025 "ignore this warning.",
1026 epcoupl_names[ir->epc]);
1027 warning(wi, warn_buf);
1033 if (ir->epc > epcNO)
1035 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1037 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.");
1043 if (ir->epc == epcMTTK)
1045 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1049 /* ELECTROSTATICS */
1050 /* More checks are in triple check (grompp.c) */
1052 if (ir->coulombtype == eelSWITCH)
1054 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1055 "artifacts, advice: use coulombtype = %s",
1056 eel_names[ir->coulombtype],
1057 eel_names[eelRF_ZERO]);
1058 warning(wi, warn_buf);
1061 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1063 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);
1064 warning(wi, warn_buf);
1065 ir->epsilon_rf = ir->epsilon_r;
1066 ir->epsilon_r = 1.0;
1069 if (ir->epsilon_r == 0)
1072 "It is pointless to use long-range electrostatics with infinite relative permittivity."
1073 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1074 CHECK(EEL_FULL(ir->coulombtype));
1077 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1079 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1080 CHECK(ir->epsilon_r < 0);
1083 if (EEL_RF(ir->coulombtype))
1085 /* reaction field (at the cut-off) */
1087 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1089 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1090 eel_names[ir->coulombtype]);
1091 warning(wi, warn_buf);
1092 ir->epsilon_rf = 0.0;
1095 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1096 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1097 (ir->epsilon_r == 0));
1098 if (ir->epsilon_rf == ir->epsilon_r)
1100 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1101 eel_names[ir->coulombtype]);
1102 warning(wi, warn_buf);
1105 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1106 * means the interaction is zero outside rcoulomb, but it helps to
1107 * provide accurate energy conservation.
1109 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1111 if (ir_coulomb_switched(ir))
1114 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1115 eel_names[ir->coulombtype]);
1116 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1119 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1121 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1123 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1124 eel_names[ir->coulombtype]);
1125 CHECK(ir->rlist > ir->rcoulomb);
1129 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1132 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1133 CHECK( ir->coulomb_modifier != eintmodNONE);
1135 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1138 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1139 CHECK( ir->vdw_modifier != eintmodNONE);
1142 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1143 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1146 "The switch/shift interaction settings are just for compatibility; you will get better "
1147 "performance from applying potential modifiers to your interactions!\n");
1148 warning_note(wi, warn_buf);
1151 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1153 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1155 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1156 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.",
1157 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1158 warning(wi, warn_buf);
1162 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1164 if (ir->rvdw_switch == 0)
1166 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.");
1167 warning(wi, warn_buf);
1171 if (EEL_FULL(ir->coulombtype))
1173 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1174 ir->coulombtype == eelPMEUSERSWITCH)
1176 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1177 eel_names[ir->coulombtype]);
1178 CHECK(ir->rcoulomb > ir->rlist);
1180 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1182 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1185 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1186 "For optimal energy conservation,consider using\n"
1187 "a potential modifier.", eel_names[ir->coulombtype]);
1188 CHECK(ir->rcoulomb != ir->rlist);
1193 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1195 // TODO: Move these checks into the ewald module with the options class
1197 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1199 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1201 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
1202 warning_error(wi, warn_buf);
1206 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1208 if (ir->ewald_geometry == eewg3D)
1210 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1211 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1212 warning(wi, warn_buf);
1214 /* This check avoids extra pbc coding for exclusion corrections */
1215 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1216 CHECK(ir->wall_ewald_zfac < 2);
1218 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1219 EEL_FULL(ir->coulombtype))
1221 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1222 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1223 warning(wi, warn_buf);
1225 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1227 if (ir->cutoff_scheme == ecutsVERLET)
1229 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1230 eel_names[ir->coulombtype]);
1231 warning(wi, warn_buf);
1235 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",
1236 eel_names[ir->coulombtype]);
1237 warning_note(wi, warn_buf);
1241 if (ir_vdw_switched(ir))
1243 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1244 CHECK(ir->rvdw_switch >= ir->rvdw);
1246 if (ir->rvdw_switch < 0.5*ir->rvdw)
1248 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.",
1249 ir->rvdw_switch, ir->rvdw);
1250 warning_note(wi, warn_buf);
1253 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1255 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1257 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1258 CHECK(ir->rlist > ir->rvdw);
1262 if (ir->vdwtype == evdwPME)
1264 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1266 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1267 evdw_names[ir->vdwtype],
1268 eintmod_names[eintmodPOTSHIFT],
1269 eintmod_names[eintmodNONE]);
1270 warning_error(wi, err_buf);
1274 if (ir->cutoff_scheme == ecutsGROUP)
1276 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1277 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1279 warning_note(wi, "With exact cut-offs, rlist should be "
1280 "larger than rcoulomb and rvdw, so that there "
1281 "is a buffer region for particle motion "
1282 "between neighborsearch steps");
1285 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1287 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1288 warning_note(wi, warn_buf);
1290 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1292 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1293 warning_note(wi, warn_buf);
1297 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1299 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.");
1302 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1305 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1308 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1310 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1313 /* ENERGY CONSERVATION */
1314 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1316 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1318 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1319 evdw_names[evdwSHIFT]);
1320 warning_note(wi, warn_buf);
1322 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1324 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1325 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1326 warning_note(wi, warn_buf);
1330 /* IMPLICIT SOLVENT */
1331 if (ir->coulombtype == eelGB_NOTUSED)
1333 sprintf(warn_buf, "Invalid option %s for coulombtype",
1334 eel_names[ir->coulombtype]);
1335 warning_error(wi, warn_buf);
1340 if (ir->cutoff_scheme != ecutsGROUP)
1342 warning_error(wi, "QMMM is currently only supported with cutoff-scheme=group");
1344 if (!EI_DYNAMICS(ir->eI))
1347 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1348 warning_error(wi, buf);
1354 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1358 /* interpret a number of doubles from a string and put them in an array,
1359 after allocating space for them.
1360 str = the input string
1361 n = the (pre-allocated) number of doubles read
1362 r = the output array of doubles. */
1363 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1365 auto values = gmx::splitString(str);
1369 for (int i = 0; i < *n; i++)
1373 (*r)[i] = gmx::fromString<real>(values[i]);
1375 catch (gmx::GromacsException &)
1377 warning_error(wi, "Invalid value " + values[i] + " in string in mdp file. Expected a real number.");
1383 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1386 int i, j, max_n_lambda, nweights, nfep[efptNR];
1387 t_lambda *fep = ir->fepvals;
1388 t_expanded *expand = ir->expandedvals;
1389 real **count_fep_lambdas;
1390 bool bOneLambda = TRUE;
1392 snew(count_fep_lambdas, efptNR);
1394 /* FEP input processing */
1395 /* first, identify the number of lambda values for each type.
1396 All that are nonzero must have the same number */
1398 for (i = 0; i < efptNR; i++)
1400 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1403 /* now, determine the number of components. All must be either zero, or equal. */
1406 for (i = 0; i < efptNR; i++)
1408 if (nfep[i] > max_n_lambda)
1410 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1411 must have the same number if its not zero.*/
1416 for (i = 0; i < efptNR; i++)
1420 ir->fepvals->separate_dvdl[i] = FALSE;
1422 else if (nfep[i] == max_n_lambda)
1424 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1425 respect to the temperature currently */
1427 ir->fepvals->separate_dvdl[i] = TRUE;
1432 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1433 nfep[i], efpt_names[i], max_n_lambda);
1436 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1437 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1439 /* the number of lambdas is the number we've read in, which is either zero
1440 or the same for all */
1441 fep->n_lambda = max_n_lambda;
1443 /* allocate space for the array of lambda values */
1444 snew(fep->all_lambda, efptNR);
1445 /* if init_lambda is defined, we need to set lambda */
1446 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1448 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1450 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1451 for (i = 0; i < efptNR; i++)
1453 snew(fep->all_lambda[i], fep->n_lambda);
1454 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1457 for (j = 0; j < fep->n_lambda; j++)
1459 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1461 sfree(count_fep_lambdas[i]);
1464 sfree(count_fep_lambdas);
1466 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1467 bookkeeping -- for now, init_lambda */
1469 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1471 for (i = 0; i < fep->n_lambda; i++)
1473 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1477 /* check to see if only a single component lambda is defined, and soft core is defined.
1478 In this case, turn on coulomb soft core */
1480 if (max_n_lambda == 0)
1486 for (i = 0; i < efptNR; i++)
1488 if ((nfep[i] != 0) && (i != efptFEP))
1494 if ((bOneLambda) && (fep->sc_alpha > 0))
1496 fep->bScCoul = TRUE;
1499 /* Fill in the others with the efptFEP if they are not explicitly
1500 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1501 they are all zero. */
1503 for (i = 0; i < efptNR; i++)
1505 if ((nfep[i] == 0) && (i != efptFEP))
1507 for (j = 0; j < fep->n_lambda; j++)
1509 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1515 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1516 if (fep->sc_r_power == 48)
1518 if (fep->sc_alpha > 0.1)
1520 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1524 /* now read in the weights */
1525 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1528 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1530 else if (nweights != fep->n_lambda)
1532 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1533 nweights, fep->n_lambda);
1535 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1537 expand->nstexpanded = fep->nstdhdl;
1538 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1543 static void do_simtemp_params(t_inputrec *ir)
1546 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1547 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1551 convertYesNos(warninp_t /*wi*/, gmx::ArrayRef<const std::string> inputs, const char * /*name*/, gmx_bool *outputs)
1554 for (const auto &input : inputs)
1556 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1561 template <typename T> void
1562 convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, T *outputs)
1565 for (const auto &input : inputs)
1569 outputs[i] = gmx::fromStdString<T>(input);
1571 catch (gmx::GromacsException &)
1573 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of integers separated by spaces.",
1575 warning_error(wi, message);
1582 convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, real *outputs)
1585 for (const auto &input : inputs)
1589 outputs[i] = gmx::fromString<real>(input);
1591 catch (gmx::GromacsException &)
1593 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of real numbers separated by spaces.",
1595 warning_error(wi, message);
1602 convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char *name, rvec *outputs)
1605 for (const auto &input : inputs)
1609 outputs[i][d] = gmx::fromString<real>(input);
1611 catch (gmx::GromacsException &)
1613 auto message = gmx::formatString("Invalid value for mdp option %s. %s should only consist of real numbers separated by spaces.",
1615 warning_error(wi, message);
1626 static void do_wall_params(t_inputrec *ir,
1627 char *wall_atomtype, char *wall_density,
1631 opts->wall_atomtype[0] = nullptr;
1632 opts->wall_atomtype[1] = nullptr;
1634 ir->wall_atomtype[0] = -1;
1635 ir->wall_atomtype[1] = -1;
1636 ir->wall_density[0] = 0;
1637 ir->wall_density[1] = 0;
1641 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1642 if (wallAtomTypes.size() != size_t(ir->nwall))
1644 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu",
1645 ir->nwall, wallAtomTypes.size());
1647 for (int i = 0; i < ir->nwall; i++)
1649 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1652 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1654 auto wallDensity = gmx::splitString(wall_density);
1655 if (wallDensity.size() != size_t(ir->nwall))
1657 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall, wallDensity.size());
1659 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1660 for (int i = 0; i < ir->nwall; i++)
1662 if (ir->wall_density[i] <= 0)
1664 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1671 static void add_wall_energrps(SimulationGroups *groups, int nwall, t_symtab *symtab)
1675 AtomGroupIndices *grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1676 for (int i = 0; i < nwall; i++)
1678 groups->groupNames.emplace_back(
1681 gmx::formatString("wall%d", i).c_str()));
1682 grps->emplace_back(groups->groupNames.size() - 1);
1687 static void read_expandedparams(std::vector<t_inpfile> *inp,
1688 t_expanded *expand, warninp_t wi)
1690 /* read expanded ensemble parameters */
1691 printStringNewline(inp, "expanded ensemble variables");
1692 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1693 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1694 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1695 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1696 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1697 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1698 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1699 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1700 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1701 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1702 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1703 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1704 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1705 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1706 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1707 expand->bSymmetrizedTMatrix = (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1708 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1709 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1710 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1711 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1712 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1713 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1714 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1717 /*! \brief Return whether an end state with the given coupling-lambda
1718 * value describes fully-interacting VDW.
1720 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1721 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1723 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1725 return (couple_lambda_value == ecouplamVDW ||
1726 couple_lambda_value == ecouplamVDWQ);
1732 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1735 explicit MdpErrorHandler(warninp_t wi)
1736 : wi_(wi), mapping_(nullptr)
1740 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1742 mapping_ = &mapping;
1745 bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context) override
1747 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1748 getOptionName(context).c_str()));
1749 std::string message = gmx::formatExceptionMessageToString(*ex);
1750 warning_error(wi_, message.c_str());
1755 std::string getOptionName(const gmx::KeyValueTreePath &context)
1757 if (mapping_ != nullptr)
1759 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1760 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1763 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1768 const gmx::IKeyValueTreeBackMapping *mapping_;
1773 void get_ir(const char *mdparin, const char *mdparout,
1774 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1775 WriteMdpHeader writeMdpHeader, warninp_t wi)
1778 double dumdub[2][6];
1780 char warn_buf[STRLEN];
1781 t_lambda *fep = ir->fepvals;
1782 t_expanded *expand = ir->expandedvals;
1784 const char *no_names[] = { "no", nullptr };
1786 init_inputrec_strings();
1787 gmx::TextInputFile stream(mdparin);
1788 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1790 snew(dumstr[0], STRLEN);
1791 snew(dumstr[1], STRLEN);
1793 if (-1 == search_einp(inp, "cutoff-scheme"))
1796 "%s did not specify a value for the .mdp option "
1797 "\"cutoff-scheme\". Probably it was first intended for use "
1798 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1799 "introduced, but the group scheme was still the default. "
1800 "The default is now the Verlet scheme, so you will observe "
1801 "different behaviour.", mdparin);
1802 warning_note(wi, warn_buf);
1805 /* ignore the following deprecated commands */
1806 replace_inp_entry(inp, "title", nullptr);
1807 replace_inp_entry(inp, "cpp", nullptr);
1808 replace_inp_entry(inp, "domain-decomposition", nullptr);
1809 replace_inp_entry(inp, "andersen-seed", nullptr);
1810 replace_inp_entry(inp, "dihre", nullptr);
1811 replace_inp_entry(inp, "dihre-fc", nullptr);
1812 replace_inp_entry(inp, "dihre-tau", nullptr);
1813 replace_inp_entry(inp, "nstdihreout", nullptr);
1814 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1815 replace_inp_entry(inp, "optimize-fft", nullptr);
1816 replace_inp_entry(inp, "adress_type", nullptr);
1817 replace_inp_entry(inp, "adress_const_wf", nullptr);
1818 replace_inp_entry(inp, "adress_ex_width", nullptr);
1819 replace_inp_entry(inp, "adress_hy_width", nullptr);
1820 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1821 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1822 replace_inp_entry(inp, "adress_site", nullptr);
1823 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1824 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1825 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1826 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1827 replace_inp_entry(inp, "rlistlong", nullptr);
1828 replace_inp_entry(inp, "nstcalclr", nullptr);
1829 replace_inp_entry(inp, "pull-print-com2", nullptr);
1830 replace_inp_entry(inp, "gb-algorithm", nullptr);
1831 replace_inp_entry(inp, "nstgbradii", nullptr);
1832 replace_inp_entry(inp, "rgbradii", nullptr);
1833 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1834 replace_inp_entry(inp, "gb-saltconc", nullptr);
1835 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1836 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1837 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1838 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1839 replace_inp_entry(inp, "sa-algorithm", nullptr);
1840 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1842 /* replace the following commands with the clearer new versions*/
1843 replace_inp_entry(inp, "unconstrained-start", "continuation");
1844 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1845 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1846 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1847 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1848 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1849 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1851 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1852 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1853 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1854 setStringEntry(&inp, "include", opts->include, nullptr);
1855 printStringNoNewline(&inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1856 setStringEntry(&inp, "define", opts->define, nullptr);
1858 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1859 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1860 printStringNoNewline(&inp, "Start time and timestep in ps");
1861 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1862 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1863 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1864 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1865 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1866 printStringNoNewline(&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1867 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1868 printStringNoNewline(&inp, "mode for center of mass motion removal");
1869 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1870 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1871 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1872 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1873 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1875 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1876 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1877 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1878 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1881 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1882 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1883 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1884 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1885 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1886 ir->niter = get_eint(&inp, "niter", 20, wi);
1887 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1888 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1889 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1890 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1891 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1893 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1894 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1896 /* Output options */
1897 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1898 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1899 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1900 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1901 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1902 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1903 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1904 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1905 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1906 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1907 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1908 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1909 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1910 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1911 printStringNoNewline(&inp, "default, all atoms will be written.");
1912 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1913 printStringNoNewline(&inp, "Selection of energy groups");
1914 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1916 /* Neighbor searching */
1917 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1918 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1919 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1920 printStringNoNewline(&inp, "nblist update frequency");
1921 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1922 printStringNoNewline(&inp, "ns algorithm (simple or grid)");
1923 ir->ns_type = get_eeenum(&inp, "ns-type", ens_names, wi);
1924 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1925 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1926 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1927 printStringNoNewline(&inp, "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1928 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1929 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1930 printStringNoNewline(&inp, "nblist cut-off");
1931 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1932 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1934 /* Electrostatics */
1935 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1936 printStringNoNewline(&inp, "Method for doing electrostatics");
1937 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1938 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1939 printStringNoNewline(&inp, "cut-off lengths");
1940 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1941 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1942 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
1943 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1944 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1945 printStringNoNewline(&inp, "Method for doing Van der Waals");
1946 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1947 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1948 printStringNoNewline(&inp, "cut-off lengths");
1949 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1950 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1951 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1952 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1953 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1954 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1955 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1956 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1957 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1958 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1959 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1960 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1961 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1962 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1963 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1964 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1965 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1966 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1967 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1968 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1969 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1971 /* Implicit solvation is no longer supported, but we need grompp
1972 to be able to refuse old .mdp files that would have built a tpr
1973 to run it. Thus, only "no" is accepted. */
1974 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
1976 /* Coupling stuff */
1977 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
1978 printStringNoNewline(&inp, "Temperature coupling");
1979 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
1980 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
1981 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
1982 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
1983 printStringNoNewline(&inp, "Groups to couple separately");
1984 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
1985 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
1986 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
1987 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
1988 printStringNoNewline(&inp, "pressure coupling");
1989 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
1990 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
1991 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
1992 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
1993 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
1994 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
1995 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
1996 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
1997 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2000 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2001 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2002 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2003 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2004 printStringNoNewline(&inp, "QM method");
2005 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2006 printStringNoNewline(&inp, "QMMM scheme");
2007 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2008 printStringNoNewline(&inp, "QM basisset");
2009 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2010 printStringNoNewline(&inp, "QM charge");
2011 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2012 printStringNoNewline(&inp, "QM multiplicity");
2013 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2014 printStringNoNewline(&inp, "Surface Hopping");
2015 setStringEntry(&inp, "SH", is->bSH, nullptr);
2016 printStringNoNewline(&inp, "CAS space options");
2017 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2018 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2019 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2020 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2021 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2022 printStringNoNewline(&inp, "Scale factor for MM charges");
2023 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2025 /* Simulated annealing */
2026 printStringNewline(&inp, "SIMULATED ANNEALING");
2027 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2028 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2029 printStringNoNewline(&inp, "Number of time points to use for specifying annealing in each group");
2030 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2031 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2032 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2033 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2034 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2037 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2038 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2039 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2040 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2043 printStringNewline(&inp, "OPTIONS FOR BONDS");
2044 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2045 printStringNoNewline(&inp, "Type of constraint algorithm");
2046 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2047 printStringNoNewline(&inp, "Do not constrain the start configuration");
2048 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2049 printStringNoNewline(&inp, "Use successive overrelaxation to reduce the number of shake iterations");
2050 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2051 printStringNoNewline(&inp, "Relative tolerance of shake");
2052 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2053 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2054 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2055 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2056 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2057 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2058 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2059 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2060 printStringNoNewline(&inp, "rotates over more degrees than");
2061 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2062 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2063 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2065 /* Energy group exclusions */
2066 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2067 printStringNoNewline(&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2068 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2071 printStringNewline(&inp, "WALLS");
2072 printStringNoNewline(&inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2073 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2074 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2075 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2076 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2077 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2078 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2081 printStringNewline(&inp, "COM PULLING");
2082 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2086 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2090 NOTE: needs COM pulling input */
2091 printStringNewline(&inp, "AWH biasing");
2092 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2097 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2101 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2105 /* Enforced rotation */
2106 printStringNewline(&inp, "ENFORCED ROTATION");
2107 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2108 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2112 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2115 /* Interactive MD */
2117 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2118 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2119 if (is->imd_grp[0] != '\0')
2126 printStringNewline(&inp, "NMR refinement stuff");
2127 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2128 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2129 printStringNoNewline(&inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2130 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2131 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2132 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2133 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2134 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2135 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2136 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2137 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2138 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2139 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2140 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2141 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2142 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2143 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2144 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2146 /* free energy variables */
2147 printStringNewline(&inp, "Free energy variables");
2148 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2149 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2150 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2151 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2152 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2154 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2156 it was not entered */
2157 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2158 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2159 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2160 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2161 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2162 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2163 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2164 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2165 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2166 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2167 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2168 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2169 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2170 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2171 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2172 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2173 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2174 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2175 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2176 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2177 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2178 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2179 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2180 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2182 /* Non-equilibrium MD stuff */
2183 printStringNewline(&inp, "Non-equilibrium MD stuff");
2184 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2185 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2186 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2187 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2188 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2189 setStringEntry(&inp, "deform", is->deform, nullptr);
2191 /* simulated tempering variables */
2192 printStringNewline(&inp, "simulated tempering variables");
2193 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2194 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2195 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2196 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2198 /* expanded ensemble variables */
2199 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2201 read_expandedparams(&inp, expand, wi);
2204 /* Electric fields */
2206 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2207 gmx::KeyValueTreeTransformer transform;
2208 transform.rules()->addRule()
2209 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2210 mdModules->initMdpTransform(transform.rules());
2211 for (const auto &path : transform.mappedPaths())
2213 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2214 mark_einp_set(inp, path[0].c_str());
2216 MdpErrorHandler errorHandler(wi);
2218 = transform.transform(convertedValues, &errorHandler);
2219 ir->params = new gmx::KeyValueTreeObject(result.object());
2220 mdModules->adjustInputrecBasedOnModules(ir);
2221 errorHandler.setBackMapping(result.backMapping());
2222 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2225 /* Ion/water position swapping ("computational electrophysiology") */
2226 printStringNewline(&inp, "Ion/water position swapping for computational electrophysiology setups");
2227 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2228 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2229 if (ir->eSwapCoords != eswapNO)
2236 printStringNoNewline(&inp, "Swap attempt frequency");
2237 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2238 printStringNoNewline(&inp, "Number of ion types to be controlled");
2239 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2242 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2244 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2245 snew(ir->swap->grp, ir->swap->ngrp);
2246 for (i = 0; i < ir->swap->ngrp; i++)
2248 snew(ir->swap->grp[i].molname, STRLEN);
2250 printStringNoNewline(&inp, "Two index groups that contain the compartment-partitioning atoms");
2251 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2252 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2253 printStringNoNewline(&inp, "Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2254 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2255 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2257 printStringNoNewline(&inp, "Name of solvent molecules");
2258 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2260 printStringNoNewline(&inp, "Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2261 printStringNoNewline(&inp, "Note that the split cylinder settings do not have an influence on the swapping protocol,");
2262 printStringNoNewline(&inp, "however, if correctly defined, the permeation events are recorded per channel");
2263 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2264 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2265 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2266 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2267 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2268 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2270 printStringNoNewline(&inp, "Average the number of ions per compartment over these many swap attempt steps");
2271 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2273 printStringNoNewline(&inp, "Names of the ion types that can be exchanged with solvent molecules,");
2274 printStringNoNewline(&inp, "and the requested number of ions of this type in compartments A and B");
2275 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2276 for (i = 0; i < nIonTypes; i++)
2278 int ig = eSwapFixedGrpNR + i;
2280 sprintf(buf, "iontype%d-name", i);
2281 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2282 sprintf(buf, "iontype%d-in-A", i);
2283 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2284 sprintf(buf, "iontype%d-in-B", i);
2285 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2288 printStringNoNewline(&inp, "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2289 printStringNoNewline(&inp, "at maximum distance (= bulk concentration) to the split group layers. However,");
2290 printStringNoNewline(&inp, "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2291 printStringNoNewline(&inp, "towards one of the compartment-partitioning layers (at +/- 1.0).");
2292 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2293 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2294 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2295 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2297 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2300 printStringNoNewline(&inp, "Start to swap ions if threshold difference to requested count is reached");
2301 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2304 /* AdResS is no longer supported, but we need grompp to be able to
2305 refuse to process old .mdp files that used it. */
2306 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2308 /* User defined thingies */
2309 printStringNewline(&inp, "User defined thingies");
2310 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2311 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2312 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2313 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2314 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2315 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2316 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2317 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2318 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2319 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2323 gmx::TextOutputFile stream(mdparout);
2324 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2326 // Transform module data into a flat key-value tree for output.
2327 gmx::KeyValueTreeBuilder builder;
2328 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2329 mdModules->buildMdpOutput(&builderObject);
2331 gmx::TextWriter writer(&stream);
2332 writeKeyValueTreeAsMdp(&writer, builder.build());
2337 /* Process options if necessary */
2338 for (m = 0; m < 2; m++)
2340 for (i = 0; i < 2*DIM; i++)
2349 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2351 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2353 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2355 case epctSEMIISOTROPIC:
2356 case epctSURFACETENSION:
2357 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2359 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2361 dumdub[m][YY] = dumdub[m][XX];
2363 case epctANISOTROPIC:
2364 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2365 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2366 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2368 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2372 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2373 epcoupltype_names[ir->epct]);
2377 clear_mat(ir->ref_p);
2378 clear_mat(ir->compress);
2379 for (i = 0; i < DIM; i++)
2381 ir->ref_p[i][i] = dumdub[1][i];
2382 ir->compress[i][i] = dumdub[0][i];
2384 if (ir->epct == epctANISOTROPIC)
2386 ir->ref_p[XX][YY] = dumdub[1][3];
2387 ir->ref_p[XX][ZZ] = dumdub[1][4];
2388 ir->ref_p[YY][ZZ] = dumdub[1][5];
2389 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2391 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2393 ir->compress[XX][YY] = dumdub[0][3];
2394 ir->compress[XX][ZZ] = dumdub[0][4];
2395 ir->compress[YY][ZZ] = dumdub[0][5];
2396 for (i = 0; i < DIM; i++)
2398 for (m = 0; m < i; m++)
2400 ir->ref_p[i][m] = ir->ref_p[m][i];
2401 ir->compress[i][m] = ir->compress[m][i];
2406 if (ir->comm_mode == ecmNO)
2411 opts->couple_moltype = nullptr;
2412 if (strlen(is->couple_moltype) > 0)
2414 if (ir->efep != efepNO)
2416 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2417 if (opts->couple_lam0 == opts->couple_lam1)
2419 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2421 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2422 opts->couple_lam1 == ecouplamNONE))
2424 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2429 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2432 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2433 if (ir->efep != efepNO)
2435 if (fep->delta_lambda > 0)
2437 ir->efep = efepSLOWGROWTH;
2441 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2443 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2444 warning_note(wi, "Old option for dhdl-print-energy given: "
2445 "changing \"yes\" to \"total\"\n");
2448 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2450 /* always print out the energy to dhdl if we are doing
2451 expanded ensemble, since we need the total energy for
2452 analysis if the temperature is changing. In some
2453 conditions one may only want the potential energy, so
2454 we will allow that if the appropriate mdp setting has
2455 been enabled. Otherwise, total it is:
2457 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2460 if ((ir->efep != efepNO) || ir->bSimTemp)
2462 ir->bExpanded = FALSE;
2463 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2465 ir->bExpanded = TRUE;
2467 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2468 if (ir->bSimTemp) /* done after fep params */
2470 do_simtemp_params(ir);
2473 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2474 * setup and not on the old way of specifying the free-energy setup,
2475 * we should check for using soft-core when not needed, since that
2476 * can complicate the sampling significantly.
2477 * Note that we only check for the automated coupling setup.
2478 * If the (advanced) user does FEP through manual topology changes,
2479 * this check will not be triggered.
2481 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2482 ir->fepvals->sc_alpha != 0 &&
2483 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2484 couple_lambda_has_vdw_on(opts->couple_lam1)))
2486 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.");
2491 ir->fepvals->n_lambda = 0;
2494 /* WALL PARAMETERS */
2496 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2498 /* ORIENTATION RESTRAINT PARAMETERS */
2500 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2502 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2505 /* DEFORMATION PARAMETERS */
2507 clear_mat(ir->deform);
2508 for (i = 0; i < 6; i++)
2513 double gmx_unused canary;
2514 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2515 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2516 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2518 if (strlen(is->deform) > 0 && ndeform != 6)
2520 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2522 for (i = 0; i < 3; i++)
2524 ir->deform[i][i] = dumdub[0][i];
2526 ir->deform[YY][XX] = dumdub[0][3];
2527 ir->deform[ZZ][XX] = dumdub[0][4];
2528 ir->deform[ZZ][YY] = dumdub[0][5];
2529 if (ir->epc != epcNO)
2531 for (i = 0; i < 3; i++)
2533 for (j = 0; j <= i; j++)
2535 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2537 warning_error(wi, "A box element has deform set and compressibility > 0");
2541 for (i = 0; i < 3; i++)
2543 for (j = 0; j < i; j++)
2545 if (ir->deform[i][j] != 0)
2547 for (m = j; m < DIM; m++)
2549 if (ir->compress[m][j] != 0)
2551 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.");
2552 warning(wi, warn_buf);
2560 /* Ion/water position swapping checks */
2561 if (ir->eSwapCoords != eswapNO)
2563 if (ir->swap->nstswap < 1)
2565 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2567 if (ir->swap->nAverage < 1)
2569 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2571 if (ir->swap->threshold < 1.0)
2573 warning_error(wi, "Ion count threshold must be at least 1.\n");
2581 static int search_QMstring(const char *s, int ng, const char *gn[])
2583 /* same as normal search_string, but this one searches QM strings */
2586 for (i = 0; (i < ng); i++)
2588 if (gmx_strcasecmp(s, gn[i]) == 0)
2594 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2595 } /* search_QMstring */
2597 /* We would like gn to be const as well, but C doesn't allow this */
2598 /* TODO this is utility functionality (search for the index of a
2599 string in a collection), so should be refactored and located more
2601 int search_string(const char *s, int ng, char *gn[])
2605 for (i = 0; (i < ng); i++)
2607 if (gmx_strcasecmp(s, gn[i]) == 0)
2614 "Group %s referenced in the .mdp file was not found in the index file.\n"
2615 "Group names must match either [moleculetype] names or custom index group\n"
2616 "names, in which case you must supply an index file to the '-n' option\n"
2621 static bool do_numbering(int natoms, SimulationGroups *groups,
2622 gmx::ArrayRef<std::string> groupsFromMdpFile,
2623 t_blocka *block, char *gnames[],
2624 SimulationAtomGroupType gtype, int restnm,
2625 int grptp, bool bVerbose,
2628 unsigned short *cbuf;
2629 AtomGroupIndices *grps = &(groups->groups[gtype]);
2630 int j, gid, aj, ognr, ntot = 0;
2633 char warn_buf[STRLEN];
2635 title = shortName(gtype);
2638 /* Mark all id's as not set */
2639 for (int i = 0; (i < natoms); i++)
2644 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2646 /* Lookup the group name in the block structure */
2647 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2648 if ((grptp != egrptpONE) || (i == 0))
2650 grps->emplace_back(gid);
2653 /* Now go over the atoms in the group */
2654 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2659 /* Range checking */
2660 if ((aj < 0) || (aj >= natoms))
2662 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2664 /* Lookup up the old group number */
2668 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2669 aj+1, title, ognr+1, i+1);
2673 /* Store the group number in buffer */
2674 if (grptp == egrptpONE)
2687 /* Now check whether we have done all atoms */
2691 if (grptp == egrptpALL)
2693 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2694 natoms-ntot, title);
2696 else if (grptp == egrptpPART)
2698 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2699 natoms-ntot, title);
2700 warning_note(wi, warn_buf);
2702 /* Assign all atoms currently unassigned to a rest group */
2703 for (j = 0; (j < natoms); j++)
2705 if (cbuf[j] == NOGID)
2707 cbuf[j] = grps->size();
2711 if (grptp != egrptpPART)
2716 "Making dummy/rest group for %s containing %d elements\n",
2717 title, natoms-ntot);
2719 /* Add group name "rest" */
2720 grps->emplace_back(restnm);
2722 /* Assign the rest name to all atoms not currently assigned to a group */
2723 for (j = 0; (j < natoms); j++)
2725 if (cbuf[j] == NOGID)
2727 // group size was not updated before this here, so need to use -1.
2728 cbuf[j] = grps->size() - 1;
2734 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2736 /* All atoms are part of one (or no) group, no index required */
2737 groups->groupNumbers[gtype].clear();
2741 for (int j = 0; (j < natoms); j++)
2743 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2749 return (bRest && grptp == egrptpPART);
2752 static void calc_nrdf(const gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2755 pull_params_t *pull;
2756 int natoms, imin, jmin;
2757 int *nrdf2, *na_vcm, na_tot;
2758 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2763 * First calc 3xnr-atoms for each group
2764 * then subtract half a degree of freedom for each constraint
2766 * Only atoms and nuclei contribute to the degrees of freedom...
2771 const SimulationGroups &groups = mtop->groups;
2772 natoms = mtop->natoms;
2774 /* Allocate one more for a possible rest group */
2775 /* We need to sum degrees of freedom into doubles,
2776 * since floats give too low nrdf's above 3 million atoms.
2778 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size()+1);
2779 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()+1);
2780 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()+1);
2781 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()+1);
2782 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()+1);
2784 for (int i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2788 for (int i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval])+1; i++)
2791 clear_ivec(dof_vcm[i]);
2793 nrdf_vcm_sub[i] = 0;
2795 snew(nrdf2, natoms);
2796 for (const AtomProxy atomP : AtomRange(*mtop))
2798 const t_atom &local = atomP.atom();
2799 int i = atomP.globalAtomNumber();
2801 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2803 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2804 for (int d = 0; d < DIM; d++)
2806 if (opts->nFreeze[g][d] == 0)
2808 /* Add one DOF for particle i (counted as 2*1) */
2810 /* VCM group i has dim d as a DOF */
2811 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] = 1;
2814 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] += 0.5*nrdf2[i];
2815 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] += 0.5*nrdf2[i];
2820 for (const gmx_molblock_t &molb : mtop->molblock)
2822 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2823 const t_atom *atom = molt.atoms.atom;
2824 for (int mol = 0; mol < molb.nmol; mol++)
2826 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2828 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2829 for (int i = 0; i < molt.ilist[ftype].size(); )
2831 /* Subtract degrees of freedom for the constraints,
2832 * if the particles still have degrees of freedom left.
2833 * If one of the particles is a vsite or a shell, then all
2834 * constraint motion will go there, but since they do not
2835 * contribute to the constraints the degrees of freedom do not
2838 int ai = as + ia[i + 1];
2839 int aj = as + ia[i + 2];
2840 if (((atom[ia[i + 1]].ptype == eptNucleus) ||
2841 (atom[ia[i + 1]].ptype == eptAtom)) &&
2842 ((atom[ia[i + 2]].ptype == eptNucleus) ||
2843 (atom[ia[i + 2]].ptype == eptAtom)))
2861 imin = std::min(imin, nrdf2[ai]);
2862 jmin = std::min(jmin, nrdf2[aj]);
2865 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2866 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -= 0.5*jmin;
2867 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2868 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -= 0.5*jmin;
2870 i += interaction_function[ftype].nratoms+1;
2873 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2874 for (int i = 0; i < molt.ilist[F_SETTLE].size(); )
2876 /* Subtract 1 dof from every atom in the SETTLE */
2877 for (int j = 0; j < 3; j++)
2879 int ai = as + ia[i + 1 + j];
2880 imin = std::min(2, nrdf2[ai]);
2882 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2883 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2887 as += molt.atoms.nr;
2893 /* Correct nrdf for the COM constraints.
2894 * We correct using the TC and VCM group of the first atom
2895 * in the reference and pull group. If atoms in one pull group
2896 * belong to different TC or VCM groups it is anyhow difficult
2897 * to determine the optimal nrdf assignment.
2901 for (int i = 0; i < pull->ncoord; i++)
2903 if (pull->coord[i].eType != epullCONSTRAINT)
2910 for (int j = 0; j < 2; j++)
2912 const t_pull_group *pgrp;
2914 pgrp = &pull->group[pull->coord[i].group[j]];
2918 /* Subtract 1/2 dof from each group */
2919 int ai = pgrp->ind[0];
2920 nrdf_tc [getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -= 0.5*imin;
2921 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -= 0.5*imin;
2922 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
2924 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][getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
2929 /* We need to subtract the whole DOF from group j=1 */
2936 if (ir->nstcomm != 0)
2940 /* We remove COM motion up to dim ndof_com() */
2941 ndim_rm_vcm = ndof_com(ir);
2943 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
2944 * the number of degrees of freedom in each vcm group when COM
2945 * translation is removed and 6 when rotation is removed as well.
2947 for (int j = 0; j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval])+1; j++)
2949 switch (ir->comm_mode)
2952 case ecmLINEAR_ACCELERATION_CORRECTION:
2953 nrdf_vcm_sub[j] = 0;
2954 for (int d = 0; d < ndim_rm_vcm; d++)
2963 nrdf_vcm_sub[j] = 6;
2966 gmx_incons("Checking comm_mode");
2970 for (int i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2972 /* Count the number of atoms of TC group i for every VCM group */
2973 for (int j = 0; j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval])+1; j++)
2978 for (int ai = 0; ai < natoms; ai++)
2980 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
2982 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
2986 /* Correct for VCM removal according to the fraction of each VCM
2987 * group present in this TC group.
2989 nrdf_uc = nrdf_tc[i];
2991 for (int j = 0; j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval])+1; j++)
2993 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
2995 nrdf_tc[i] += nrdf_uc*(static_cast<double>(na_vcm[j])/static_cast<double>(na_tot))*
2996 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
3001 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3003 opts->nrdf[i] = nrdf_tc[i];
3004 if (opts->nrdf[i] < 0)
3009 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3010 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3018 sfree(nrdf_vcm_sub);
3021 static bool do_egp_flag(t_inputrec *ir, SimulationGroups *groups,
3022 const char *option, const char *val, int flag)
3024 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3025 * But since this is much larger than STRLEN, such a line can not be parsed.
3026 * The real maximum is the number of names that fit in a string: STRLEN/2.
3028 #define EGP_MAX (STRLEN/2)
3032 auto names = gmx::splitString(val);
3033 if (names.size() % 2 != 0)
3035 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3037 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3039 for (size_t i = 0; i < names.size() / 2; i++)
3041 // TODO this needs to be replaced by a solution using std::find_if
3044 gmx_strcasecmp(names[2*i].c_str(), *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3050 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3051 names[2*i].c_str(), option);
3055 gmx_strcasecmp(names[2*i+1].c_str(), *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3061 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3062 names[2*i+1].c_str(), option);
3064 if ((j < nr) && (k < nr))
3066 ir->opts.egp_flags[nr*j+k] |= flag;
3067 ir->opts.egp_flags[nr*k+j] |= flag;
3076 static void make_swap_groups(
3081 int ig = -1, i = 0, gind;
3085 /* Just a quick check here, more thorough checks are in mdrun */
3086 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3088 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3091 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3092 for (ig = 0; ig < swap->ngrp; ig++)
3094 swapg = &swap->grp[ig];
3095 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3096 swapg->nat = grps->index[gind+1] - grps->index[gind];
3100 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3101 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3102 swap->grp[ig].molname, swapg->nat);
3103 snew(swapg->ind, swapg->nat);
3104 for (i = 0; i < swapg->nat; i++)
3106 swapg->ind[i] = grps->a[grps->index[gind]+i];
3111 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3117 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3122 ig = search_string(IMDgname, grps->nr, gnames);
3123 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3125 if (IMDgroup->nat > 0)
3127 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3128 IMDgname, IMDgroup->nat);
3129 snew(IMDgroup->ind, IMDgroup->nat);
3130 for (i = 0; i < IMDgroup->nat; i++)
3132 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3137 void do_index(const char* mdparin, const char *ndx,
3143 t_blocka *defaultIndexGroups;
3147 char warnbuf[STRLEN], **gnames;
3151 int i, j, k, restnm;
3152 bool bExcl, bTable, bAnneal, bRest;
3153 char warn_buf[STRLEN];
3157 fprintf(stderr, "processing index file...\n");
3161 snew(defaultIndexGroups, 1);
3162 snew(defaultIndexGroups->index, 1);
3164 atoms_all = gmx_mtop_global_atoms(mtop);
3165 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3166 done_atom(&atoms_all);
3170 defaultIndexGroups = init_index(ndx, &gnames);
3173 SimulationGroups *groups = &mtop->groups;
3174 natoms = mtop->natoms;
3175 symtab = &mtop->symtab;
3177 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3179 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3181 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3182 restnm = groups->groupNames.size() - 1;
3183 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3184 srenew(gnames, defaultIndexGroups->nr+1);
3185 gnames[restnm] = *(groups->groupNames.back());
3187 set_warning_line(wi, mdparin, -1);
3189 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3190 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3191 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3192 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size() ||
3193 temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3195 gmx_fatal(FARGS, "Invalid T coupling input: %zu groups, %zu ref-t values and "
3197 temperatureCouplingGroupNames.size(),
3198 temperatureCouplingReferenceValues.size(),
3199 temperatureCouplingTauValues.size());
3202 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3203 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3204 SimulationAtomGroupType::TemperatureCoupling,
3205 restnm, useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3206 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3208 snew(ir->opts.nrdf, nr);
3209 snew(ir->opts.tau_t, nr);
3210 snew(ir->opts.ref_t, nr);
3211 if (ir->eI == eiBD && ir->bd_fric == 0)
3213 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3216 if (useReferenceTemperature)
3218 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3220 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3224 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3225 for (i = 0; (i < nr); i++)
3227 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3229 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3230 warning_error(wi, warn_buf);
3233 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3235 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.");
3238 if (ir->opts.tau_t[i] >= 0)
3240 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3243 if (ir->etc != etcNO && ir->nsttcouple == -1)
3245 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3250 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3252 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");
3254 if (ir->epc == epcMTTK)
3256 if (ir->etc != etcNOSEHOOVER)
3258 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3262 if (ir->nstpcouple != ir->nsttcouple)
3264 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3265 ir->nstpcouple = ir->nsttcouple = mincouple;
3266 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);
3267 warning_note(wi, warn_buf);
3272 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3273 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3275 if (ETC_ANDERSEN(ir->etc))
3277 if (ir->nsttcouple != 1)
3280 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");
3281 warning_note(wi, warn_buf);
3284 nstcmin = tcouple_min_integration_steps(ir->etc);
3287 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3289 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3290 ETCOUPLTYPE(ir->etc),
3292 ir->nsttcouple*ir->delta_t);
3293 warning(wi, warn_buf);
3296 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3297 for (i = 0; (i < nr); i++)
3299 if (ir->opts.ref_t[i] < 0)
3301 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3304 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3305 if we are in this conditional) if mc_temp is negative */
3306 if (ir->expandedvals->mc_temp < 0)
3308 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3312 /* Simulated annealing for each group. There are nr groups */
3313 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3314 if (simulatedAnnealingGroupNames.size() == 1 &&
3315 gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3317 simulatedAnnealingGroupNames.resize(0);
3319 if (!simulatedAnnealingGroupNames.empty() &&
3320 gmx::ssize(simulatedAnnealingGroupNames) != nr)
3322 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3323 simulatedAnnealingGroupNames.size(), nr);
3327 snew(ir->opts.annealing, nr);
3328 snew(ir->opts.anneal_npoints, nr);
3329 snew(ir->opts.anneal_time, nr);
3330 snew(ir->opts.anneal_temp, nr);
3331 for (i = 0; i < nr; i++)
3333 ir->opts.annealing[i] = eannNO;
3334 ir->opts.anneal_npoints[i] = 0;
3335 ir->opts.anneal_time[i] = nullptr;
3336 ir->opts.anneal_temp[i] = nullptr;
3338 if (!simulatedAnnealingGroupNames.empty())
3341 for (i = 0; i < nr; i++)
3343 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3345 ir->opts.annealing[i] = eannNO;
3347 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3349 ir->opts.annealing[i] = eannSINGLE;
3352 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3354 ir->opts.annealing[i] = eannPERIODIC;
3360 /* Read the other fields too */
3361 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3362 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3364 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3365 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3367 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3368 size_t numSimulatedAnnealingFields = 0;
3369 for (i = 0; i < nr; i++)
3371 if (ir->opts.anneal_npoints[i] == 1)
3373 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3375 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3376 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3377 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3380 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3382 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3384 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3385 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3387 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3388 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3390 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3391 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3394 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3395 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3396 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3397 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp", allSimulatedAnnealingTemperatures.data());
3398 for (i = 0, k = 0; i < nr; i++)
3400 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3402 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3403 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3406 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3408 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3414 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3416 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3417 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3420 if (ir->opts.anneal_temp[i][j] < 0)
3422 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3427 /* Print out some summary information, to make sure we got it right */
3428 for (i = 0; i < nr; i++)
3430 if (ir->opts.annealing[i] != eannNO)
3432 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3433 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3434 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3435 ir->opts.anneal_npoints[i]);
3436 fprintf(stderr, "Time (ps) Temperature (K)\n");
3437 /* All terms except the last one */
3438 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3440 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3443 /* Finally the last one */
3444 j = ir->opts.anneal_npoints[i]-1;
3445 if (ir->opts.annealing[i] == eannSINGLE)
3447 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3451 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3452 if (std::fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3454 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3465 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3467 make_pull_coords(ir->pull);
3472 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3475 if (ir->eSwapCoords != eswapNO)
3477 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3480 /* Make indices for IMD session */
3483 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3486 auto accelerations = gmx::splitString(is->acc);
3487 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3488 if (accelerationGroupNames.size() * DIM != accelerations.size())
3490 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3491 accelerationGroupNames.size(), accelerations.size());
3493 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3494 SimulationAtomGroupType::Acceleration,
3495 restnm, egrptpALL_GENREST, bVerbose, wi);
3496 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3497 snew(ir->opts.acc, nr);
3498 ir->opts.ngacc = nr;
3500 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3502 auto freezeDims = gmx::splitString(is->frdim);
3503 auto freezeGroupNames = gmx::splitString(is->freeze);
3504 if (freezeDims.size() != DIM * freezeGroupNames.size())
3506 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3507 freezeGroupNames.size(), freezeDims.size());
3509 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3510 SimulationAtomGroupType::Freeze,
3511 restnm, egrptpALL_GENREST, bVerbose, wi);
3512 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3513 ir->opts.ngfrz = nr;
3514 snew(ir->opts.nFreeze, nr);
3515 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3517 for (j = 0; (j < DIM); j++, k++)
3519 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3520 if (!ir->opts.nFreeze[i][j])
3522 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3524 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3525 "(not %s)", freezeDims[k].c_str());
3526 warning(wi, warn_buf);
3531 for (; (i < nr); i++)
3533 for (j = 0; (j < DIM); j++)
3535 ir->opts.nFreeze[i][j] = 0;
3539 auto energyGroupNames = gmx::splitString(is->energy);
3540 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3541 SimulationAtomGroupType::EnergyOutput,
3542 restnm, egrptpALL_GENREST, bVerbose, wi);
3543 add_wall_energrps(groups, ir->nwall, symtab);
3544 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3545 auto vcmGroupNames = gmx::splitString(is->vcm);
3547 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3548 SimulationAtomGroupType::MassCenterVelocityRemoval,
3549 restnm, vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3552 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3553 "This may lead to artifacts.\n"
3554 "In most cases one should use one group for the whole system.");
3557 /* Now we have filled the freeze struct, so we can calculate NRDF */
3558 calc_nrdf(mtop, ir, gnames);
3560 auto user1GroupNames = gmx::splitString(is->user1);
3561 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3562 SimulationAtomGroupType::User1,
3563 restnm, egrptpALL_GENREST, bVerbose, wi);
3564 auto user2GroupNames = gmx::splitString(is->user2);
3565 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3566 SimulationAtomGroupType::User2,
3567 restnm, egrptpALL_GENREST, bVerbose, wi);
3568 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3569 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3570 SimulationAtomGroupType::CompressedPositionOutput,
3571 restnm, egrptpONE, bVerbose, wi);
3572 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3573 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3574 SimulationAtomGroupType::OrientationRestraintsFit,
3575 restnm, egrptpALL_GENREST, bVerbose, wi);
3577 /* QMMM input processing */
3578 auto qmGroupNames = gmx::splitString(is->QMMM);
3579 auto qmMethods = gmx::splitString(is->QMmethod);
3580 auto qmBasisSets = gmx::splitString(is->QMbasis);
3581 if (ir->eI != eiMimic)
3583 if (qmMethods.size() != qmGroupNames.size() ||
3584 qmBasisSets.size() != qmGroupNames.size())
3586 gmx_fatal(FARGS, "Invalid QMMM input: %zu groups %zu basissets"
3587 " and %zu methods\n", qmGroupNames.size(),
3588 qmBasisSets.size(), qmMethods.size());
3590 /* group rest, if any, is always MM! */
3591 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3592 SimulationAtomGroupType::QuantumMechanics,
3593 restnm, egrptpALL_GENREST, bVerbose, wi);
3594 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3595 ir->opts.ngQM = qmGroupNames.size();
3596 snew(ir->opts.QMmethod, nr);
3597 snew(ir->opts.QMbasis, nr);
3598 for (i = 0; i < nr; i++)
3600 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3601 * converted to the corresponding enum in names.c
3603 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(),
3606 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(),
3611 auto qmMultiplicities = gmx::splitString(is->QMmult);
3612 auto qmCharges = gmx::splitString(is->QMcharge);
3613 auto qmbSH = gmx::splitString(is->bSH);
3614 snew(ir->opts.QMmult, nr);
3615 snew(ir->opts.QMcharge, nr);
3616 snew(ir->opts.bSH, nr);
3617 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3618 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3619 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3621 auto CASelectrons = gmx::splitString(is->CASelectrons);
3622 auto CASorbitals = gmx::splitString(is->CASorbitals);
3623 snew(ir->opts.CASelectrons, nr);
3624 snew(ir->opts.CASorbitals, nr);
3625 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3626 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3628 auto SAon = gmx::splitString(is->SAon);
3629 auto SAoff = gmx::splitString(is->SAoff);
3630 auto SAsteps = gmx::splitString(is->SAsteps);
3631 snew(ir->opts.SAon, nr);
3632 snew(ir->opts.SAoff, nr);
3633 snew(ir->opts.SAsteps, nr);
3634 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3635 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3636 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3641 if (qmGroupNames.size() > 1)
3643 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3645 /* group rest, if any, is always MM! */
3646 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3647 SimulationAtomGroupType::QuantumMechanics,
3648 restnm, egrptpALL_GENREST, bVerbose, wi);
3650 ir->opts.ngQM = qmGroupNames.size();
3653 /* end of QMMM input */
3657 for (auto group : gmx::keysOf(groups->groups))
3659 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3660 for (const auto &entry : groups->groups[group])
3662 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3664 fprintf(stderr, "\n");
3668 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3669 snew(ir->opts.egp_flags, nr*nr);
3671 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3672 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3674 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3676 if (bExcl && EEL_FULL(ir->coulombtype))
3678 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3681 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3682 if (bTable && !(ir->vdwtype == evdwUSER) &&
3683 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3684 !(ir->coulombtype == eelPMEUSERSWITCH))
3686 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3689 /* final check before going out of scope if simulated tempering variables
3690 * need to be set to default values.
3692 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3694 ir->expandedvals->nstexpanded = 2*static_cast<int>(ir->opts.tau_t[0]/ir->delta_t);
3695 warning(wi, gmx::formatString("the value for nstexpanded was not specified for "
3696 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3697 "by default, but it is recommended to set it to an explicit value!",
3698 ir->expandedvals->nstexpanded));
3700 for (i = 0; (i < defaultIndexGroups->nr); i++)
3705 done_blocka(defaultIndexGroups);
3706 sfree(defaultIndexGroups);
3712 static void check_disre(const gmx_mtop_t *mtop)
3714 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3716 const gmx_ffparams_t &ffparams = mtop->ffparams;
3719 for (int i = 0; i < ffparams.numTypes(); i++)
3721 int ftype = ffparams.functype[i];
3722 if (ftype == F_DISRES)
3724 int label = ffparams.iparams[i].disres.label;
3725 if (label == old_label)
3727 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3735 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3736 "probably the parameters for multiple pairs in one restraint "
3737 "are not identical\n", ndouble);
3742 static bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3747 gmx_mtop_ilistloop_t iloop;
3756 for (d = 0; d < DIM; d++)
3758 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3760 /* Check for freeze groups */
3761 for (g = 0; g < ir->opts.ngfrz; g++)
3763 for (d = 0; d < DIM; d++)
3765 if (ir->opts.nFreeze[g][d] != 0)
3773 /* Check for position restraints */
3774 iloop = gmx_mtop_ilistloop_init(sys);
3775 while (const InteractionLists *ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3778 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3780 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3782 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3783 for (d = 0; d < DIM; d++)
3785 if (pr->posres.fcA[d] != 0)
3791 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3793 /* Check for flat-bottom posres */
3794 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3795 if (pr->fbposres.k != 0)
3797 switch (pr->fbposres.geom)
3799 case efbposresSPHERE:
3800 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3802 case efbposresCYLINDERX:
3803 AbsRef[YY] = AbsRef[ZZ] = 1;
3805 case efbposresCYLINDERY:
3806 AbsRef[XX] = AbsRef[ZZ] = 1;
3808 case efbposresCYLINDER:
3809 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3810 case efbposresCYLINDERZ:
3811 AbsRef[XX] = AbsRef[YY] = 1;
3813 case efbposresX: /* d=XX */
3814 case efbposresY: /* d=YY */
3815 case efbposresZ: /* d=ZZ */
3816 d = pr->fbposres.geom - efbposresX;
3820 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3821 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3829 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3833 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3834 bool *bC6ParametersWorkWithGeometricRules,
3835 bool *bC6ParametersWorkWithLBRules,
3836 bool *bLBRulesPossible)
3838 int ntypes, tpi, tpj;
3841 double c6i, c6j, c12i, c12j;
3842 double c6, c6_geometric, c6_LB;
3843 double sigmai, sigmaj, epsi, epsj;
3844 bool bCanDoLBRules, bCanDoGeometricRules;
3847 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3848 * force-field floating point parameters.
3851 ptr = getenv("GMX_LJCOMB_TOL");
3855 double gmx_unused canary;
3857 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3859 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3864 *bC6ParametersWorkWithLBRules = TRUE;
3865 *bC6ParametersWorkWithGeometricRules = TRUE;
3866 bCanDoLBRules = TRUE;
3867 ntypes = mtop->ffparams.atnr;
3868 snew(typecount, ntypes);
3869 gmx_mtop_count_atomtypes(mtop, state, typecount);
3870 *bLBRulesPossible = TRUE;
3871 for (tpi = 0; tpi < ntypes; ++tpi)
3873 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3874 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3875 for (tpj = tpi; tpj < ntypes; ++tpj)
3877 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3878 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3879 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3880 c6_geometric = std::sqrt(c6i * c6j);
3881 if (!gmx_numzero(c6_geometric))
3883 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3885 sigmai = gmx::sixthroot(c12i / c6i);
3886 sigmaj = gmx::sixthroot(c12j / c6j);
3887 epsi = c6i * c6i /(4.0 * c12i);
3888 epsj = c6j * c6j /(4.0 * c12j);
3889 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3893 *bLBRulesPossible = FALSE;
3894 c6_LB = c6_geometric;
3896 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3901 *bC6ParametersWorkWithLBRules = FALSE;
3904 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3906 if (!bCanDoGeometricRules)
3908 *bC6ParametersWorkWithGeometricRules = FALSE;
3916 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3919 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3921 check_combination_rule_differences(mtop, 0,
3922 &bC6ParametersWorkWithGeometricRules,
3923 &bC6ParametersWorkWithLBRules,
3925 if (ir->ljpme_combination_rule == eljpmeLB)
3927 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
3929 warning(wi, "You are using arithmetic-geometric combination rules "
3930 "in LJ-PME, but your non-bonded C6 parameters do not "
3931 "follow these rules.");
3936 if (!bC6ParametersWorkWithGeometricRules)
3938 if (ir->eDispCorr != edispcNO)
3940 warning_note(wi, "You are using geometric combination rules in "
3941 "LJ-PME, but your non-bonded C6 parameters do "
3942 "not follow these rules. "
3943 "This will introduce very small errors in the forces and energies in "
3944 "your simulations. Dispersion correction will correct total energy "
3945 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3949 warning_note(wi, "You are using geometric combination rules in "
3950 "LJ-PME, but your non-bonded C6 parameters do "
3951 "not follow these rules. "
3952 "This will introduce very small errors in the forces and energies in "
3953 "your simulations. If your system is homogeneous, consider using dispersion correction "
3954 "for the total energy and pressure.");
3960 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3963 char err_buf[STRLEN];
3968 gmx_mtop_atomloop_block_t aloopb;
3970 char warn_buf[STRLEN];
3972 set_warning_line(wi, mdparin, -1);
3974 if (ir->cutoff_scheme == ecutsVERLET &&
3975 ir->verletbuf_tol > 0 &&
3977 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3978 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3980 /* Check if a too small Verlet buffer might potentially
3981 * cause more drift than the thermostat can couple off.
3983 /* Temperature error fraction for warning and suggestion */
3984 const real T_error_warn = 0.002;
3985 const real T_error_suggest = 0.001;
3986 /* For safety: 2 DOF per atom (typical with constraints) */
3987 const real nrdf_at = 2;
3988 real T, tau, max_T_error;
3993 for (i = 0; i < ir->opts.ngtc; i++)
3995 T = std::max(T, ir->opts.ref_t[i]);
3996 tau = std::max(tau, ir->opts.tau_t[i]);
4000 /* This is a worst case estimate of the temperature error,
4001 * assuming perfect buffer estimation and no cancelation
4002 * of errors. The factor 0.5 is because energy distributes
4003 * equally over Ekin and Epot.
4005 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4006 if (max_T_error > T_error_warn)
4008 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.",
4009 ir->verletbuf_tol, T, tau,
4011 100*T_error_suggest,
4012 ir->verletbuf_tol*T_error_suggest/max_T_error);
4013 warning(wi, warn_buf);
4018 if (ETC_ANDERSEN(ir->etc))
4022 for (i = 0; i < ir->opts.ngtc; i++)
4024 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4025 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4026 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4027 i, ir->opts.tau_t[i]);
4028 CHECK(ir->opts.tau_t[i] < 0);
4031 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4033 for (i = 0; i < ir->opts.ngtc; i++)
4035 int nsteps = gmx::roundToInt(ir->opts.tau_t[i]/ir->delta_t);
4036 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);
4037 CHECK(nsteps % ir->nstcomm != 0);
4042 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4043 ir->comm_mode == ecmNO &&
4044 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4045 !ETC_ANDERSEN(ir->etc))
4047 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");
4050 if (ir->epc == epcPARRINELLORAHMAN &&
4051 ir->etc == etcNOSEHOOVER)
4054 for (int g = 0; g < ir->opts.ngtc; g++)
4056 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4058 if (ir->tau_p < 1.9*tau_t_max)
4060 std::string message =
4061 gmx::formatString("With %s T-coupling and %s p-coupling, "
4062 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4063 etcoupl_names[ir->etc],
4064 epcoupl_names[ir->epc],
4066 "tau-t", tau_t_max);
4067 warning(wi, message.c_str());
4071 /* Check for pressure coupling with absolute position restraints */
4072 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4074 absolute_reference(ir, sys, TRUE, AbsRef);
4076 for (m = 0; m < DIM; m++)
4078 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4080 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4088 aloopb = gmx_mtop_atomloop_block_init(sys);
4090 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4092 if (atom->q != 0 || atom->qB != 0)
4100 if (EEL_FULL(ir->coulombtype))
4103 "You are using full electrostatics treatment %s for a system without charges.\n"
4104 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4105 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4106 warning(wi, err_buf);
4111 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4114 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4115 "You might want to consider using %s electrostatics.\n",
4117 warning_note(wi, err_buf);
4121 /* Check if combination rules used in LJ-PME are the same as in the force field */
4122 if (EVDW_PME(ir->vdwtype))
4124 check_combination_rules(ir, sys, wi);
4127 /* Generalized reaction field */
4128 if (ir->opts.ngtc == 0)
4130 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4132 CHECK(ir->coulombtype == eelGRF);
4136 sprintf(err_buf, "When using coulombtype = %s"
4137 " ref-t for temperature coupling should be > 0",
4139 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4143 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4145 for (m = 0; (m < DIM); m++)
4147 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4156 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4157 for (const AtomProxy atomP : AtomRange(*sys))
4159 const t_atom &local = atomP.atom();
4160 int i = atomP.globalAtomNumber();
4161 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4164 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4166 for (m = 0; (m < DIM); m++)
4168 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4172 for (m = 0; (m < DIM); m++)
4174 if (fabs(acc[m]) > 1e-6)
4176 const char *dim[DIM] = { "X", "Y", "Z" };
4178 "Net Acceleration in %s direction, will %s be corrected\n",
4179 dim[m], ir->nstcomm != 0 ? "" : "not");
4180 if (ir->nstcomm != 0 && m < ndof_com(ir))
4183 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4185 ir->opts.acc[i][m] -= acc[m];
4193 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4194 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4196 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4204 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4206 if (ir->pull->coord[i].group[0] == 0 ||
4207 ir->pull->coord[i].group[1] == 0)
4209 absolute_reference(ir, sys, FALSE, AbsRef);
4210 for (m = 0; m < DIM; m++)
4212 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4214 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.");
4222 for (i = 0; i < 3; i++)
4224 for (m = 0; m <= i; m++)
4226 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4227 ir->deform[i][m] != 0)
4229 for (c = 0; c < ir->pull->ncoord; c++)
4231 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4232 ir->pull->coord[c].vec[m] != 0)
4234 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4245 void double_check(t_inputrec *ir, matrix box,
4246 bool bHasNormalConstraints,
4247 bool bHasAnyConstraints,
4251 char warn_buf[STRLEN];
4254 ptr = check_box(ir->ePBC, box);
4257 warning_error(wi, ptr);
4260 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4262 if (ir->shake_tol <= 0.0)
4264 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4266 warning_error(wi, warn_buf);
4270 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4272 /* If we have Lincs constraints: */
4273 if (ir->eI == eiMD && ir->etc == etcNO &&
4274 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4276 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4277 warning_note(wi, warn_buf);
4280 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4282 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4283 warning_note(wi, warn_buf);
4285 if (ir->epc == epcMTTK)
4287 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4291 if (bHasAnyConstraints && ir->epc == epcMTTK)
4293 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4296 if (ir->LincsWarnAngle > 90.0)
4298 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4299 warning(wi, warn_buf);
4300 ir->LincsWarnAngle = 90.0;
4303 if (ir->ePBC != epbcNONE)
4305 if (ir->nstlist == 0)
4307 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4309 if (ir->ns_type == ensGRID)
4311 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4313 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");
4314 warning_error(wi, warn_buf);
4319 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4320 if (2*ir->rlist >= min_size)
4322 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4323 warning_error(wi, warn_buf);
4326 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4333 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4337 real rvdw1, rvdw2, rcoul1, rcoul2;
4338 char warn_buf[STRLEN];
4340 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4344 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4349 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4355 if (rvdw1 + rvdw2 > ir->rlist ||
4356 rcoul1 + rcoul2 > ir->rlist)
4359 "The sum of the two largest charge group radii (%f) "
4360 "is larger than rlist (%f)\n",
4361 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4362 warning(wi, warn_buf);
4366 /* Here we do not use the zero at cut-off macro,
4367 * since user defined interactions might purposely
4368 * not be zero at the cut-off.
4370 if (ir_vdw_is_zero_at_cutoff(ir) &&
4371 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4373 sprintf(warn_buf, "The sum of the two largest charge group "
4374 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4375 "With exact cut-offs, better performance can be "
4376 "obtained with cutoff-scheme = %s, because it "
4377 "does not use charge groups at all.",
4379 ir->rlist, ir->rvdw,
4380 ecutscheme_names[ecutsVERLET]);
4383 warning(wi, warn_buf);
4387 warning_note(wi, warn_buf);
4390 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4391 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4393 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4394 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4396 ir->rlist, ir->rcoulomb,
4397 ecutscheme_names[ecutsVERLET]);
4400 warning(wi, warn_buf);
4404 warning_note(wi, warn_buf);