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50 #include "gromacs/awh/read-params.h"
51 #include "gromacs/fileio/readinp.h"
52 #include "gromacs/fileio/warninp.h"
53 #include "gromacs/gmxlib/chargegroup.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/gmxpreprocess/keyvaluetreemdpwriter.h"
56 #include "gromacs/gmxpreprocess/toputil.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/math/units.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/mdlib/calc_verletbuf.h"
61 #include "gromacs/mdrunutility/mdmodules.h"
62 #include "gromacs/mdtypes/inputrec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/mdtypes/pull-params.h"
65 #include "gromacs/options/options.h"
66 #include "gromacs/options/treesupport.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/topology/block.h"
69 #include "gromacs/topology/ifunc.h"
70 #include "gromacs/topology/index.h"
71 #include "gromacs/topology/mtop_util.h"
72 #include "gromacs/topology/symtab.h"
73 #include "gromacs/topology/topology.h"
74 #include "gromacs/utility/cstringutil.h"
75 #include "gromacs/utility/exceptions.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/filestream.h"
78 #include "gromacs/utility/gmxassert.h"
79 #include "gromacs/utility/ikeyvaluetreeerror.h"
80 #include "gromacs/utility/keyvaluetree.h"
81 #include "gromacs/utility/keyvaluetreebuilder.h"
82 #include "gromacs/utility/keyvaluetreetransform.h"
83 #include "gromacs/utility/smalloc.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(gmx_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 gmx_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);
531 /* nstexpanded should be a multiple of nstcalcenergy */
532 check_nst("nstcalcenergy", ir->nstcalcenergy,
533 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
535 /* for storing exact averages nstenergy should be
536 * a multiple of nstcalcenergy
538 check_nst("nstcalcenergy", ir->nstcalcenergy,
539 "nstenergy", &ir->nstenergy, wi);
543 if (ir->nsteps == 0 && !ir->bContinuation)
545 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
549 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
550 ir->bContinuation && ir->ld_seed != -1)
552 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)");
558 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
559 CHECK(ir->ePBC != epbcXYZ);
560 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
561 CHECK(ir->ns_type != ensGRID);
562 sprintf(err_buf, "with TPI nstlist should be larger than zero");
563 CHECK(ir->nstlist <= 0);
564 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
565 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
566 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
567 CHECK(ir->cutoff_scheme == ecutsVERLET);
571 if ( (opts->nshake > 0) && (opts->bMorse) )
574 "Using morse bond-potentials while constraining bonds is useless");
575 warning(wi, warn_buf);
578 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
579 ir->bContinuation && ir->ld_seed != -1)
581 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)");
583 /* verify simulated tempering options */
587 gmx_bool bAllTempZero = TRUE;
588 for (i = 0; i < fep->n_lambda; i++)
590 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]);
591 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
592 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
594 bAllTempZero = FALSE;
597 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
598 CHECK(bAllTempZero == TRUE);
600 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
601 CHECK(ir->eI != eiVV);
603 /* check compatability of the temperature coupling with simulated tempering */
605 if (ir->etc == etcNOSEHOOVER)
607 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
608 warning_note(wi, warn_buf);
611 /* check that the temperatures make sense */
613 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);
614 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
616 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
617 CHECK(ir->simtempvals->simtemp_high <= 0);
619 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
620 CHECK(ir->simtempvals->simtemp_low <= 0);
623 /* verify free energy options */
625 if (ir->efep != efepNO)
628 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
630 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
632 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
633 (int)fep->sc_r_power);
634 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
636 sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
637 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
639 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
640 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
642 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
643 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
645 sprintf(err_buf, "Free-energy not implemented for Ewald");
646 CHECK(ir->coulombtype == eelEWALD);
648 /* check validty of lambda inputs */
649 if (fep->n_lambda == 0)
651 /* Clear output in case of no states:*/
652 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
653 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
657 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
658 CHECK((fep->init_fep_state >= fep->n_lambda));
661 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
662 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
664 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",
665 fep->init_lambda, fep->init_fep_state);
666 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
670 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
674 for (i = 0; i < efptNR; i++)
676 if (fep->separate_dvdl[i])
681 if (n_lambda_terms > 1)
683 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.");
684 warning(wi, warn_buf);
687 if (n_lambda_terms < 2 && fep->n_lambda > 0)
690 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
694 for (j = 0; j < efptNR; j++)
696 for (i = 0; i < fep->n_lambda; i++)
698 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]);
699 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
703 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
705 for (i = 0; i < fep->n_lambda; i++)
707 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],
708 fep->all_lambda[efptCOUL][i]);
709 CHECK((fep->sc_alpha > 0) &&
710 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
711 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
712 ((fep->all_lambda[efptVDW][i] > 0.0) &&
713 (fep->all_lambda[efptVDW][i] < 1.0))));
717 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
719 real sigma, lambda, r_sc;
722 /* Maximum estimate for A and B charges equal with lambda power 1 */
724 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);
725 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.",
727 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
728 warning_note(wi, warn_buf);
731 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
732 be treated differently, but that's the next step */
734 for (i = 0; i < efptNR; i++)
736 for (j = 0; j < fep->n_lambda; j++)
738 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
739 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
744 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
748 /* checking equilibration of weights inputs for validity */
750 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
751 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
752 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
754 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
755 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
756 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
758 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
759 expand->equil_steps, elmceq_names[elmceqSTEPS]);
760 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
762 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
763 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
764 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
766 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
767 expand->equil_ratio, elmceq_names[elmceqRATIO]);
768 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
770 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
771 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
772 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
774 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
775 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
776 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
778 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
779 expand->equil_steps, elmceq_names[elmceqSTEPS]);
780 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
782 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
783 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
784 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
786 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
787 expand->equil_ratio, elmceq_names[elmceqRATIO]);
788 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
790 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
791 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
792 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
794 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
795 CHECK((expand->lmc_repeats <= 0));
796 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
797 CHECK((expand->minvarmin <= 0));
798 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
799 CHECK((expand->c_range < 0));
800 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
801 fep->init_fep_state, expand->lmc_forced_nstart);
802 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
803 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
804 CHECK((expand->lmc_forced_nstart < 0));
805 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
806 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
808 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
809 CHECK((expand->init_wl_delta < 0));
810 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
811 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
812 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
813 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
815 /* if there is no temperature control, we need to specify an MC temperature */
816 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO) && (expand->mc_temp <= 0.0))
818 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set to a positive number");
819 warning_error(wi, err_buf);
821 if (expand->nstTij > 0)
823 sprintf(err_buf, "nstlog must be non-zero");
824 CHECK(ir->nstlog == 0);
825 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
826 expand->nstTij, ir->nstlog);
827 CHECK((expand->nstTij % ir->nstlog) != 0);
832 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
833 CHECK(ir->nwall && ir->ePBC != epbcXY);
836 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
838 if (ir->ePBC == epbcNONE)
840 if (ir->epc != epcNO)
842 warning(wi, "Turning off pressure coupling for vacuum system");
848 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
849 epbc_names[ir->ePBC]);
850 CHECK(ir->epc != epcNO);
852 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
853 CHECK(EEL_FULL(ir->coulombtype));
855 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
856 epbc_names[ir->ePBC]);
857 CHECK(ir->eDispCorr != edispcNO);
860 if (ir->rlist == 0.0)
862 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
863 "with coulombtype = %s or coulombtype = %s\n"
864 "without periodic boundary conditions (pbc = %s) and\n"
865 "rcoulomb and rvdw set to zero",
866 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
867 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
868 (ir->ePBC != epbcNONE) ||
869 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
873 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
878 if (ir->nstcomm == 0)
880 ir->comm_mode = ecmNO;
882 if (ir->comm_mode != ecmNO)
886 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");
887 ir->nstcomm = abs(ir->nstcomm);
890 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
892 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
893 ir->nstcomm = ir->nstcalcenergy;
896 if (ir->comm_mode == ecmANGULAR)
898 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
899 CHECK(ir->bPeriodicMols);
900 if (ir->ePBC != epbcNONE)
902 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.");
907 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
909 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]);
910 warning_note(wi, warn_buf);
913 /* TEMPERATURE COUPLING */
914 if (ir->etc == etcYES)
916 ir->etc = etcBERENDSEN;
917 warning_note(wi, "Old option for temperature coupling given: "
918 "changing \"yes\" to \"Berendsen\"\n");
921 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
923 if (ir->opts.nhchainlength < 1)
925 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
926 ir->opts.nhchainlength = 1;
927 warning(wi, warn_buf);
930 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
932 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
933 ir->opts.nhchainlength = 1;
938 ir->opts.nhchainlength = 0;
941 if (ir->eI == eiVVAK)
943 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
945 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
948 if (ETC_ANDERSEN(ir->etc))
950 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
951 CHECK(!(EI_VV(ir->eI)));
953 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
955 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]);
956 warning_note(wi, warn_buf);
959 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]);
960 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
963 if (ir->etc == etcBERENDSEN)
965 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
966 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
967 warning_note(wi, warn_buf);
970 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
971 && ir->epc == epcBERENDSEN)
973 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
974 "true ensemble for the thermostat");
975 warning(wi, warn_buf);
978 /* PRESSURE COUPLING */
979 if (ir->epc == epcISOTROPIC)
981 ir->epc = epcBERENDSEN;
982 warning_note(wi, "Old option for pressure coupling given: "
983 "changing \"Isotropic\" to \"Berendsen\"\n");
986 if (ir->epc != epcNO)
988 dt_pcoupl = ir->nstpcouple*ir->delta_t;
990 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
991 CHECK(ir->tau_p <= 0);
993 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
995 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
996 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
997 warning(wi, warn_buf);
1000 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1001 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1002 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1003 ir->compress[ZZ][ZZ] < 0 ||
1004 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1005 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1007 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1010 "You are generating velocities so I am assuming you "
1011 "are equilibrating a system. You are using "
1012 "%s pressure coupling, but this can be "
1013 "unstable for equilibration. If your system crashes, try "
1014 "equilibrating first with Berendsen pressure coupling. If "
1015 "you are not equilibrating the system, you can probably "
1016 "ignore this warning.",
1017 epcoupl_names[ir->epc]);
1018 warning(wi, warn_buf);
1024 if (ir->epc > epcNO)
1026 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1028 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.");
1034 if (ir->epc == epcMTTK)
1036 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1040 /* ELECTROSTATICS */
1041 /* More checks are in triple check (grompp.c) */
1043 if (ir->coulombtype == eelSWITCH)
1045 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1046 "artifacts, advice: use coulombtype = %s",
1047 eel_names[ir->coulombtype],
1048 eel_names[eelRF_ZERO]);
1049 warning(wi, warn_buf);
1052 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1054 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);
1055 warning(wi, warn_buf);
1056 ir->epsilon_rf = ir->epsilon_r;
1057 ir->epsilon_r = 1.0;
1060 if (ir->epsilon_r == 0)
1063 "It is pointless to use long-range electrostatics with infinite relative permittivity."
1064 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1065 CHECK(EEL_FULL(ir->coulombtype));
1068 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1070 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1071 CHECK(ir->epsilon_r < 0);
1074 if (EEL_RF(ir->coulombtype))
1076 /* reaction field (at the cut-off) */
1078 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1080 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1081 eel_names[ir->coulombtype]);
1082 warning(wi, warn_buf);
1083 ir->epsilon_rf = 0.0;
1086 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1087 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1088 (ir->epsilon_r == 0));
1089 if (ir->epsilon_rf == ir->epsilon_r)
1091 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1092 eel_names[ir->coulombtype]);
1093 warning(wi, warn_buf);
1096 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1097 * means the interaction is zero outside rcoulomb, but it helps to
1098 * provide accurate energy conservation.
1100 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1102 if (ir_coulomb_switched(ir))
1105 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1106 eel_names[ir->coulombtype]);
1107 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1110 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1112 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1114 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1115 eel_names[ir->coulombtype]);
1116 CHECK(ir->rlist > ir->rcoulomb);
1120 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1123 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1124 CHECK( ir->coulomb_modifier != eintmodNONE);
1126 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1129 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1130 CHECK( ir->vdw_modifier != eintmodNONE);
1133 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1134 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1137 "The switch/shift interaction settings are just for compatibility; you will get better "
1138 "performance from applying potential modifiers to your interactions!\n");
1139 warning_note(wi, warn_buf);
1142 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1144 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1146 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1147 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.",
1148 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1149 warning(wi, warn_buf);
1153 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1155 if (ir->rvdw_switch == 0)
1157 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.");
1158 warning(wi, warn_buf);
1162 if (EEL_FULL(ir->coulombtype))
1164 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1165 ir->coulombtype == eelPMEUSERSWITCH)
1167 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1168 eel_names[ir->coulombtype]);
1169 CHECK(ir->rcoulomb > ir->rlist);
1171 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1173 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1176 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1177 "For optimal energy conservation,consider using\n"
1178 "a potential modifier.", eel_names[ir->coulombtype]);
1179 CHECK(ir->rcoulomb != ir->rlist);
1184 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1186 // TODO: Move these checks into the ewald module with the options class
1188 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1190 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1192 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
1193 warning_error(wi, warn_buf);
1197 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1199 if (ir->ewald_geometry == eewg3D)
1201 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1202 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1203 warning(wi, warn_buf);
1205 /* This check avoids extra pbc coding for exclusion corrections */
1206 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1207 CHECK(ir->wall_ewald_zfac < 2);
1209 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1210 EEL_FULL(ir->coulombtype))
1212 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1213 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1214 warning(wi, warn_buf);
1216 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1218 if (ir->cutoff_scheme == ecutsVERLET)
1220 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1221 eel_names[ir->coulombtype]);
1222 warning(wi, warn_buf);
1226 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",
1227 eel_names[ir->coulombtype]);
1228 warning_note(wi, warn_buf);
1232 if (ir_vdw_switched(ir))
1234 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1235 CHECK(ir->rvdw_switch >= ir->rvdw);
1237 if (ir->rvdw_switch < 0.5*ir->rvdw)
1239 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.",
1240 ir->rvdw_switch, ir->rvdw);
1241 warning_note(wi, warn_buf);
1244 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1246 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1248 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1249 CHECK(ir->rlist > ir->rvdw);
1253 if (ir->vdwtype == evdwPME)
1255 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1257 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1258 evdw_names[ir->vdwtype],
1259 eintmod_names[eintmodPOTSHIFT],
1260 eintmod_names[eintmodNONE]);
1261 warning_error(wi, err_buf);
1265 if (ir->cutoff_scheme == ecutsGROUP)
1267 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1268 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1270 warning_note(wi, "With exact cut-offs, rlist should be "
1271 "larger than rcoulomb and rvdw, so that there "
1272 "is a buffer region for particle motion "
1273 "between neighborsearch steps");
1276 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1278 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1279 warning_note(wi, warn_buf);
1281 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1283 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1284 warning_note(wi, warn_buf);
1288 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1290 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.");
1293 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1296 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1299 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1301 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1304 /* ENERGY CONSERVATION */
1305 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1307 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1309 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1310 evdw_names[evdwSHIFT]);
1311 warning_note(wi, warn_buf);
1313 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1315 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1316 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1317 warning_note(wi, warn_buf);
1321 /* IMPLICIT SOLVENT */
1322 if (ir->coulombtype == eelGB_NOTUSED)
1324 sprintf(warn_buf, "Invalid option %s for coulombtype",
1325 eel_names[ir->coulombtype]);
1326 warning_error(wi, warn_buf);
1331 if (ir->cutoff_scheme != ecutsGROUP)
1333 warning_error(wi, "QMMM is currently only supported with cutoff-scheme=group");
1335 if (!EI_DYNAMICS(ir->eI))
1338 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1339 warning_error(wi, buf);
1345 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1349 /* count the number of text elemets separated by whitespace in a string.
1350 str = the input string
1351 maxptr = the maximum number of allowed elements
1352 ptr = the output array of pointers to the first character of each element
1353 returns: the number of elements. */
1354 int str_nelem(const char *str, int maxptr, char *ptr[])
1359 copy0 = gmx_strdup(str);
1362 while (*copy != '\0')
1366 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1374 while ((*copy != '\0') && !isspace(*copy))
1393 /* interpret a number of doubles from a string and put them in an array,
1394 after allocating space for them.
1395 str = the input string
1396 n = the (pre-allocated) number of doubles read
1397 r = the output array of doubles. */
1398 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1403 char warn_buf[STRLEN];
1405 *n = str_nelem(str, MAXPTR, ptr);
1408 for (i = 0; i < *n; i++)
1410 (*r)[i] = strtod(ptr[i], &endptr);
1413 sprintf(warn_buf, "Invalid value %s in string in mdp file. Expected a real number.", ptr[i]);
1414 warning_error(wi, warn_buf);
1419 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1422 int i, j, max_n_lambda, nweights, nfep[efptNR];
1423 t_lambda *fep = ir->fepvals;
1424 t_expanded *expand = ir->expandedvals;
1425 real **count_fep_lambdas;
1426 gmx_bool bOneLambda = TRUE;
1428 snew(count_fep_lambdas, efptNR);
1430 /* FEP input processing */
1431 /* first, identify the number of lambda values for each type.
1432 All that are nonzero must have the same number */
1434 for (i = 0; i < efptNR; i++)
1436 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1439 /* now, determine the number of components. All must be either zero, or equal. */
1442 for (i = 0; i < efptNR; i++)
1444 if (nfep[i] > max_n_lambda)
1446 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1447 must have the same number if its not zero.*/
1452 for (i = 0; i < efptNR; i++)
1456 ir->fepvals->separate_dvdl[i] = FALSE;
1458 else if (nfep[i] == max_n_lambda)
1460 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1461 respect to the temperature currently */
1463 ir->fepvals->separate_dvdl[i] = TRUE;
1468 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1469 nfep[i], efpt_names[i], max_n_lambda);
1472 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1473 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1475 /* the number of lambdas is the number we've read in, which is either zero
1476 or the same for all */
1477 fep->n_lambda = max_n_lambda;
1479 /* allocate space for the array of lambda values */
1480 snew(fep->all_lambda, efptNR);
1481 /* if init_lambda is defined, we need to set lambda */
1482 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1484 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1486 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1487 for (i = 0; i < efptNR; i++)
1489 snew(fep->all_lambda[i], fep->n_lambda);
1490 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1493 for (j = 0; j < fep->n_lambda; j++)
1495 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1497 sfree(count_fep_lambdas[i]);
1500 sfree(count_fep_lambdas);
1502 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1503 bookkeeping -- for now, init_lambda */
1505 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1507 for (i = 0; i < fep->n_lambda; i++)
1509 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1513 /* check to see if only a single component lambda is defined, and soft core is defined.
1514 In this case, turn on coulomb soft core */
1516 if (max_n_lambda == 0)
1522 for (i = 0; i < efptNR; i++)
1524 if ((nfep[i] != 0) && (i != efptFEP))
1530 if ((bOneLambda) && (fep->sc_alpha > 0))
1532 fep->bScCoul = TRUE;
1535 /* Fill in the others with the efptFEP if they are not explicitly
1536 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1537 they are all zero. */
1539 for (i = 0; i < efptNR; i++)
1541 if ((nfep[i] == 0) && (i != efptFEP))
1543 for (j = 0; j < fep->n_lambda; j++)
1545 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1551 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1552 if (fep->sc_r_power == 48)
1554 if (fep->sc_alpha > 0.1)
1556 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1560 /* now read in the weights */
1561 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1564 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1566 else if (nweights != fep->n_lambda)
1568 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1569 nweights, fep->n_lambda);
1571 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1573 expand->nstexpanded = fep->nstdhdl;
1574 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1576 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1578 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1579 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1580 2*tau_t just to be careful so it's not to frequent */
1585 static void do_simtemp_params(t_inputrec *ir)
1588 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1589 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1592 static void do_wall_params(t_inputrec *ir,
1593 char *wall_atomtype, char *wall_density,
1597 char *names[MAXPTR];
1600 opts->wall_atomtype[0] = nullptr;
1601 opts->wall_atomtype[1] = nullptr;
1603 ir->wall_atomtype[0] = -1;
1604 ir->wall_atomtype[1] = -1;
1605 ir->wall_density[0] = 0;
1606 ir->wall_density[1] = 0;
1610 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1611 if (nstr != ir->nwall)
1613 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1616 for (i = 0; i < ir->nwall; i++)
1618 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1621 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1623 nstr = str_nelem(wall_density, MAXPTR, names);
1624 if (nstr != ir->nwall)
1626 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1628 for (i = 0; i < ir->nwall; i++)
1630 if (sscanf(names[i], "%lf", &dbl) != 1)
1632 gmx_fatal(FARGS, "Could not parse wall-density value from string '%s'", names[i]);
1636 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1638 ir->wall_density[i] = dbl;
1644 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1652 srenew(groups->grpname, groups->ngrpname+nwall);
1653 grps = &(groups->grps[egcENER]);
1654 srenew(grps->nm_ind, grps->nr+nwall);
1655 for (i = 0; i < nwall; i++)
1657 sprintf(str, "wall%d", i);
1658 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1659 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1664 static void read_expandedparams(std::vector<t_inpfile> *inp,
1665 t_expanded *expand, warninp_t wi)
1667 /* read expanded ensemble parameters */
1668 printStringNewline(inp, "expanded ensemble variables");
1669 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1670 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1671 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1672 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1673 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1674 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1675 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1676 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1677 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1678 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1679 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1680 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1681 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1682 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1683 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1684 expand->bSymmetrizedTMatrix = get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi);
1685 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1686 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1687 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1688 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1689 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1690 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1691 expand->bWLoneovert = get_eeenum(inp, "wl-oneovert", yesno_names, wi);
1694 /*! \brief Return whether an end state with the given coupling-lambda
1695 * value describes fully-interacting VDW.
1697 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1698 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1700 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1702 return (couple_lambda_value == ecouplamVDW ||
1703 couple_lambda_value == ecouplamVDWQ);
1709 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1712 explicit MdpErrorHandler(warninp_t wi)
1713 : wi_(wi), mapping_(nullptr)
1717 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1719 mapping_ = &mapping;
1722 virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
1724 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1725 getOptionName(context).c_str()));
1726 std::string message = gmx::formatExceptionMessageToString(*ex);
1727 warning_error(wi_, message.c_str());
1732 std::string getOptionName(const gmx::KeyValueTreePath &context)
1734 if (mapping_ != nullptr)
1736 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1737 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1740 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1745 const gmx::IKeyValueTreeBackMapping *mapping_;
1750 void get_ir(const char *mdparin, const char *mdparout,
1751 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1752 WriteMdpHeader writeMdpHeader, warninp_t wi)
1755 double dumdub[2][6];
1757 char warn_buf[STRLEN];
1758 t_lambda *fep = ir->fepvals;
1759 t_expanded *expand = ir->expandedvals;
1761 const char *no_names[] = { "no", nullptr };
1763 init_inputrec_strings();
1764 gmx::TextInputFile stream(mdparin);
1765 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1767 snew(dumstr[0], STRLEN);
1768 snew(dumstr[1], STRLEN);
1770 if (-1 == search_einp(inp, "cutoff-scheme"))
1773 "%s did not specify a value for the .mdp option "
1774 "\"cutoff-scheme\". Probably it was first intended for use "
1775 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1776 "introduced, but the group scheme was still the default. "
1777 "The default is now the Verlet scheme, so you will observe "
1778 "different behaviour.", mdparin);
1779 warning_note(wi, warn_buf);
1782 /* ignore the following deprecated commands */
1783 replace_inp_entry(inp, "title", nullptr);
1784 replace_inp_entry(inp, "cpp", nullptr);
1785 replace_inp_entry(inp, "domain-decomposition", nullptr);
1786 replace_inp_entry(inp, "andersen-seed", nullptr);
1787 replace_inp_entry(inp, "dihre", nullptr);
1788 replace_inp_entry(inp, "dihre-fc", nullptr);
1789 replace_inp_entry(inp, "dihre-tau", nullptr);
1790 replace_inp_entry(inp, "nstdihreout", nullptr);
1791 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1792 replace_inp_entry(inp, "optimize-fft", nullptr);
1793 replace_inp_entry(inp, "adress_type", nullptr);
1794 replace_inp_entry(inp, "adress_const_wf", nullptr);
1795 replace_inp_entry(inp, "adress_ex_width", nullptr);
1796 replace_inp_entry(inp, "adress_hy_width", nullptr);
1797 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1798 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1799 replace_inp_entry(inp, "adress_site", nullptr);
1800 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1801 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1802 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1803 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1804 replace_inp_entry(inp, "rlistlong", nullptr);
1805 replace_inp_entry(inp, "nstcalclr", nullptr);
1806 replace_inp_entry(inp, "pull-print-com2", nullptr);
1807 replace_inp_entry(inp, "gb-algorithm", nullptr);
1808 replace_inp_entry(inp, "nstgbradii", nullptr);
1809 replace_inp_entry(inp, "rgbradii", nullptr);
1810 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1811 replace_inp_entry(inp, "gb-saltconc", nullptr);
1812 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1813 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1814 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1815 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1816 replace_inp_entry(inp, "sa-algorithm", nullptr);
1817 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1819 /* replace the following commands with the clearer new versions*/
1820 replace_inp_entry(inp, "unconstrained-start", "continuation");
1821 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1822 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1823 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1824 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1825 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1826 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1828 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1829 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1830 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1831 setStringEntry(&inp, "include", opts->include, nullptr);
1832 printStringNoNewline(&inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1833 setStringEntry(&inp, "define", opts->define, nullptr);
1835 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1836 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1837 printStringNoNewline(&inp, "Start time and timestep in ps");
1838 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1839 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1840 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1841 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1842 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1843 printStringNoNewline(&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1844 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1845 printStringNoNewline(&inp, "mode for center of mass motion removal");
1846 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1847 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1848 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1849 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1850 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1852 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1853 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1854 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1855 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1858 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1859 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1860 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1861 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1862 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1863 ir->niter = get_eint(&inp, "niter", 20, wi);
1864 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1865 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1866 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1867 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1868 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1870 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1871 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1873 /* Output options */
1874 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1875 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1876 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1877 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1878 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1879 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1880 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1881 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1882 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1883 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1884 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1885 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1886 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1887 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1888 printStringNoNewline(&inp, "default, all atoms will be written.");
1889 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1890 printStringNoNewline(&inp, "Selection of energy groups");
1891 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1893 /* Neighbor searching */
1894 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1895 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1896 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1897 printStringNoNewline(&inp, "nblist update frequency");
1898 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1899 printStringNoNewline(&inp, "ns algorithm (simple or grid)");
1900 ir->ns_type = get_eeenum(&inp, "ns-type", ens_names, wi);
1901 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1902 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1903 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi);
1904 printStringNoNewline(&inp, "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1905 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1906 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1907 printStringNoNewline(&inp, "nblist cut-off");
1908 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1909 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1911 /* Electrostatics */
1912 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1913 printStringNoNewline(&inp, "Method for doing electrostatics");
1914 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1915 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1916 printStringNoNewline(&inp, "cut-off lengths");
1917 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1918 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1919 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
1920 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1921 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1922 printStringNoNewline(&inp, "Method for doing Van der Waals");
1923 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1924 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1925 printStringNoNewline(&inp, "cut-off lengths");
1926 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1927 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1928 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1929 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1930 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1931 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1932 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1933 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1934 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1935 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1936 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1937 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1938 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1939 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1940 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1941 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1942 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1943 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1944 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1945 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1946 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1948 /* Implicit solvation is no longer supported, but we need grompp
1949 to be able to refuse old .mdp files that would have built a tpr
1950 to run it. Thus, only "no" is accepted. */
1951 ir->implicit_solvent = get_eeenum(&inp, "implicit-solvent", no_names, wi);
1953 /* Coupling stuff */
1954 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
1955 printStringNoNewline(&inp, "Temperature coupling");
1956 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
1957 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
1958 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
1959 ir->bPrintNHChains = get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi);
1960 printStringNoNewline(&inp, "Groups to couple separately");
1961 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
1962 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
1963 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
1964 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
1965 printStringNoNewline(&inp, "pressure coupling");
1966 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
1967 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
1968 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
1969 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
1970 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
1971 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
1972 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
1973 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
1974 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
1977 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
1978 ir->bQMMM = get_eeenum(&inp, "QMMM", yesno_names, wi);
1979 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
1980 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
1981 printStringNoNewline(&inp, "QM method");
1982 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
1983 printStringNoNewline(&inp, "QMMM scheme");
1984 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
1985 printStringNoNewline(&inp, "QM basisset");
1986 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
1987 printStringNoNewline(&inp, "QM charge");
1988 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
1989 printStringNoNewline(&inp, "QM multiplicity");
1990 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
1991 printStringNoNewline(&inp, "Surface Hopping");
1992 setStringEntry(&inp, "SH", is->bSH, nullptr);
1993 printStringNoNewline(&inp, "CAS space options");
1994 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
1995 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
1996 setStringEntry(&inp, "SAon", is->SAon, nullptr);
1997 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
1998 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
1999 printStringNoNewline(&inp, "Scale factor for MM charges");
2000 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2002 /* Simulated annealing */
2003 printStringNewline(&inp, "SIMULATED ANNEALING");
2004 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2005 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2006 printStringNoNewline(&inp, "Number of time points to use for specifying annealing in each group");
2007 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2008 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2009 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2010 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2011 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2014 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2015 opts->bGenVel = get_eeenum(&inp, "gen-vel", yesno_names, wi);
2016 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2017 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2020 printStringNewline(&inp, "OPTIONS FOR BONDS");
2021 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2022 printStringNoNewline(&inp, "Type of constraint algorithm");
2023 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2024 printStringNoNewline(&inp, "Do not constrain the start configuration");
2025 ir->bContinuation = get_eeenum(&inp, "continuation", yesno_names, wi);
2026 printStringNoNewline(&inp, "Use successive overrelaxation to reduce the number of shake iterations");
2027 ir->bShakeSOR = get_eeenum(&inp, "Shake-SOR", yesno_names, wi);
2028 printStringNoNewline(&inp, "Relative tolerance of shake");
2029 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2030 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2031 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2032 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2033 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2034 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2035 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2036 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2037 printStringNoNewline(&inp, "rotates over more degrees than");
2038 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2039 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2040 opts->bMorse = get_eeenum(&inp, "morse", yesno_names, wi);
2042 /* Energy group exclusions */
2043 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2044 printStringNoNewline(&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2045 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2048 printStringNewline(&inp, "WALLS");
2049 printStringNoNewline(&inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2050 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2051 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2052 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2053 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2054 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2055 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2058 printStringNewline(&inp, "COM PULLING");
2059 ir->bPull = get_eeenum(&inp, "pull", yesno_names, wi);
2063 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2067 NOTE: needs COM pulling input */
2068 printStringNewline(&inp, "AWH biasing");
2069 ir->bDoAwh = get_eeenum(&inp, "awh", yesno_names, wi);
2074 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2078 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2082 /* Enforced rotation */
2083 printStringNewline(&inp, "ENFORCED ROTATION");
2084 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2085 ir->bRot = get_eeenum(&inp, "rotation", yesno_names, wi);
2089 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2092 /* Interactive MD */
2094 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2095 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2096 if (is->imd_grp[0] != '\0')
2103 printStringNewline(&inp, "NMR refinement stuff");
2104 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2105 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2106 printStringNoNewline(&inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2107 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2108 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2109 ir->bDisreMixed = get_eeenum(&inp, "disre-mixed", yesno_names, wi);
2110 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2111 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2112 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2113 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2114 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2115 opts->bOrire = get_eeenum(&inp, "orire", yesno_names, wi);
2116 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2117 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2118 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2119 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2120 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2121 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2123 /* free energy variables */
2124 printStringNewline(&inp, "Free energy variables");
2125 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2126 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2127 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2128 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2129 opts->bCoupleIntra = get_eeenum(&inp, "couple-intramol", yesno_names, wi);
2131 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2133 it was not entered */
2134 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2135 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2136 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2137 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2138 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2139 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2140 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2141 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2142 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2143 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2144 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2145 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2146 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2147 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2148 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2149 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2150 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2151 fep->bScCoul = get_eeenum(&inp, "sc-coul", yesno_names, wi);
2152 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2153 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2154 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2155 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2156 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2157 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2159 /* Non-equilibrium MD stuff */
2160 printStringNewline(&inp, "Non-equilibrium MD stuff");
2161 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2162 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2163 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2164 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2165 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2166 setStringEntry(&inp, "deform", is->deform, nullptr);
2168 /* simulated tempering variables */
2169 printStringNewline(&inp, "simulated tempering variables");
2170 ir->bSimTemp = get_eeenum(&inp, "simulated-tempering", yesno_names, wi);
2171 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2172 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2173 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2175 /* expanded ensemble variables */
2176 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2178 read_expandedparams(&inp, expand, wi);
2181 /* Electric fields */
2183 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2184 gmx::KeyValueTreeTransformer transform;
2185 transform.rules()->addRule()
2186 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2187 mdModules->initMdpTransform(transform.rules());
2188 for (const auto &path : transform.mappedPaths())
2190 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2191 mark_einp_set(inp, path[0].c_str());
2193 MdpErrorHandler errorHandler(wi);
2195 = transform.transform(convertedValues, &errorHandler);
2196 ir->params = new gmx::KeyValueTreeObject(result.object());
2197 mdModules->adjustInputrecBasedOnModules(ir);
2198 errorHandler.setBackMapping(result.backMapping());
2199 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2202 /* Ion/water position swapping ("computational electrophysiology") */
2203 printStringNewline(&inp, "Ion/water position swapping for computational electrophysiology setups");
2204 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2205 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2206 if (ir->eSwapCoords != eswapNO)
2213 printStringNoNewline(&inp, "Swap attempt frequency");
2214 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2215 printStringNoNewline(&inp, "Number of ion types to be controlled");
2216 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2219 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2221 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2222 snew(ir->swap->grp, ir->swap->ngrp);
2223 for (i = 0; i < ir->swap->ngrp; i++)
2225 snew(ir->swap->grp[i].molname, STRLEN);
2227 printStringNoNewline(&inp, "Two index groups that contain the compartment-partitioning atoms");
2228 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2229 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2230 printStringNoNewline(&inp, "Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2231 ir->swap->massw_split[0] = get_eeenum(&inp, "massw-split0", yesno_names, wi);
2232 ir->swap->massw_split[1] = get_eeenum(&inp, "massw-split1", yesno_names, wi);
2234 printStringNoNewline(&inp, "Name of solvent molecules");
2235 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2237 printStringNoNewline(&inp, "Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2238 printStringNoNewline(&inp, "Note that the split cylinder settings do not have an influence on the swapping protocol,");
2239 printStringNoNewline(&inp, "however, if correctly defined, the permeation events are recorded per channel");
2240 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2241 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2242 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2243 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2244 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2245 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2247 printStringNoNewline(&inp, "Average the number of ions per compartment over these many swap attempt steps");
2248 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2250 printStringNoNewline(&inp, "Names of the ion types that can be exchanged with solvent molecules,");
2251 printStringNoNewline(&inp, "and the requested number of ions of this type in compartments A and B");
2252 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2253 for (i = 0; i < nIonTypes; i++)
2255 int ig = eSwapFixedGrpNR + i;
2257 sprintf(buf, "iontype%d-name", i);
2258 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2259 sprintf(buf, "iontype%d-in-A", i);
2260 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2261 sprintf(buf, "iontype%d-in-B", i);
2262 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2265 printStringNoNewline(&inp, "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2266 printStringNoNewline(&inp, "at maximum distance (= bulk concentration) to the split group layers. However,");
2267 printStringNoNewline(&inp, "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2268 printStringNoNewline(&inp, "towards one of the compartment-partitioning layers (at +/- 1.0).");
2269 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2270 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2271 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2272 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2274 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2277 printStringNoNewline(&inp, "Start to swap ions if threshold difference to requested count is reached");
2278 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2281 /* AdResS is no longer supported, but we need grompp to be able to
2282 refuse to process old .mdp files that used it. */
2283 ir->bAdress = get_eeenum(&inp, "adress", no_names, wi);
2285 /* User defined thingies */
2286 printStringNewline(&inp, "User defined thingies");
2287 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2288 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2289 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2290 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2291 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2292 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2293 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2294 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2295 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2296 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2300 gmx::TextOutputFile stream(mdparout);
2301 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2303 // Transform module data into a flat key-value tree for output.
2304 gmx::KeyValueTreeBuilder builder;
2305 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2306 mdModules->buildMdpOutput(&builderObject);
2308 gmx::TextWriter writer(&stream);
2309 writeKeyValueTreeAsMdp(&writer, builder.build());
2314 /* Process options if necessary */
2315 for (m = 0; m < 2; m++)
2317 for (i = 0; i < 2*DIM; i++)
2326 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2328 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2330 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2332 case epctSEMIISOTROPIC:
2333 case epctSURFACETENSION:
2334 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2336 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2338 dumdub[m][YY] = dumdub[m][XX];
2340 case epctANISOTROPIC:
2341 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2342 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2343 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2345 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2349 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2350 epcoupltype_names[ir->epct]);
2354 clear_mat(ir->ref_p);
2355 clear_mat(ir->compress);
2356 for (i = 0; i < DIM; i++)
2358 ir->ref_p[i][i] = dumdub[1][i];
2359 ir->compress[i][i] = dumdub[0][i];
2361 if (ir->epct == epctANISOTROPIC)
2363 ir->ref_p[XX][YY] = dumdub[1][3];
2364 ir->ref_p[XX][ZZ] = dumdub[1][4];
2365 ir->ref_p[YY][ZZ] = dumdub[1][5];
2366 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2368 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2370 ir->compress[XX][YY] = dumdub[0][3];
2371 ir->compress[XX][ZZ] = dumdub[0][4];
2372 ir->compress[YY][ZZ] = dumdub[0][5];
2373 for (i = 0; i < DIM; i++)
2375 for (m = 0; m < i; m++)
2377 ir->ref_p[i][m] = ir->ref_p[m][i];
2378 ir->compress[i][m] = ir->compress[m][i];
2383 if (ir->comm_mode == ecmNO)
2388 opts->couple_moltype = nullptr;
2389 if (strlen(is->couple_moltype) > 0)
2391 if (ir->efep != efepNO)
2393 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2394 if (opts->couple_lam0 == opts->couple_lam1)
2396 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2398 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2399 opts->couple_lam1 == ecouplamNONE))
2401 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2406 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2409 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2410 if (ir->efep != efepNO)
2412 if (fep->delta_lambda > 0)
2414 ir->efep = efepSLOWGROWTH;
2418 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2420 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2421 warning_note(wi, "Old option for dhdl-print-energy given: "
2422 "changing \"yes\" to \"total\"\n");
2425 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2427 /* always print out the energy to dhdl if we are doing
2428 expanded ensemble, since we need the total energy for
2429 analysis if the temperature is changing. In some
2430 conditions one may only want the potential energy, so
2431 we will allow that if the appropriate mdp setting has
2432 been enabled. Otherwise, total it is:
2434 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2437 if ((ir->efep != efepNO) || ir->bSimTemp)
2439 ir->bExpanded = FALSE;
2440 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2442 ir->bExpanded = TRUE;
2444 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2445 if (ir->bSimTemp) /* done after fep params */
2447 do_simtemp_params(ir);
2450 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2451 * setup and not on the old way of specifying the free-energy setup,
2452 * we should check for using soft-core when not needed, since that
2453 * can complicate the sampling significantly.
2454 * Note that we only check for the automated coupling setup.
2455 * If the (advanced) user does FEP through manual topology changes,
2456 * this check will not be triggered.
2458 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2459 ir->fepvals->sc_alpha != 0 &&
2460 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2461 couple_lambda_has_vdw_on(opts->couple_lam1)))
2463 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.");
2468 ir->fepvals->n_lambda = 0;
2471 /* WALL PARAMETERS */
2473 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2475 /* ORIENTATION RESTRAINT PARAMETERS */
2477 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
2479 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2482 /* DEFORMATION PARAMETERS */
2484 clear_mat(ir->deform);
2485 for (i = 0; i < 6; i++)
2490 double gmx_unused canary;
2491 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2492 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2493 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2495 if (strlen(is->deform) > 0 && ndeform != 6)
2497 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2499 for (i = 0; i < 3; i++)
2501 ir->deform[i][i] = dumdub[0][i];
2503 ir->deform[YY][XX] = dumdub[0][3];
2504 ir->deform[ZZ][XX] = dumdub[0][4];
2505 ir->deform[ZZ][YY] = dumdub[0][5];
2506 if (ir->epc != epcNO)
2508 for (i = 0; i < 3; i++)
2510 for (j = 0; j <= i; j++)
2512 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2514 warning_error(wi, "A box element has deform set and compressibility > 0");
2518 for (i = 0; i < 3; i++)
2520 for (j = 0; j < i; j++)
2522 if (ir->deform[i][j] != 0)
2524 for (m = j; m < DIM; m++)
2526 if (ir->compress[m][j] != 0)
2528 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.");
2529 warning(wi, warn_buf);
2537 /* Ion/water position swapping checks */
2538 if (ir->eSwapCoords != eswapNO)
2540 if (ir->swap->nstswap < 1)
2542 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2544 if (ir->swap->nAverage < 1)
2546 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2548 if (ir->swap->threshold < 1.0)
2550 warning_error(wi, "Ion count threshold must be at least 1.\n");
2558 static int search_QMstring(const char *s, int ng, const char *gn[])
2560 /* same as normal search_string, but this one searches QM strings */
2563 for (i = 0; (i < ng); i++)
2565 if (gmx_strcasecmp(s, gn[i]) == 0)
2571 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2572 } /* search_QMstring */
2574 /* We would like gn to be const as well, but C doesn't allow this */
2575 /* TODO this is utility functionality (search for the index of a
2576 string in a collection), so should be refactored and located more
2578 int search_string(const char *s, int ng, char *gn[])
2582 for (i = 0; (i < ng); i++)
2584 if (gmx_strcasecmp(s, gn[i]) == 0)
2591 "Group %s referenced in the .mdp file was not found in the index file.\n"
2592 "Group names must match either [moleculetype] names or custom index group\n"
2593 "names, in which case you must supply an index file to the '-n' option\n"
2598 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2599 t_blocka *block, char *gnames[],
2600 int gtype, int restnm,
2601 int grptp, gmx_bool bVerbose,
2604 unsigned short *cbuf;
2605 t_grps *grps = &(groups->grps[gtype]);
2606 int i, j, gid, aj, ognr, ntot = 0;
2609 char warn_buf[STRLEN];
2613 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2616 title = gtypes[gtype];
2619 /* Mark all id's as not set */
2620 for (i = 0; (i < natoms); i++)
2625 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2626 for (i = 0; (i < ng); i++)
2628 /* Lookup the group name in the block structure */
2629 gid = search_string(ptrs[i], block->nr, gnames);
2630 if ((grptp != egrptpONE) || (i == 0))
2632 grps->nm_ind[grps->nr++] = gid;
2636 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2639 /* Now go over the atoms in the group */
2640 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2645 /* Range checking */
2646 if ((aj < 0) || (aj >= natoms))
2648 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2650 /* Lookup up the old group number */
2654 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2655 aj+1, title, ognr+1, i+1);
2659 /* Store the group number in buffer */
2660 if (grptp == egrptpONE)
2673 /* Now check whether we have done all atoms */
2677 if (grptp == egrptpALL)
2679 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2680 natoms-ntot, title);
2682 else if (grptp == egrptpPART)
2684 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2685 natoms-ntot, title);
2686 warning_note(wi, warn_buf);
2688 /* Assign all atoms currently unassigned to a rest group */
2689 for (j = 0; (j < natoms); j++)
2691 if (cbuf[j] == NOGID)
2697 if (grptp != egrptpPART)
2702 "Making dummy/rest group for %s containing %d elements\n",
2703 title, natoms-ntot);
2705 /* Add group name "rest" */
2706 grps->nm_ind[grps->nr] = restnm;
2708 /* Assign the rest name to all atoms not currently assigned to a group */
2709 for (j = 0; (j < natoms); j++)
2711 if (cbuf[j] == NOGID)
2720 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2722 /* All atoms are part of one (or no) group, no index required */
2723 groups->ngrpnr[gtype] = 0;
2724 groups->grpnr[gtype] = nullptr;
2728 groups->ngrpnr[gtype] = natoms;
2729 snew(groups->grpnr[gtype], natoms);
2730 for (j = 0; (j < natoms); j++)
2732 groups->grpnr[gtype][j] = cbuf[j];
2738 return (bRest && grptp == egrptpPART);
2741 static void calc_nrdf(const gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2744 const gmx_groups_t *groups;
2745 pull_params_t *pull;
2746 int natoms, ai, aj, i, j, d, g, imin, jmin;
2748 int *nrdf2, *na_vcm, na_tot;
2749 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2751 gmx_mtop_atomloop_all_t aloop;
2755 * First calc 3xnr-atoms for each group
2756 * then subtract half a degree of freedom for each constraint
2758 * Only atoms and nuclei contribute to the degrees of freedom...
2763 groups = &mtop->groups;
2764 natoms = mtop->natoms;
2766 /* Allocate one more for a possible rest group */
2767 /* We need to sum degrees of freedom into doubles,
2768 * since floats give too low nrdf's above 3 million atoms.
2770 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2771 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2772 snew(dof_vcm, groups->grps[egcVCM].nr+1);
2773 snew(na_vcm, groups->grps[egcVCM].nr+1);
2774 snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
2776 for (i = 0; i < groups->grps[egcTC].nr; i++)
2780 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2783 clear_ivec(dof_vcm[i]);
2785 nrdf_vcm_sub[i] = 0;
2788 snew(nrdf2, natoms);
2789 aloop = gmx_mtop_atomloop_all_init(mtop);
2791 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2794 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2796 g = ggrpnr(groups, egcFREEZE, i);
2797 for (d = 0; d < DIM; d++)
2799 if (opts->nFreeze[g][d] == 0)
2801 /* Add one DOF for particle i (counted as 2*1) */
2803 /* VCM group i has dim d as a DOF */
2804 dof_vcm[ggrpnr(groups, egcVCM, i)][d] = 1;
2807 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2808 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2813 for (const gmx_molblock_t &molb : mtop->molblock)
2815 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2816 atom = molt.atoms.atom;
2817 for (mol = 0; mol < molb.nmol; mol++)
2819 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2821 ia = molt.ilist[ftype].iatoms;
2822 for (i = 0; i < molt.ilist[ftype].nr; )
2824 /* Subtract degrees of freedom for the constraints,
2825 * if the particles still have degrees of freedom left.
2826 * If one of the particles is a vsite or a shell, then all
2827 * constraint motion will go there, but since they do not
2828 * contribute to the constraints the degrees of freedom do not
2833 if (((atom[ia[1]].ptype == eptNucleus) ||
2834 (atom[ia[1]].ptype == eptAtom)) &&
2835 ((atom[ia[2]].ptype == eptNucleus) ||
2836 (atom[ia[2]].ptype == eptAtom)))
2854 imin = std::min(imin, nrdf2[ai]);
2855 jmin = std::min(jmin, nrdf2[aj]);
2858 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2859 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2860 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2861 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2863 ia += interaction_function[ftype].nratoms+1;
2864 i += interaction_function[ftype].nratoms+1;
2867 ia = molt.ilist[F_SETTLE].iatoms;
2868 for (i = 0; i < molt.ilist[F_SETTLE].nr; )
2870 /* Subtract 1 dof from every atom in the SETTLE */
2871 for (j = 0; j < 3; j++)
2874 imin = std::min(2, nrdf2[ai]);
2876 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2877 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2882 as += molt.atoms.nr;
2888 /* Correct nrdf for the COM constraints.
2889 * We correct using the TC and VCM group of the first atom
2890 * in the reference and pull group. If atoms in one pull group
2891 * belong to different TC or VCM groups it is anyhow difficult
2892 * to determine the optimal nrdf assignment.
2896 for (i = 0; i < pull->ncoord; i++)
2898 if (pull->coord[i].eType != epullCONSTRAINT)
2905 for (j = 0; j < 2; j++)
2907 const t_pull_group *pgrp;
2909 pgrp = &pull->group[pull->coord[i].group[j]];
2913 /* Subtract 1/2 dof from each group */
2915 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2916 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2917 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2919 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->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
2924 /* We need to subtract the whole DOF from group j=1 */
2931 if (ir->nstcomm != 0)
2935 /* We remove COM motion up to dim ndof_com() */
2936 ndim_rm_vcm = ndof_com(ir);
2938 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
2939 * the number of degrees of freedom in each vcm group when COM
2940 * translation is removed and 6 when rotation is removed as well.
2942 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2944 switch (ir->comm_mode)
2947 case ecmLINEAR_ACCELERATION_CORRECTION:
2948 nrdf_vcm_sub[j] = 0;
2949 for (d = 0; d < ndim_rm_vcm; d++)
2958 nrdf_vcm_sub[j] = 6;
2961 gmx_incons("Checking comm_mode");
2965 for (i = 0; i < groups->grps[egcTC].nr; i++)
2967 /* Count the number of atoms of TC group i for every VCM group */
2968 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2973 for (ai = 0; ai < natoms; ai++)
2975 if (ggrpnr(groups, egcTC, ai) == i)
2977 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2981 /* Correct for VCM removal according to the fraction of each VCM
2982 * group present in this TC group.
2984 nrdf_uc = nrdf_tc[i];
2987 fprintf(debug, "T-group[%d] nrdf_uc = %g\n", i, nrdf_uc);
2990 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2992 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
2994 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2995 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
2999 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
3000 j, nrdf_vcm[j], nrdf_tc[i]);
3005 for (i = 0; (i < groups->grps[egcTC].nr); i++)
3007 opts->nrdf[i] = nrdf_tc[i];
3008 if (opts->nrdf[i] < 0)
3013 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3014 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3022 sfree(nrdf_vcm_sub);
3025 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3026 const char *option, const char *val, int flag)
3028 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3029 * But since this is much larger than STRLEN, such a line can not be parsed.
3030 * The real maximum is the number of names that fit in a string: STRLEN/2.
3032 #define EGP_MAX (STRLEN/2)
3033 int nelem, i, j, k, nr;
3034 char *names[EGP_MAX];
3038 gnames = groups->grpname;
3040 nelem = str_nelem(val, EGP_MAX, names);
3043 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3045 nr = groups->grps[egcENER].nr;
3047 for (i = 0; i < nelem/2; i++)
3051 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3057 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3058 names[2*i], option);
3062 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3068 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3069 names[2*i+1], option);
3071 if ((j < nr) && (k < nr))
3073 ir->opts.egp_flags[nr*j+k] |= flag;
3074 ir->opts.egp_flags[nr*k+j] |= flag;
3083 static void make_swap_groups(
3088 int ig = -1, i = 0, gind;
3092 /* Just a quick check here, more thorough checks are in mdrun */
3093 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3095 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3098 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3099 for (ig = 0; ig < swap->ngrp; ig++)
3101 swapg = &swap->grp[ig];
3102 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3103 swapg->nat = grps->index[gind+1] - grps->index[gind];
3107 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3108 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3109 swap->grp[ig].molname, swapg->nat);
3110 snew(swapg->ind, swapg->nat);
3111 for (i = 0; i < swapg->nat; i++)
3113 swapg->ind[i] = grps->a[grps->index[gind]+i];
3118 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3124 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3129 ig = search_string(IMDgname, grps->nr, gnames);
3130 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3132 if (IMDgroup->nat > 0)
3134 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3135 IMDgname, IMDgroup->nat);
3136 snew(IMDgroup->ind, IMDgroup->nat);
3137 for (i = 0; i < IMDgroup->nat; i++)
3139 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3145 void do_index(const char* mdparin, const char *ndx,
3152 gmx_groups_t *groups;
3156 char warnbuf[STRLEN], **gnames;
3157 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3160 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3161 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3162 int i, j, k, restnm;
3163 gmx_bool bExcl, bTable, bAnneal, bRest;
3164 int nQMmethod, nQMbasis, nQMg;
3165 char warn_buf[STRLEN];
3170 fprintf(stderr, "processing index file...\n");
3175 snew(grps->index, 1);
3177 atoms_all = gmx_mtop_global_atoms(mtop);
3178 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3179 done_atom(&atoms_all);
3183 grps = init_index(ndx, &gnames);
3186 groups = &mtop->groups;
3187 natoms = mtop->natoms;
3188 symtab = &mtop->symtab;
3190 snew(groups->grpname, grps->nr+1);
3192 for (i = 0; (i < grps->nr); i++)
3194 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3196 groups->grpname[i] = put_symtab(symtab, "rest");
3198 srenew(gnames, grps->nr+1);
3199 gnames[restnm] = *(groups->grpname[i]);
3200 groups->ngrpname = grps->nr+1;
3202 set_warning_line(wi, mdparin, -1);
3204 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3205 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3206 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3207 if ((ntau_t != ntcg) || (nref_t != ntcg))
3209 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3210 "%d tau-t values", ntcg, nref_t, ntau_t);
3213 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3214 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3215 restnm, useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3216 nr = groups->grps[egcTC].nr;
3218 snew(ir->opts.nrdf, nr);
3219 snew(ir->opts.tau_t, nr);
3220 snew(ir->opts.ref_t, nr);
3221 if (ir->eI == eiBD && ir->bd_fric == 0)
3223 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3226 if (useReferenceTemperature)
3230 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3234 for (i = 0; (i < nr); i++)
3236 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3239 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3241 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3243 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3244 warning_error(wi, warn_buf);
3247 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3249 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.");
3252 if (ir->opts.tau_t[i] >= 0)
3254 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3257 if (ir->etc != etcNO && ir->nsttcouple == -1)
3259 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3264 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3266 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");
3268 if (ir->epc == epcMTTK)
3270 if (ir->etc != etcNOSEHOOVER)
3272 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3276 if (ir->nstpcouple != ir->nsttcouple)
3278 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3279 ir->nstpcouple = ir->nsttcouple = mincouple;
3280 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);
3281 warning_note(wi, warn_buf);
3286 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3287 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3289 if (ETC_ANDERSEN(ir->etc))
3291 if (ir->nsttcouple != 1)
3294 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");
3295 warning_note(wi, warn_buf);
3298 nstcmin = tcouple_min_integration_steps(ir->etc);
3301 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3303 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3304 ETCOUPLTYPE(ir->etc),
3306 ir->nsttcouple*ir->delta_t);
3307 warning(wi, warn_buf);
3310 for (i = 0; (i < nr); i++)
3312 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3315 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3317 if (ir->opts.ref_t[i] < 0)
3319 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3322 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3323 if we are in this conditional) if mc_temp is negative */
3324 if (ir->expandedvals->mc_temp < 0)
3326 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3330 /* Simulated annealing for each group. There are nr groups */
3331 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3332 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3336 if (nSA > 0 && nSA != nr)
3338 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3342 snew(ir->opts.annealing, nr);
3343 snew(ir->opts.anneal_npoints, nr);
3344 snew(ir->opts.anneal_time, nr);
3345 snew(ir->opts.anneal_temp, nr);
3346 for (i = 0; i < nr; i++)
3348 ir->opts.annealing[i] = eannNO;
3349 ir->opts.anneal_npoints[i] = 0;
3350 ir->opts.anneal_time[i] = nullptr;
3351 ir->opts.anneal_temp[i] = nullptr;
3356 for (i = 0; i < nr; i++)
3358 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3360 ir->opts.annealing[i] = eannNO;
3362 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3364 ir->opts.annealing[i] = eannSINGLE;
3367 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3369 ir->opts.annealing[i] = eannPERIODIC;
3375 /* Read the other fields too */
3376 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3377 if (nSA_points != nSA)
3379 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3381 for (k = 0, i = 0; i < nr; i++)
3383 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3386 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3388 if (ir->opts.anneal_npoints[i] == 1)
3390 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3392 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3393 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3394 k += ir->opts.anneal_npoints[i];
3397 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3400 gmx_fatal(FARGS, "Found %d annealing-time values, wanted %d\n", nSA_time, k);
3402 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3405 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3408 for (i = 0, k = 0; i < nr; i++)
3411 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3413 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3416 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3418 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3421 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3425 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3427 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3433 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3435 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3436 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3439 if (ir->opts.anneal_temp[i][j] < 0)
3441 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3446 /* Print out some summary information, to make sure we got it right */
3447 for (i = 0, k = 0; i < nr; i++)
3449 if (ir->opts.annealing[i] != eannNO)
3451 j = groups->grps[egcTC].nm_ind[i];
3452 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3453 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3454 ir->opts.anneal_npoints[i]);
3455 fprintf(stderr, "Time (ps) Temperature (K)\n");
3456 /* All terms except the last one */
3457 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3459 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3462 /* Finally the last one */
3463 j = ir->opts.anneal_npoints[i]-1;
3464 if (ir->opts.annealing[i] == eannSINGLE)
3466 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3470 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3471 if (std::fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3473 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3484 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3486 make_pull_coords(ir->pull);
3491 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3494 if (ir->eSwapCoords != eswapNO)
3496 make_swap_groups(ir->swap, grps, gnames);
3499 /* Make indices for IMD session */
3502 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3505 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3506 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3507 if (nacg*DIM != nacc)
3509 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3512 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3513 restnm, egrptpALL_GENREST, bVerbose, wi);
3514 nr = groups->grps[egcACC].nr;
3515 snew(ir->opts.acc, nr);
3516 ir->opts.ngacc = nr;
3518 for (i = k = 0; (i < nacg); i++)
3520 for (j = 0; (j < DIM); j++, k++)
3522 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3525 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3529 for (; (i < nr); i++)
3531 for (j = 0; (j < DIM); j++)
3533 ir->opts.acc[i][j] = 0;
3537 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3538 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3539 if (nfrdim != DIM*nfreeze)
3541 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3544 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3545 restnm, egrptpALL_GENREST, bVerbose, wi);
3546 nr = groups->grps[egcFREEZE].nr;
3547 ir->opts.ngfrz = nr;
3548 snew(ir->opts.nFreeze, nr);
3549 for (i = k = 0; (i < nfreeze); i++)
3551 for (j = 0; (j < DIM); j++, k++)
3553 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3554 if (!ir->opts.nFreeze[i][j])
3556 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3558 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3559 "(not %s)", ptr1[k]);
3560 warning(wi, warn_buf);
3565 for (; (i < nr); i++)
3567 for (j = 0; (j < DIM); j++)
3569 ir->opts.nFreeze[i][j] = 0;
3573 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3574 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3575 restnm, egrptpALL_GENREST, bVerbose, wi);
3576 add_wall_energrps(groups, ir->nwall, symtab);
3577 ir->opts.ngener = groups->grps[egcENER].nr;
3578 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3580 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3581 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3584 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3585 "This may lead to artifacts.\n"
3586 "In most cases one should use one group for the whole system.");
3589 /* Now we have filled the freeze struct, so we can calculate NRDF */
3590 calc_nrdf(mtop, ir, gnames);
3592 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3593 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3594 restnm, egrptpALL_GENREST, bVerbose, wi);
3595 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3596 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3597 restnm, egrptpALL_GENREST, bVerbose, wi);
3598 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3599 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3600 restnm, egrptpONE, bVerbose, wi);
3601 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3602 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3603 restnm, egrptpALL_GENREST, bVerbose, wi);
3605 /* QMMM input processing */
3606 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3607 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3608 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3609 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3611 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3612 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3614 /* group rest, if any, is always MM! */
3615 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3616 restnm, egrptpALL_GENREST, bVerbose, wi);
3617 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3618 ir->opts.ngQM = nQMg;
3619 snew(ir->opts.QMmethod, nr);
3620 snew(ir->opts.QMbasis, nr);
3621 for (i = 0; i < nr; i++)
3623 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3624 * converted to the corresponding enum in names.c
3626 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3628 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3632 str_nelem(is->QMmult, MAXPTR, ptr1);
3633 str_nelem(is->QMcharge, MAXPTR, ptr2);
3634 str_nelem(is->bSH, MAXPTR, ptr3);
3635 snew(ir->opts.QMmult, nr);
3636 snew(ir->opts.QMcharge, nr);
3637 snew(ir->opts.bSH, nr);
3639 for (i = 0; i < nr; i++)
3641 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3644 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3646 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3649 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3651 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3654 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3655 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3656 snew(ir->opts.CASelectrons, nr);
3657 snew(ir->opts.CASorbitals, nr);
3658 for (i = 0; i < nr; i++)
3660 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3663 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3665 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3668 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3672 str_nelem(is->SAon, MAXPTR, ptr1);
3673 str_nelem(is->SAoff, MAXPTR, ptr2);
3674 str_nelem(is->SAsteps, MAXPTR, ptr3);
3675 snew(ir->opts.SAon, nr);
3676 snew(ir->opts.SAoff, nr);
3677 snew(ir->opts.SAsteps, nr);
3679 for (i = 0; i < nr; i++)
3681 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3684 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3686 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3689 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3691 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3694 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3697 /* end of QMMM input */
3701 for (i = 0; (i < egcNR); i++)
3703 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3704 for (j = 0; (j < groups->grps[i].nr); j++)
3706 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3708 fprintf(stderr, "\n");
3712 nr = groups->grps[egcENER].nr;
3713 snew(ir->opts.egp_flags, nr*nr);
3715 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3716 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3718 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3720 if (bExcl && EEL_FULL(ir->coulombtype))
3722 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3725 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3726 if (bTable && !(ir->vdwtype == evdwUSER) &&
3727 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3728 !(ir->coulombtype == eelPMEUSERSWITCH))
3730 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3733 for (i = 0; (i < grps->nr); i++)
3745 static void check_disre(gmx_mtop_t *mtop)
3747 gmx_ffparams_t *ffparams;
3748 t_functype *functype;
3750 int i, ndouble, ftype;
3751 int label, old_label;
3753 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3755 ffparams = &mtop->ffparams;
3756 functype = ffparams->functype;
3757 ip = ffparams->iparams;
3760 for (i = 0; i < ffparams->ntypes; i++)
3762 ftype = functype[i];
3763 if (ftype == F_DISRES)
3765 label = ip[i].disres.label;
3766 if (label == old_label)
3768 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3776 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3777 "probably the parameters for multiple pairs in one restraint "
3778 "are not identical\n", ndouble);
3783 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3784 gmx_bool posres_only,
3788 gmx_mtop_ilistloop_t iloop;
3789 const t_ilist *ilist;
3798 for (d = 0; d < DIM; d++)
3800 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3802 /* Check for freeze groups */
3803 for (g = 0; g < ir->opts.ngfrz; g++)
3805 for (d = 0; d < DIM; d++)
3807 if (ir->opts.nFreeze[g][d] != 0)
3815 /* Check for position restraints */
3816 iloop = gmx_mtop_ilistloop_init(sys);
3817 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3820 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3822 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3824 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3825 for (d = 0; d < DIM; d++)
3827 if (pr->posres.fcA[d] != 0)
3833 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3835 /* Check for flat-bottom posres */
3836 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3837 if (pr->fbposres.k != 0)
3839 switch (pr->fbposres.geom)
3841 case efbposresSPHERE:
3842 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3844 case efbposresCYLINDERX:
3845 AbsRef[YY] = AbsRef[ZZ] = 1;
3847 case efbposresCYLINDERY:
3848 AbsRef[XX] = AbsRef[ZZ] = 1;
3850 case efbposresCYLINDER:
3851 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3852 case efbposresCYLINDERZ:
3853 AbsRef[XX] = AbsRef[YY] = 1;
3855 case efbposresX: /* d=XX */
3856 case efbposresY: /* d=YY */
3857 case efbposresZ: /* d=ZZ */
3858 d = pr->fbposres.geom - efbposresX;
3862 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3863 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3871 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3875 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3876 gmx_bool *bC6ParametersWorkWithGeometricRules,
3877 gmx_bool *bC6ParametersWorkWithLBRules,
3878 gmx_bool *bLBRulesPossible)
3880 int ntypes, tpi, tpj;
3883 double c6i, c6j, c12i, c12j;
3884 double c6, c6_geometric, c6_LB;
3885 double sigmai, sigmaj, epsi, epsj;
3886 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3889 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3890 * force-field floating point parameters.
3893 ptr = getenv("GMX_LJCOMB_TOL");
3897 double gmx_unused canary;
3899 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3901 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3906 *bC6ParametersWorkWithLBRules = TRUE;
3907 *bC6ParametersWorkWithGeometricRules = TRUE;
3908 bCanDoLBRules = TRUE;
3909 ntypes = mtop->ffparams.atnr;
3910 snew(typecount, ntypes);
3911 gmx_mtop_count_atomtypes(mtop, state, typecount);
3912 *bLBRulesPossible = TRUE;
3913 for (tpi = 0; tpi < ntypes; ++tpi)
3915 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3916 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3917 for (tpj = tpi; tpj < ntypes; ++tpj)
3919 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3920 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3921 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3922 c6_geometric = std::sqrt(c6i * c6j);
3923 if (!gmx_numzero(c6_geometric))
3925 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3927 sigmai = gmx::sixthroot(c12i / c6i);
3928 sigmaj = gmx::sixthroot(c12j / c6j);
3929 epsi = c6i * c6i /(4.0 * c12i);
3930 epsj = c6j * c6j /(4.0 * c12j);
3931 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3935 *bLBRulesPossible = FALSE;
3936 c6_LB = c6_geometric;
3938 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3941 if (FALSE == bCanDoLBRules)
3943 *bC6ParametersWorkWithLBRules = FALSE;
3946 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3948 if (FALSE == bCanDoGeometricRules)
3950 *bC6ParametersWorkWithGeometricRules = FALSE;
3958 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3961 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3963 check_combination_rule_differences(mtop, 0,
3964 &bC6ParametersWorkWithGeometricRules,
3965 &bC6ParametersWorkWithLBRules,
3967 if (ir->ljpme_combination_rule == eljpmeLB)
3969 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3971 warning(wi, "You are using arithmetic-geometric combination rules "
3972 "in LJ-PME, but your non-bonded C6 parameters do not "
3973 "follow these rules.");
3978 if (FALSE == bC6ParametersWorkWithGeometricRules)
3980 if (ir->eDispCorr != edispcNO)
3982 warning_note(wi, "You are using geometric combination rules in "
3983 "LJ-PME, but your non-bonded C6 parameters do "
3984 "not follow these rules. "
3985 "This will introduce very small errors in the forces and energies in "
3986 "your simulations. Dispersion correction will correct total energy "
3987 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3991 warning_note(wi, "You are using geometric combination rules in "
3992 "LJ-PME, but your non-bonded C6 parameters do "
3993 "not follow these rules. "
3994 "This will introduce very small errors in the forces and energies in "
3995 "your simulations. If your system is homogeneous, consider using dispersion correction "
3996 "for the total energy and pressure.");
4002 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4005 char err_buf[STRLEN];
4007 gmx_bool bCharge, bAcc;
4010 gmx_mtop_atomloop_block_t aloopb;
4011 gmx_mtop_atomloop_all_t aloop;
4013 char warn_buf[STRLEN];
4015 set_warning_line(wi, mdparin, -1);
4017 if (ir->cutoff_scheme == ecutsVERLET &&
4018 ir->verletbuf_tol > 0 &&
4020 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4021 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4023 /* Check if a too small Verlet buffer might potentially
4024 * cause more drift than the thermostat can couple off.
4026 /* Temperature error fraction for warning and suggestion */
4027 const real T_error_warn = 0.002;
4028 const real T_error_suggest = 0.001;
4029 /* For safety: 2 DOF per atom (typical with constraints) */
4030 const real nrdf_at = 2;
4031 real T, tau, max_T_error;
4036 for (i = 0; i < ir->opts.ngtc; i++)
4038 T = std::max(T, ir->opts.ref_t[i]);
4039 tau = std::max(tau, ir->opts.tau_t[i]);
4043 /* This is a worst case estimate of the temperature error,
4044 * assuming perfect buffer estimation and no cancelation
4045 * of errors. The factor 0.5 is because energy distributes
4046 * equally over Ekin and Epot.
4048 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4049 if (max_T_error > T_error_warn)
4051 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.",
4052 ir->verletbuf_tol, T, tau,
4054 100*T_error_suggest,
4055 ir->verletbuf_tol*T_error_suggest/max_T_error);
4056 warning(wi, warn_buf);
4061 if (ETC_ANDERSEN(ir->etc))
4065 for (i = 0; i < ir->opts.ngtc; i++)
4067 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4068 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4069 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4070 i, ir->opts.tau_t[i]);
4071 CHECK(ir->opts.tau_t[i] < 0);
4074 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4076 for (i = 0; i < ir->opts.ngtc; i++)
4078 int nsteps = static_cast<int>(ir->opts.tau_t[i]/ir->delta_t + 0.5);
4079 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);
4080 CHECK(nsteps % ir->nstcomm != 0);
4085 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4086 ir->comm_mode == ecmNO &&
4087 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4088 !ETC_ANDERSEN(ir->etc))
4090 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");
4093 /* Check for pressure coupling with absolute position restraints */
4094 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4096 absolute_reference(ir, sys, TRUE, AbsRef);
4098 for (m = 0; m < DIM; m++)
4100 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4102 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4110 aloopb = gmx_mtop_atomloop_block_init(sys);
4112 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4114 if (atom->q != 0 || atom->qB != 0)
4122 if (EEL_FULL(ir->coulombtype))
4125 "You are using full electrostatics treatment %s for a system without charges.\n"
4126 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4127 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4128 warning(wi, err_buf);
4133 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4136 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4137 "You might want to consider using %s electrostatics.\n",
4139 warning_note(wi, err_buf);
4143 /* Check if combination rules used in LJ-PME are the same as in the force field */
4144 if (EVDW_PME(ir->vdwtype))
4146 check_combination_rules(ir, sys, wi);
4149 /* Generalized reaction field */
4150 if (ir->opts.ngtc == 0)
4152 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4154 CHECK(ir->coulombtype == eelGRF);
4158 sprintf(err_buf, "When using coulombtype = %s"
4159 " ref-t for temperature coupling should be > 0",
4161 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4165 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4167 for (m = 0; (m < DIM); m++)
4169 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4178 snew(mgrp, sys->groups.grps[egcACC].nr);
4179 aloop = gmx_mtop_atomloop_all_init(sys);
4181 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4183 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4186 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4188 for (m = 0; (m < DIM); m++)
4190 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4194 for (m = 0; (m < DIM); m++)
4196 if (fabs(acc[m]) > 1e-6)
4198 const char *dim[DIM] = { "X", "Y", "Z" };
4200 "Net Acceleration in %s direction, will %s be corrected\n",
4201 dim[m], ir->nstcomm != 0 ? "" : "not");
4202 if (ir->nstcomm != 0 && m < ndof_com(ir))
4205 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4207 ir->opts.acc[i][m] -= acc[m];
4215 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4216 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4218 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4226 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4228 if (ir->pull->coord[i].group[0] == 0 ||
4229 ir->pull->coord[i].group[1] == 0)
4231 absolute_reference(ir, sys, FALSE, AbsRef);
4232 for (m = 0; m < DIM; m++)
4234 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4236 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.");
4244 for (i = 0; i < 3; i++)
4246 for (m = 0; m <= i; m++)
4248 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4249 ir->deform[i][m] != 0)
4251 for (c = 0; c < ir->pull->ncoord; c++)
4253 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4254 ir->pull->coord[c].vec[m] != 0)
4256 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4267 void double_check(t_inputrec *ir, matrix box,
4268 gmx_bool bHasNormalConstraints,
4269 gmx_bool bHasAnyConstraints,
4273 char warn_buf[STRLEN];
4276 ptr = check_box(ir->ePBC, box);
4279 warning_error(wi, ptr);
4282 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4284 if (ir->shake_tol <= 0.0)
4286 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4288 warning_error(wi, warn_buf);
4292 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4294 /* If we have Lincs constraints: */
4295 if (ir->eI == eiMD && ir->etc == etcNO &&
4296 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4298 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4299 warning_note(wi, warn_buf);
4302 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4304 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4305 warning_note(wi, warn_buf);
4307 if (ir->epc == epcMTTK)
4309 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4313 if (bHasAnyConstraints && ir->epc == epcMTTK)
4315 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4318 if (ir->LincsWarnAngle > 90.0)
4320 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4321 warning(wi, warn_buf);
4322 ir->LincsWarnAngle = 90.0;
4325 if (ir->ePBC != epbcNONE)
4327 if (ir->nstlist == 0)
4329 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4331 if (ir->ns_type == ensGRID)
4333 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4335 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");
4336 warning_error(wi, warn_buf);
4341 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4342 if (2*ir->rlist >= min_size)
4344 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4345 warning_error(wi, warn_buf);
4348 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4355 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4359 real rvdw1, rvdw2, rcoul1, rcoul2;
4360 char warn_buf[STRLEN];
4362 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4366 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4371 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4377 if (rvdw1 + rvdw2 > ir->rlist ||
4378 rcoul1 + rcoul2 > ir->rlist)
4381 "The sum of the two largest charge group radii (%f) "
4382 "is larger than rlist (%f)\n",
4383 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4384 warning(wi, warn_buf);
4388 /* Here we do not use the zero at cut-off macro,
4389 * since user defined interactions might purposely
4390 * not be zero at the cut-off.
4392 if (ir_vdw_is_zero_at_cutoff(ir) &&
4393 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4395 sprintf(warn_buf, "The sum of the two largest charge group "
4396 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4397 "With exact cut-offs, better performance can be "
4398 "obtained with cutoff-scheme = %s, because it "
4399 "does not use charge groups at all.",
4401 ir->rlist, ir->rvdw,
4402 ecutscheme_names[ecutsVERLET]);
4405 warning(wi, warn_buf);
4409 warning_note(wi, warn_buf);
4412 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4413 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4415 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4416 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4418 ir->rlist, ir->rcoulomb,
4419 ecutscheme_names[ecutsVERLET]);
4422 warning(wi, warn_buf);
4426 warning_note(wi, warn_buf);