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51 #include "gromacs/applied_forces/awh/read_params.h"
52 #include "gromacs/fileio/readinp.h"
53 #include "gromacs/fileio/warninp.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/gmxpreprocess/toputil.h"
56 #include "gromacs/math/functions.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/mdlib/calc_verletbuf.h"
60 #include "gromacs/mdrun/mdmodules.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/mdtypes/multipletimestepping.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/selection/indexutil.h"
69 #include "gromacs/topology/block.h"
70 #include "gromacs/topology/ifunc.h"
71 #include "gromacs/topology/index.h"
72 #include "gromacs/topology/mtop_util.h"
73 #include "gromacs/topology/symtab.h"
74 #include "gromacs/topology/topology.h"
75 #include "gromacs/utility/arrayref.h"
76 #include "gromacs/utility/cstringutil.h"
77 #include "gromacs/utility/exceptions.h"
78 #include "gromacs/utility/fatalerror.h"
79 #include "gromacs/utility/filestream.h"
80 #include "gromacs/utility/gmxassert.h"
81 #include "gromacs/utility/ikeyvaluetreeerror.h"
82 #include "gromacs/utility/keyvaluetree.h"
83 #include "gromacs/utility/keyvaluetreebuilder.h"
84 #include "gromacs/utility/keyvaluetreemdpwriter.h"
85 #include "gromacs/utility/keyvaluetreetransform.h"
86 #include "gromacs/utility/mdmodulenotification.h"
87 #include "gromacs/utility/smalloc.h"
88 #include "gromacs/utility/strconvert.h"
89 #include "gromacs/utility/stringcompare.h"
90 #include "gromacs/utility/stringutil.h"
91 #include "gromacs/utility/textwriter.h"
96 /* Resource parameters
97 * Do not change any of these until you read the instruction
98 * in readinp.h. Some cpp's do not take spaces after the backslash
99 * (like the c-shell), which will give you a very weird compiler
103 struct gmx_inputrec_strings
105 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
106 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
107 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
108 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
109 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
110 char fep_lambda[efptNR][STRLEN];
111 char lambda_weights[STRLEN];
112 std::vector<std::string> pullGroupNames;
113 std::vector<std::string> rotateGroupNames;
114 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
117 static gmx_inputrec_strings* inputrecStrings = nullptr;
119 void init_inputrec_strings()
124 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
125 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
127 inputrecStrings = new gmx_inputrec_strings();
130 void done_inputrec_strings()
132 delete inputrecStrings;
133 inputrecStrings = nullptr;
139 egrptpALL, /* All particles have to be a member of a group. */
140 egrptpALL_GENREST, /* A rest group with name is generated for particles *
141 * that are not part of any group. */
142 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
143 * for the rest group. */
144 egrptpONE /* Merge all selected groups into one group, *
145 * make a rest group for the remaining particles. */
148 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
149 "h-angles", "all-angles", nullptr };
151 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
153 static void GetSimTemps(int ntemps, t_simtemp* simtemp, double* temperature_lambdas)
158 for (i = 0; i < ntemps; i++)
160 /* simple linear scaling -- allows more control */
161 if (simtemp->eSimTempScale == esimtempLINEAR)
163 simtemp->temperatures[i] =
165 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
167 else if (simtemp->eSimTempScale
168 == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
170 simtemp->temperatures[i] = simtemp->simtemp_low
171 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
172 static_cast<real>((1.0 * i) / (ntemps - 1)));
174 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
176 simtemp->temperatures[i] = simtemp->simtemp_low
177 + (simtemp->simtemp_high - simtemp->simtemp_low)
178 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
183 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
184 gmx_fatal(FARGS, "%s", errorstr);
190 static void _low_check(bool b, const char* s, warninp_t wi)
194 warning_error(wi, s);
198 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
202 if (*p > 0 && *p % nst != 0)
204 /* Round up to the next multiple of nst */
205 *p = ((*p) / nst + 1) * nst;
206 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
211 static int lcd(int n1, int n2)
216 for (i = 2; (i <= n1 && i <= n2); i++)
218 if (n1 % i == 0 && n2 % i == 0)
227 //! Convert legacy mdp entries to modern ones.
228 static void process_interaction_modifier(int* eintmod)
230 if (*eintmod == eintmodPOTSHIFT_VERLET_UNSUPPORTED)
232 *eintmod = eintmodPOTSHIFT;
236 static void checkMtsRequirement(const t_inputrec& ir, const char* param, const int nstValue, warninp_t wi)
238 GMX_RELEASE_ASSERT(ir.mtsLevels.size() >= 2, "Need at least two levels for MTS");
239 const int mtsFactor = ir.mtsLevels.back().stepFactor;
240 if (nstValue % mtsFactor != 0)
242 auto message = gmx::formatString(
243 "With MTS, %s = %d should be a multiple of mts-factor = %d", param, nstValue, mtsFactor);
244 warning_error(wi, message.c_str());
248 static void setupMtsLevels(gmx::ArrayRef<gmx::MtsLevel> mtsLevels,
249 const t_inputrec& ir,
250 const t_gromppopts& opts,
253 /* MD-VV has no MTS support yet.
254 * SD1 needs different scaling coefficients for the different MTS forces
255 * and the different forces are currently not available in ForceBuffers.
259 auto message = gmx::formatString(
260 "Multiple time stepping is only supported with integrator %s", ei_names[eiMD]);
261 warning_error(wi, message.c_str());
263 if (opts.numMtsLevels != 2)
265 warning_error(wi, "Only mts-levels = 2 is supported");
269 const std::vector<std::string> inputForceGroups = gmx::splitString(opts.mtsLevel2Forces);
270 auto& forceGroups = mtsLevels[1].forceGroups;
271 for (const auto& inputForceGroup : inputForceGroups)
275 for (const auto& forceGroupName : gmx::mtsForceGroupNames)
277 if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
279 forceGroups.set(nameIndex);
287 gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str());
288 warning_error(wi, message.c_str());
292 if (mtsLevels[1].stepFactor <= 1)
294 gmx_fatal(FARGS, "mts-factor should be larger than 1");
297 // Make the level 0 use the complement of the force groups of group 1
298 mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
299 mtsLevels[0].stepFactor = 1;
301 if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
302 && !mtsLevels[1].forceGroups[static_cast<int>(gmx::MtsForceGroups::LongrangeNonbonded)])
305 "With long-range electrostatics and/or LJ treatment, the long-range part "
306 "has to be part of the mts-level2-forces");
309 if (ir.nstcalcenergy > 0)
311 checkMtsRequirement(ir, "nstcalcenergy", ir.nstcalcenergy, wi);
313 checkMtsRequirement(ir, "nstenergy", ir.nstenergy, wi);
314 checkMtsRequirement(ir, "nstlog", ir.nstlog, wi);
315 if (ir.efep != efepNO)
317 checkMtsRequirement(ir, "nstdhdl", ir.fepvals->nstdhdl, wi);
322 const int pullMtsLevel = gmx::forceGroupMtsLevel(ir.mtsLevels, gmx::MtsForceGroups::Pull);
323 if (ir.pull->nstxout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
325 warning_error(wi, "pull-nstxout should be a multiple of mts-factor");
327 if (ir.pull->nstfout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
329 warning_error(wi, "pull-nstfout should be a multiple of mts-factor");
335 void check_ir(const char* mdparin,
336 const gmx::MdModulesNotifier& mdModulesNotifier,
340 /* Check internal consistency.
341 * NOTE: index groups are not set here yet, don't check things
342 * like temperature coupling group options here, but in triple_check
345 /* Strange macro: first one fills the err_buf, and then one can check
346 * the condition, which will print the message and increase the error
349 #define CHECK(b) _low_check(b, err_buf, wi)
350 char err_buf[256], warn_buf[STRLEN];
353 t_lambda* fep = ir->fepvals;
354 t_expanded* expand = ir->expandedvals;
356 set_warning_line(wi, mdparin, -1);
358 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
360 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
361 warning_error(wi, warn_buf);
364 /* BASIC CUT-OFF STUFF */
365 if (ir->rcoulomb < 0)
367 warning_error(wi, "rcoulomb should be >= 0");
371 warning_error(wi, "rvdw should be >= 0");
373 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
375 warning_error(wi, "rlist should be >= 0");
378 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
379 "neighbour-list update scheme for efficient buffering for improved energy "
380 "conservation, please use the Verlet cut-off scheme instead.)");
381 CHECK(ir->nstlist < 0);
383 process_interaction_modifier(&ir->coulomb_modifier);
384 process_interaction_modifier(&ir->vdw_modifier);
386 if (ir->cutoff_scheme == ecutsGROUP)
389 "The group cutoff scheme has been removed since GROMACS 2020. "
390 "Please use the Verlet cutoff scheme.");
392 if (ir->cutoff_scheme == ecutsVERLET)
396 /* Normal Verlet type neighbor-list, currently only limited feature support */
397 if (inputrec2nboundeddim(ir) < 3)
399 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
402 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
403 if (ir->rcoulomb != ir->rvdw)
405 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
406 // for PME load balancing, we can support this exception.
407 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
408 && ir->rcoulomb > ir->rvdw);
409 if (!bUsesPmeTwinRangeKernel)
412 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
413 "rcoulomb>rvdw with PME electrostatics)");
417 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
419 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
421 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
424 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
426 evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
427 warning_note(wi, warn_buf);
429 ir->vdwtype = evdwCUT;
433 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
434 evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
435 warning_error(wi, warn_buf);
439 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
442 "With Verlet lists only cut-off and PME LJ interactions are supported");
444 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
445 || ir->coulombtype == eelEWALD))
448 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
449 "electrostatics are supported");
451 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
453 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
454 warning_error(wi, warn_buf);
457 if (EEL_USER(ir->coulombtype))
459 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
460 eel_names[ir->coulombtype]);
461 warning_error(wi, warn_buf);
464 if (ir->nstlist <= 0)
466 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
469 if (ir->nstlist < 10)
472 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
473 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
477 rc_max = std::max(ir->rvdw, ir->rcoulomb);
481 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
482 ir->verletbuf_tol = 0;
485 else if (ir->verletbuf_tol <= 0)
487 if (ir->verletbuf_tol == 0)
489 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
492 if (ir->rlist < rc_max)
495 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
498 if (ir->rlist == rc_max && ir->nstlist > 1)
502 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
503 "buffer. The cluster pair list does have a buffering effect, but choosing "
504 "a larger rlist might be necessary for good energy conservation.");
509 if (ir->rlist > rc_max)
512 "You have set rlist larger than the interaction cut-off, but you also "
513 "have verlet-buffer-tolerance > 0. Will set rlist using "
514 "verlet-buffer-tolerance.");
517 if (ir->nstlist == 1)
519 /* No buffer required */
524 if (EI_DYNAMICS(ir->eI))
526 if (inputrec2nboundeddim(ir) < 3)
529 "The box volume is required for calculating rlist from the "
530 "energy drift with verlet-buffer-tolerance > 0. You are "
531 "using at least one unbounded dimension, so no volume can be "
532 "computed. Either use a finite box, or set rlist yourself "
533 "together with verlet-buffer-tolerance = -1.");
535 /* Set rlist temporarily so we can continue processing */
540 /* Set the buffer to 5% of the cut-off */
541 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
547 /* GENERAL INTEGRATOR STUFF */
550 if (ir->etc != etcNO)
552 if (EI_RANDOM(ir->eI))
555 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
556 "implicitly. See the documentation for more information on which "
557 "parameters affect temperature for %s.",
558 etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
563 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
565 etcoupl_names[ir->etc], ei_names[ir->eI]);
567 warning_note(wi, warn_buf);
571 if (ir->eI == eiVVAK)
574 "Integrator method %s is implemented primarily for validation purposes; for "
575 "molecular dynamics, you should probably be using %s or %s",
576 ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
577 warning_note(wi, warn_buf);
579 if (!EI_DYNAMICS(ir->eI))
581 if (ir->epc != epcNO)
584 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
585 epcoupl_names[ir->epc], ei_names[ir->eI]);
586 warning_note(wi, warn_buf);
590 if (EI_DYNAMICS(ir->eI))
592 if (ir->nstcalcenergy < 0)
594 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
595 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
597 /* nstcalcenergy larger than nstener does not make sense.
598 * We ideally want nstcalcenergy=nstener.
602 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
606 ir->nstcalcenergy = ir->nstenergy;
610 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
611 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
612 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
615 const char* nsten = "nstenergy";
616 const char* nstdh = "nstdhdl";
617 const char* min_name = nsten;
618 int min_nst = ir->nstenergy;
620 /* find the smallest of ( nstenergy, nstdhdl ) */
621 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
622 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
624 min_nst = ir->fepvals->nstdhdl;
627 /* If the user sets nstenergy small, we should respect that */
628 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
630 warning_note(wi, warn_buf);
631 ir->nstcalcenergy = min_nst;
634 if (ir->epc != epcNO)
636 if (ir->nstpcouple < 0)
638 ir->nstpcouple = ir_optimal_nstpcouple(ir);
640 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
643 "With multiple time stepping, nstpcouple should be a mutiple of "
648 if (ir->nstcalcenergy > 0)
650 if (ir->efep != efepNO)
652 /* nstdhdl should be a multiple of nstcalcenergy */
653 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
657 /* nstexpanded should be a multiple of nstcalcenergy */
658 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
659 &ir->expandedvals->nstexpanded, wi);
661 /* for storing exact averages nstenergy should be
662 * a multiple of nstcalcenergy
664 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
667 // Inquire all MdModules, if their parameters match with the energy
668 // calculation frequency
669 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
670 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
672 // Emit all errors from the energy calculation frequency checks
673 for (const std::string& energyFrequencyErrorMessage :
674 energyCalculationFrequencyErrors.errorMessages())
676 warning_error(wi, energyFrequencyErrorMessage);
680 if (ir->nsteps == 0 && !ir->bContinuation)
683 "For a correct single-point energy evaluation with nsteps = 0, use "
684 "continuation = yes to avoid constraining the input coordinates.");
688 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
691 "You are doing a continuation with SD or BD, make sure that ld_seed is "
692 "different from the previous run (using ld_seed=-1 will ensure this)");
698 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
699 CHECK(ir->pbcType != PbcType::Xyz);
700 sprintf(err_buf, "with TPI nstlist should be larger than zero");
701 CHECK(ir->nstlist <= 0);
702 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
703 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
707 if ((opts->nshake > 0) && (opts->bMorse))
709 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
710 warning(wi, warn_buf);
713 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
716 "You are doing a continuation with SD or BD, make sure that ld_seed is "
717 "different from the previous run (using ld_seed=-1 will ensure this)");
719 /* verify simulated tempering options */
723 bool bAllTempZero = TRUE;
724 for (i = 0; i < fep->n_lambda; i++)
726 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
727 efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
728 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
729 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
731 bAllTempZero = FALSE;
734 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
735 CHECK(bAllTempZero == TRUE);
737 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
738 CHECK(ir->eI != eiVV);
740 /* check compatability of the temperature coupling with simulated tempering */
742 if (ir->etc == etcNOSEHOOVER)
745 "Nose-Hoover based temperature control such as [%s] my not be "
746 "entirelyconsistent with simulated tempering",
747 etcoupl_names[ir->etc]);
748 warning_note(wi, warn_buf);
751 /* check that the temperatures make sense */
754 "Higher simulated tempering temperature (%g) must be >= than the simulated "
755 "tempering lower temperature (%g)",
756 ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
757 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
759 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
760 ir->simtempvals->simtemp_high);
761 CHECK(ir->simtempvals->simtemp_high <= 0);
763 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
764 ir->simtempvals->simtemp_low);
765 CHECK(ir->simtempvals->simtemp_low <= 0);
768 /* verify free energy options */
770 if (ir->efep != efepNO)
773 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
774 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
777 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
779 static_cast<int>(fep->sc_r_power));
780 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
783 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
786 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
788 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
790 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
792 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
793 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
795 sprintf(err_buf, "Free-energy not implemented for Ewald");
796 CHECK(ir->coulombtype == eelEWALD);
798 /* check validty of lambda inputs */
799 if (fep->n_lambda == 0)
801 /* Clear output in case of no states:*/
802 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
803 fep->init_fep_state);
804 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
808 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
809 fep->init_fep_state, fep->n_lambda - 1);
810 CHECK((fep->init_fep_state >= fep->n_lambda));
814 "Lambda state must be set, either with init-lambda-state or with init-lambda");
815 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
818 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
819 "init-lambda-state or with init-lambda, but not both",
820 fep->init_lambda, fep->init_fep_state);
821 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
824 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
828 for (i = 0; i < efptNR; i++)
830 if (fep->separate_dvdl[i])
835 if (n_lambda_terms > 1)
838 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
839 "use init-lambda to set lambda state (except for slow growth). Use "
840 "init-lambda-state instead.");
841 warning(wi, warn_buf);
844 if (n_lambda_terms < 2 && fep->n_lambda > 0)
847 "init-lambda is deprecated for setting lambda state (except for slow "
848 "growth). Use init-lambda-state instead.");
852 for (j = 0; j < efptNR; j++)
854 for (i = 0; i < fep->n_lambda; i++)
856 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
857 efpt_names[j], fep->all_lambda[j][i]);
858 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
862 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
864 for (i = 0; i < fep->n_lambda; i++)
867 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
868 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
869 "crashes, and is not supported.",
870 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
871 CHECK((fep->sc_alpha > 0)
872 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
873 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
877 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
879 real sigma, lambda, r_sc;
882 /* Maximum estimate for A and B charges equal with lambda power 1 */
884 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
885 1.0 / fep->sc_r_power);
887 "With PME there is a minor soft core effect present at the cut-off, "
888 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
889 "energy conservation, but usually other effects dominate. With a common sigma "
890 "value of %g nm the fraction of the particle-particle potential at the cut-off "
891 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
892 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
893 warning_note(wi, warn_buf);
896 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
897 be treated differently, but that's the next step */
899 for (i = 0; i < efptNR; i++)
901 for (j = 0; j < fep->n_lambda; j++)
903 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
904 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
909 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
913 /* checking equilibration of weights inputs for validity */
916 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
918 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
919 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
922 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
924 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
925 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
928 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
929 expand->equil_steps, elmceq_names[elmceqSTEPS]);
930 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
933 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
934 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
935 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
938 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
939 expand->equil_ratio, elmceq_names[elmceqRATIO]);
940 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
943 "weight-equil-number-all-lambda (%d) must be a positive integer if "
944 "lmc-weights-equil=%s",
945 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
946 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
949 "weight-equil-number-samples (%d) must be a positive integer if "
950 "lmc-weights-equil=%s",
951 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
952 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
955 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
956 expand->equil_steps, elmceq_names[elmceqSTEPS]);
957 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
959 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
960 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
961 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
963 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
964 expand->equil_ratio, elmceq_names[elmceqRATIO]);
965 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
967 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
968 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
969 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
971 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
972 CHECK((expand->lmc_repeats <= 0));
973 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
974 CHECK((expand->minvarmin <= 0));
975 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
976 CHECK((expand->c_range < 0));
978 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
980 fep->init_fep_state, expand->lmc_forced_nstart);
981 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
982 && (expand->elmcmove != elmcmoveNO));
983 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
984 CHECK((expand->lmc_forced_nstart < 0));
985 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
986 fep->init_fep_state);
987 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
989 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
990 CHECK((expand->init_wl_delta < 0));
991 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
992 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
993 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
994 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
996 /* if there is no temperature control, we need to specify an MC temperature */
997 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
998 && (expand->mc_temp <= 0.0))
1001 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
1002 "to a positive number");
1003 warning_error(wi, err_buf);
1005 if (expand->nstTij > 0)
1007 sprintf(err_buf, "nstlog must be non-zero");
1008 CHECK(ir->nstlog == 0);
1009 // Avoid modulus by zero in the case that already triggered an error exit.
1010 if (ir->nstlog != 0)
1013 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
1014 expand->nstTij, ir->nstlog);
1015 CHECK((expand->nstTij % ir->nstlog) != 0);
1021 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
1022 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
1025 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
1027 if (ir->pbcType == PbcType::No)
1029 if (ir->epc != epcNO)
1031 warning(wi, "Turning off pressure coupling for vacuum system");
1037 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
1038 c_pbcTypeNames[ir->pbcType].c_str());
1039 CHECK(ir->epc != epcNO);
1041 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1042 CHECK(EEL_FULL(ir->coulombtype));
1044 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
1045 c_pbcTypeNames[ir->pbcType].c_str());
1046 CHECK(ir->eDispCorr != edispcNO);
1049 if (ir->rlist == 0.0)
1052 "can only have neighborlist cut-off zero (=infinite)\n"
1053 "with coulombtype = %s or coulombtype = %s\n"
1054 "without periodic boundary conditions (pbc = %s) and\n"
1055 "rcoulomb and rvdw set to zero",
1056 eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
1057 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
1058 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1060 if (ir->nstlist > 0)
1063 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1064 "nstype=simple and only one MPI rank");
1069 if (ir->nstcomm == 0)
1071 // TODO Change this behaviour. There should be exactly one way
1072 // to turn off an algorithm.
1073 ir->comm_mode = ecmNO;
1075 if (ir->comm_mode != ecmNO)
1077 if (ir->nstcomm < 0)
1079 // TODO Such input was once valid. Now that we've been
1080 // helpful for a few years, we should reject such input,
1081 // lest we have to support every historical decision
1084 "If you want to remove the rotation around the center of mass, you should set "
1085 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1086 "its absolute value");
1087 ir->nstcomm = abs(ir->nstcomm);
1090 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1093 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1094 "nstcomm to nstcalcenergy");
1095 ir->nstcomm = ir->nstcalcenergy;
1098 if (ir->comm_mode == ecmANGULAR)
1101 "Can not remove the rotation around the center of mass with periodic "
1103 CHECK(ir->bPeriodicMols);
1104 if (ir->pbcType != PbcType::No)
1107 "Removing the rotation around the center of mass in a periodic system, "
1108 "this can lead to artifacts. Only use this on a single (cluster of) "
1109 "molecules. This cluster should not cross periodic boundaries.");
1114 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
1117 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1118 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1121 warning_note(wi, warn_buf);
1124 /* TEMPERATURE COUPLING */
1125 if (ir->etc == etcYES)
1127 ir->etc = etcBERENDSEN;
1129 "Old option for temperature coupling given: "
1130 "changing \"yes\" to \"Berendsen\"\n");
1133 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1135 if (ir->opts.nhchainlength < 1)
1138 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1140 ir->opts.nhchainlength);
1141 ir->opts.nhchainlength = 1;
1142 warning(wi, warn_buf);
1145 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1149 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1150 ir->opts.nhchainlength = 1;
1155 ir->opts.nhchainlength = 0;
1158 if (ir->eI == eiVVAK)
1161 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1164 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1167 if (ETC_ANDERSEN(ir->etc))
1169 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1170 etcoupl_names[ir->etc], ei_names[ir->eI]);
1171 CHECK(!(EI_VV(ir->eI)));
1173 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1176 "Center of mass removal not necessary for %s. All velocities of coupled "
1177 "groups are rerandomized periodically, so flying ice cube errors will not "
1179 etcoupl_names[ir->etc]);
1180 warning_note(wi, warn_buf);
1184 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1185 "randomized every time step",
1186 ir->nstcomm, etcoupl_names[ir->etc]);
1187 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1190 if (ir->etc == etcBERENDSEN)
1193 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1194 "might want to consider using the %s thermostat.",
1195 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1196 warning_note(wi, warn_buf);
1199 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1202 "Using Berendsen pressure coupling invalidates the "
1203 "true ensemble for the thermostat");
1204 warning(wi, warn_buf);
1207 /* PRESSURE COUPLING */
1208 if (ir->epc == epcISOTROPIC)
1210 ir->epc = epcBERENDSEN;
1212 "Old option for pressure coupling given: "
1213 "changing \"Isotropic\" to \"Berendsen\"\n");
1216 if (ir->epc != epcNO)
1218 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1220 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1221 CHECK(ir->tau_p <= 0);
1223 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1226 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1227 "times larger than nstpcouple*dt (%g)",
1228 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1229 warning(wi, warn_buf);
1233 "compressibility must be > 0 when using pressure"
1235 EPCOUPLTYPE(ir->epc));
1236 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1237 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1238 && ir->compress[ZZ][YY] <= 0));
1240 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1243 "You are generating velocities so I am assuming you "
1244 "are equilibrating a system. You are using "
1245 "%s pressure coupling, but this can be "
1246 "unstable for equilibration. If your system crashes, try "
1247 "equilibrating first with Berendsen pressure coupling. If "
1248 "you are not equilibrating the system, you can probably "
1249 "ignore this warning.",
1250 epcoupl_names[ir->epc]);
1251 warning(wi, warn_buf);
1257 if (ir->epc == epcMTTK)
1259 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1263 /* ELECTROSTATICS */
1264 /* More checks are in triple check (grompp.c) */
1266 if (ir->coulombtype == eelSWITCH)
1269 "coulombtype = %s is only for testing purposes and can lead to serious "
1270 "artifacts, advice: use coulombtype = %s",
1271 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1272 warning(wi, warn_buf);
1275 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1278 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1279 "format and exchanging epsilon-r and epsilon-rf",
1281 warning(wi, warn_buf);
1282 ir->epsilon_rf = ir->epsilon_r;
1283 ir->epsilon_r = 1.0;
1286 if (ir->epsilon_r == 0)
1289 "It is pointless to use long-range electrostatics with infinite relative "
1291 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1293 CHECK(EEL_FULL(ir->coulombtype));
1296 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1298 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1299 CHECK(ir->epsilon_r < 0);
1302 if (EEL_RF(ir->coulombtype))
1304 /* reaction field (at the cut-off) */
1306 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1309 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1310 eel_names[ir->coulombtype]);
1311 warning(wi, warn_buf);
1312 ir->epsilon_rf = 0.0;
1315 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1316 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1317 if (ir->epsilon_rf == ir->epsilon_r)
1319 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1320 eel_names[ir->coulombtype]);
1321 warning(wi, warn_buf);
1324 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1325 * means the interaction is zero outside rcoulomb, but it helps to
1326 * provide accurate energy conservation.
1328 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1330 if (ir_coulomb_switched(ir))
1333 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1334 "potential modifier options!",
1335 eel_names[ir->coulombtype]);
1336 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1340 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1343 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1344 "secondary coulomb-modifier.");
1345 CHECK(ir->coulomb_modifier != eintmodNONE);
1347 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1350 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1351 "secondary vdw-modifier.");
1352 CHECK(ir->vdw_modifier != eintmodNONE);
1355 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1356 || ir->vdwtype == evdwSHIFT)
1359 "The switch/shift interaction settings are just for compatibility; you will get "
1361 "performance from applying potential modifiers to your interactions!\n");
1362 warning_note(wi, warn_buf);
1365 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1367 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1369 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1371 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1372 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1373 "will be good regardless, since ewald_rtol = %g.",
1374 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1375 warning(wi, warn_buf);
1379 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1381 if (ir->rvdw_switch == 0)
1384 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1385 "potential. This suggests it was not set in the mdp, which can lead to large "
1386 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1387 "switching range.");
1388 warning(wi, warn_buf);
1392 if (EEL_FULL(ir->coulombtype))
1394 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1395 || ir->coulombtype == eelPMEUSERSWITCH)
1397 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1398 eel_names[ir->coulombtype]);
1399 CHECK(ir->rcoulomb > ir->rlist);
1403 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1405 // TODO: Move these checks into the ewald module with the options class
1407 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1409 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1411 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1412 eel_names[ir->coulombtype], orderMin, orderMax);
1413 warning_error(wi, warn_buf);
1417 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1419 if (ir->ewald_geometry == eewg3D)
1421 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1422 c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
1423 warning(wi, warn_buf);
1425 /* This check avoids extra pbc coding for exclusion corrections */
1426 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1427 CHECK(ir->wall_ewald_zfac < 2);
1429 if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
1431 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1432 eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
1433 warning(wi, warn_buf);
1435 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1437 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1438 CHECK(ir->bPeriodicMols);
1439 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1440 warning_note(wi, warn_buf);
1442 "With epsilon_surface > 0 you can only use domain decomposition "
1443 "when there are only small molecules with all bonds constrained (mdrun will check "
1445 warning_note(wi, warn_buf);
1448 if (ir_vdw_switched(ir))
1450 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1451 CHECK(ir->rvdw_switch >= ir->rvdw);
1453 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1456 "You are applying a switch function to vdw forces or potentials from %g to %g "
1457 "nm, which is more than half the interaction range, whereas switch functions "
1458 "are intended to act only close to the cut-off.",
1459 ir->rvdw_switch, ir->rvdw);
1460 warning_note(wi, warn_buf);
1464 if (ir->vdwtype == evdwPME)
1466 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1468 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1469 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1470 warning_error(wi, err_buf);
1474 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1477 "You have selected user tables with dispersion correction, the dispersion "
1478 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1479 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1480 "really want dispersion correction to -C6/r^6.");
1483 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1485 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1488 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1490 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1493 /* IMPLICIT SOLVENT */
1494 if (ir->coulombtype == eelGB_NOTUSED)
1496 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1497 warning_error(wi, warn_buf);
1502 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1507 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1511 /* interpret a number of doubles from a string and put them in an array,
1512 after allocating space for them.
1513 str = the input string
1514 n = the (pre-allocated) number of doubles read
1515 r = the output array of doubles. */
1516 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1518 auto values = gmx::splitString(str);
1522 for (int i = 0; i < *n; i++)
1526 (*r)[i] = gmx::fromString<real>(values[i]);
1528 catch (gmx::GromacsException&)
1530 warning_error(wi, "Invalid value " + values[i]
1531 + " in string in mdp file. Expected a real number.");
1537 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1540 int i, j, max_n_lambda, nweights, nfep[efptNR];
1541 t_lambda* fep = ir->fepvals;
1542 t_expanded* expand = ir->expandedvals;
1543 real** count_fep_lambdas;
1544 bool bOneLambda = TRUE;
1546 snew(count_fep_lambdas, efptNR);
1548 /* FEP input processing */
1549 /* first, identify the number of lambda values for each type.
1550 All that are nonzero must have the same number */
1552 for (i = 0; i < efptNR; i++)
1554 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1557 /* now, determine the number of components. All must be either zero, or equal. */
1560 for (i = 0; i < efptNR; i++)
1562 if (nfep[i] > max_n_lambda)
1564 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1565 must have the same number if its not zero.*/
1570 for (i = 0; i < efptNR; i++)
1574 ir->fepvals->separate_dvdl[i] = FALSE;
1576 else if (nfep[i] == max_n_lambda)
1578 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1579 the derivative with respect to the temperature currently */
1581 ir->fepvals->separate_dvdl[i] = TRUE;
1587 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1589 nfep[i], efpt_names[i], max_n_lambda);
1592 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1593 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1595 /* the number of lambdas is the number we've read in, which is either zero
1596 or the same for all */
1597 fep->n_lambda = max_n_lambda;
1599 /* allocate space for the array of lambda values */
1600 snew(fep->all_lambda, efptNR);
1601 /* if init_lambda is defined, we need to set lambda */
1602 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1604 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1606 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1607 for (i = 0; i < efptNR; i++)
1609 snew(fep->all_lambda[i], fep->n_lambda);
1610 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1613 for (j = 0; j < fep->n_lambda; j++)
1615 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1617 sfree(count_fep_lambdas[i]);
1620 sfree(count_fep_lambdas);
1622 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1623 internal bookkeeping -- for now, init_lambda */
1625 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1627 for (i = 0; i < fep->n_lambda; i++)
1629 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1633 /* check to see if only a single component lambda is defined, and soft core is defined.
1634 In this case, turn on coulomb soft core */
1636 if (max_n_lambda == 0)
1642 for (i = 0; i < efptNR; i++)
1644 if ((nfep[i] != 0) && (i != efptFEP))
1650 if ((bOneLambda) && (fep->sc_alpha > 0))
1652 fep->bScCoul = TRUE;
1655 /* Fill in the others with the efptFEP if they are not explicitly
1656 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1657 they are all zero. */
1659 for (i = 0; i < efptNR; i++)
1661 if ((nfep[i] == 0) && (i != efptFEP))
1663 for (j = 0; j < fep->n_lambda; j++)
1665 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1671 /* now read in the weights */
1672 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1675 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1677 else if (nweights != fep->n_lambda)
1679 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1680 nweights, fep->n_lambda);
1682 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1684 expand->nstexpanded = fep->nstdhdl;
1685 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1690 static void do_simtemp_params(t_inputrec* ir)
1693 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1694 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1697 template<typename T>
1698 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1701 for (const auto& input : inputs)
1705 outputs[i] = gmx::fromStdString<T>(input);
1707 catch (gmx::GromacsException&)
1709 auto message = gmx::formatString(
1710 "Invalid value for mdp option %s. %s should only consist of integers separated "
1713 warning_error(wi, message);
1719 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1722 for (const auto& input : inputs)
1726 outputs[i] = gmx::fromString<real>(input);
1728 catch (gmx::GromacsException&)
1730 auto message = gmx::formatString(
1731 "Invalid value for mdp option %s. %s should only consist of real numbers "
1732 "separated by spaces.",
1734 warning_error(wi, message);
1740 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1743 for (const auto& input : inputs)
1747 outputs[i][d] = gmx::fromString<real>(input);
1749 catch (gmx::GromacsException&)
1751 auto message = gmx::formatString(
1752 "Invalid value for mdp option %s. %s should only consist of real numbers "
1753 "separated by spaces.",
1755 warning_error(wi, message);
1766 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1768 opts->wall_atomtype[0] = nullptr;
1769 opts->wall_atomtype[1] = nullptr;
1771 ir->wall_atomtype[0] = -1;
1772 ir->wall_atomtype[1] = -1;
1773 ir->wall_density[0] = 0;
1774 ir->wall_density[1] = 0;
1778 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1779 if (wallAtomTypes.size() != size_t(ir->nwall))
1781 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1782 wallAtomTypes.size());
1784 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1785 for (int i = 0; i < ir->nwall; i++)
1787 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1790 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1792 auto wallDensity = gmx::splitString(wall_density);
1793 if (wallDensity.size() != size_t(ir->nwall))
1795 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1796 wallDensity.size());
1798 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1799 for (int i = 0; i < ir->nwall; i++)
1801 if (ir->wall_density[i] <= 0)
1803 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1810 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1814 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1815 for (int i = 0; i < nwall; i++)
1817 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1818 grps->emplace_back(groups->groupNames.size() - 1);
1823 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1825 /* read expanded ensemble parameters */
1826 printStringNewline(inp, "expanded ensemble variables");
1827 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1828 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1829 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1830 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1831 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1832 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1833 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1834 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1835 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1836 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1837 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1838 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1839 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1840 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1841 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1842 expand->bSymmetrizedTMatrix =
1843 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1844 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1845 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1846 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1847 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1848 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1849 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1850 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1853 /*! \brief Return whether an end state with the given coupling-lambda
1854 * value describes fully-interacting VDW.
1856 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1857 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1859 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1861 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1867 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1870 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1872 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1874 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1877 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1878 std::string message = gmx::formatExceptionMessageToString(*ex);
1879 warning_error(wi_, message.c_str());
1884 std::string getOptionName(const gmx::KeyValueTreePath& context)
1886 if (mapping_ != nullptr)
1888 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1889 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1892 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1897 const gmx::IKeyValueTreeBackMapping* mapping_;
1902 void get_ir(const char* mdparin,
1903 const char* mdparout,
1904 gmx::MDModules* mdModules,
1907 WriteMdpHeader writeMdpHeader,
1911 double dumdub[2][6];
1913 char warn_buf[STRLEN];
1914 t_lambda* fep = ir->fepvals;
1915 t_expanded* expand = ir->expandedvals;
1917 const char* no_names[] = { "no", nullptr };
1919 init_inputrec_strings();
1920 gmx::TextInputFile stream(mdparin);
1921 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1923 snew(dumstr[0], STRLEN);
1924 snew(dumstr[1], STRLEN);
1926 /* ignore the following deprecated commands */
1927 replace_inp_entry(inp, "title", nullptr);
1928 replace_inp_entry(inp, "cpp", nullptr);
1929 replace_inp_entry(inp, "domain-decomposition", nullptr);
1930 replace_inp_entry(inp, "andersen-seed", nullptr);
1931 replace_inp_entry(inp, "dihre", nullptr);
1932 replace_inp_entry(inp, "dihre-fc", nullptr);
1933 replace_inp_entry(inp, "dihre-tau", nullptr);
1934 replace_inp_entry(inp, "nstdihreout", nullptr);
1935 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1936 replace_inp_entry(inp, "optimize-fft", nullptr);
1937 replace_inp_entry(inp, "adress_type", nullptr);
1938 replace_inp_entry(inp, "adress_const_wf", nullptr);
1939 replace_inp_entry(inp, "adress_ex_width", nullptr);
1940 replace_inp_entry(inp, "adress_hy_width", nullptr);
1941 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1942 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1943 replace_inp_entry(inp, "adress_site", nullptr);
1944 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1945 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1946 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1947 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1948 replace_inp_entry(inp, "rlistlong", nullptr);
1949 replace_inp_entry(inp, "nstcalclr", nullptr);
1950 replace_inp_entry(inp, "pull-print-com2", nullptr);
1951 replace_inp_entry(inp, "gb-algorithm", nullptr);
1952 replace_inp_entry(inp, "nstgbradii", nullptr);
1953 replace_inp_entry(inp, "rgbradii", nullptr);
1954 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1955 replace_inp_entry(inp, "gb-saltconc", nullptr);
1956 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1957 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1958 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1959 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1960 replace_inp_entry(inp, "sa-algorithm", nullptr);
1961 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1962 replace_inp_entry(inp, "ns-type", nullptr);
1964 /* replace the following commands with the clearer new versions*/
1965 replace_inp_entry(inp, "unconstrained-start", "continuation");
1966 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1967 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1968 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1969 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1970 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1971 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1973 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1974 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1975 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1976 setStringEntry(&inp, "include", opts->include, nullptr);
1977 printStringNoNewline(
1978 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1979 setStringEntry(&inp, "define", opts->define, nullptr);
1981 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1982 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1983 printStringNoNewline(&inp, "Start time and timestep in ps");
1984 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1985 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1986 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1987 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1988 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1989 printStringNoNewline(
1990 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1991 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1992 printStringNoNewline(&inp, "Multiple time-stepping");
1993 ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
1996 opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
1997 ir->mtsLevels.resize(2);
1998 gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
1999 opts->mtsLevel2Forces = setStringEntry(&inp, "mts-level2-forces",
2000 "longrange-nonbonded nonbonded pair dihedral");
2001 mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
2003 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2004 if (!EI_DYNAMICS(ir->eI))
2007 ir->mtsLevels.clear();
2010 printStringNoNewline(&inp, "mode for center of mass motion removal");
2011 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
2012 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2013 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2014 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2015 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2017 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2018 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2019 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2020 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2023 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2024 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2025 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2026 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2027 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2028 ir->niter = get_eint(&inp, "niter", 20, wi);
2029 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2030 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2031 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2032 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2033 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2035 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2036 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2038 /* Output options */
2039 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2040 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2041 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2042 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2043 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2044 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2045 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2046 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2047 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2048 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2049 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2050 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2051 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2052 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2053 printStringNoNewline(&inp, "default, all atoms will be written.");
2054 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2055 printStringNoNewline(&inp, "Selection of energy groups");
2056 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2058 /* Neighbor searching */
2059 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2060 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2061 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
2062 printStringNoNewline(&inp, "nblist update frequency");
2063 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2064 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2065 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2066 std::vector<const char*> pbcTypesNamesChar;
2067 for (const auto& pbcTypeName : c_pbcTypeNames)
2069 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2071 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2072 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
2073 printStringNoNewline(&inp,
2074 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2075 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2076 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2077 printStringNoNewline(&inp, "nblist cut-off");
2078 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2079 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2081 /* Electrostatics */
2082 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2083 printStringNoNewline(&inp, "Method for doing electrostatics");
2084 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
2085 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
2086 printStringNoNewline(&inp, "cut-off lengths");
2087 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2088 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2089 printStringNoNewline(&inp,
2090 "Relative dielectric constant for the medium and the reaction field");
2091 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2092 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2093 printStringNoNewline(&inp, "Method for doing Van der Waals");
2094 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
2095 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
2096 printStringNoNewline(&inp, "cut-off lengths");
2097 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2098 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2099 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2100 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
2101 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2102 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2103 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2104 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2105 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2106 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2107 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2108 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2109 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2110 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2111 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2112 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2113 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2114 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2115 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2116 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2117 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2119 /* Implicit solvation is no longer supported, but we need grompp
2120 to be able to refuse old .mdp files that would have built a tpr
2121 to run it. Thus, only "no" is accepted. */
2122 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2124 /* Coupling stuff */
2125 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2126 printStringNoNewline(&inp, "Temperature coupling");
2127 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2128 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2129 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2130 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2131 printStringNoNewline(&inp, "Groups to couple separately");
2132 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2133 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2134 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2135 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2136 printStringNoNewline(&inp, "pressure coupling");
2137 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2138 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2139 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2140 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2141 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2142 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2143 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2144 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2145 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2148 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2149 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2150 printStringNoNewline(&inp, "Groups treated with MiMiC");
2151 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2153 /* Simulated annealing */
2154 printStringNewline(&inp, "SIMULATED ANNEALING");
2155 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2156 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2157 printStringNoNewline(&inp,
2158 "Number of time points to use for specifying annealing in each group");
2159 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2160 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2161 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2162 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2163 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2166 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2167 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2168 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2169 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2172 printStringNewline(&inp, "OPTIONS FOR BONDS");
2173 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2174 printStringNoNewline(&inp, "Type of constraint algorithm");
2175 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2176 printStringNoNewline(&inp, "Do not constrain the start configuration");
2177 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2178 printStringNoNewline(&inp,
2179 "Use successive overrelaxation to reduce the number of shake iterations");
2180 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2181 printStringNoNewline(&inp, "Relative tolerance of shake");
2182 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2183 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2184 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2185 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2186 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2187 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2188 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2189 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2190 printStringNoNewline(&inp, "rotates over more degrees than");
2191 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2192 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2193 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2195 /* Energy group exclusions */
2196 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2197 printStringNoNewline(
2198 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2199 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2202 printStringNewline(&inp, "WALLS");
2203 printStringNoNewline(
2204 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2205 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2206 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2207 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2208 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2209 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2210 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2213 printStringNewline(&inp, "COM PULLING");
2214 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2217 ir->pull = std::make_unique<pull_params_t>();
2218 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2222 for (int c = 0; c < ir->pull->ncoord; c++)
2224 if (ir->pull->coord[c].eType == epullCONSTRAINT)
2227 "Constraint COM pulling is not supported in combination with "
2228 "multiple time stepping");
2236 NOTE: needs COM pulling or free energy input */
2237 printStringNewline(&inp, "AWH biasing");
2238 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2241 ir->awhParams = gmx::readAwhParams(&inp, wi);
2244 /* Enforced rotation */
2245 printStringNewline(&inp, "ENFORCED ROTATION");
2246 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2247 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2251 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2254 /* Interactive MD */
2256 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2257 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2258 if (inputrecStrings->imd_grp[0] != '\0')
2265 printStringNewline(&inp, "NMR refinement stuff");
2266 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2267 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2268 printStringNoNewline(
2269 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2270 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2271 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2272 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2273 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2274 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2275 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2276 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2277 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2278 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2279 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2280 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2281 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2282 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2283 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2284 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2286 /* free energy variables */
2287 printStringNewline(&inp, "Free energy variables");
2288 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2289 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2290 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2291 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2292 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2294 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2296 it was not entered */
2297 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2298 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2299 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2300 setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
2301 setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
2302 setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
2303 setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
2304 setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
2305 setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
2306 setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
2307 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2308 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2309 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2310 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2311 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2312 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2313 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2314 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2315 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2316 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2317 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2318 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2319 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2320 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2322 /* Non-equilibrium MD stuff */
2323 printStringNewline(&inp, "Non-equilibrium MD stuff");
2324 setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
2325 setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
2326 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2327 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2328 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2329 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2331 /* simulated tempering variables */
2332 printStringNewline(&inp, "simulated tempering variables");
2333 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2334 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2335 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2336 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2338 /* expanded ensemble variables */
2339 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2341 read_expandedparams(&inp, expand, wi);
2344 /* Electric fields */
2346 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2347 gmx::KeyValueTreeTransformer transform;
2348 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2349 mdModules->initMdpTransform(transform.rules());
2350 for (const auto& path : transform.mappedPaths())
2352 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2353 mark_einp_set(inp, path[0].c_str());
2355 MdpErrorHandler errorHandler(wi);
2356 auto result = transform.transform(convertedValues, &errorHandler);
2357 ir->params = new gmx::KeyValueTreeObject(result.object());
2358 mdModules->adjustInputrecBasedOnModules(ir);
2359 errorHandler.setBackMapping(result.backMapping());
2360 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2363 /* Ion/water position swapping ("computational electrophysiology") */
2364 printStringNewline(&inp,
2365 "Ion/water position swapping for computational electrophysiology setups");
2366 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2367 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2368 if (ir->eSwapCoords != eswapNO)
2375 printStringNoNewline(&inp, "Swap attempt frequency");
2376 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2377 printStringNoNewline(&inp, "Number of ion types to be controlled");
2378 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2381 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2383 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2384 snew(ir->swap->grp, ir->swap->ngrp);
2385 for (i = 0; i < ir->swap->ngrp; i++)
2387 snew(ir->swap->grp[i].molname, STRLEN);
2389 printStringNoNewline(&inp,
2390 "Two index groups that contain the compartment-partitioning atoms");
2391 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2392 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2393 printStringNoNewline(&inp,
2394 "Use center of mass of split groups (yes/no), otherwise center of "
2395 "geometry is used");
2396 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2397 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2399 printStringNoNewline(&inp, "Name of solvent molecules");
2400 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2402 printStringNoNewline(&inp,
2403 "Split cylinder: radius, upper and lower extension (nm) (this will "
2404 "define the channels)");
2405 printStringNoNewline(&inp,
2406 "Note that the split cylinder settings do not have an influence on "
2407 "the swapping protocol,");
2408 printStringNoNewline(
2410 "however, if correctly defined, the permeation events are recorded per channel");
2411 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2412 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2413 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2414 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2415 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2416 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2418 printStringNoNewline(
2420 "Average the number of ions per compartment over these many swap attempt steps");
2421 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2423 printStringNoNewline(
2424 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2425 printStringNoNewline(
2426 &inp, "and the requested number of ions of this type in compartments A and B");
2427 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2428 for (i = 0; i < nIonTypes; i++)
2430 int ig = eSwapFixedGrpNR + i;
2432 sprintf(buf, "iontype%d-name", i);
2433 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2434 sprintf(buf, "iontype%d-in-A", i);
2435 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2436 sprintf(buf, "iontype%d-in-B", i);
2437 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2440 printStringNoNewline(
2442 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2443 printStringNoNewline(
2445 "at maximum distance (= bulk concentration) to the split group layers. However,");
2446 printStringNoNewline(&inp,
2447 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2448 "layer from the middle at 0.0");
2449 printStringNoNewline(&inp,
2450 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2451 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2452 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2453 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2454 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2456 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2459 printStringNoNewline(
2460 &inp, "Start to swap ions if threshold difference to requested count is reached");
2461 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2464 /* AdResS is no longer supported, but we need grompp to be able to
2465 refuse to process old .mdp files that used it. */
2466 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2468 /* User defined thingies */
2469 printStringNewline(&inp, "User defined thingies");
2470 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2471 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2472 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2473 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2474 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2475 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2476 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2477 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2478 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2479 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2483 gmx::TextOutputFile stream(mdparout);
2484 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2486 // Transform module data into a flat key-value tree for output.
2487 gmx::KeyValueTreeBuilder builder;
2488 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2489 mdModules->buildMdpOutput(&builderObject);
2491 gmx::TextWriter writer(&stream);
2492 writeKeyValueTreeAsMdp(&writer, builder.build());
2497 /* Process options if necessary */
2498 for (m = 0; m < 2; m++)
2500 for (i = 0; i < 2 * DIM; i++)
2509 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2513 "Pressure coupling incorrect number of values (I need exactly 1)");
2515 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2517 case epctSEMIISOTROPIC:
2518 case epctSURFACETENSION:
2519 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2523 "Pressure coupling incorrect number of values (I need exactly 2)");
2525 dumdub[m][YY] = dumdub[m][XX];
2527 case epctANISOTROPIC:
2528 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2529 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2534 "Pressure coupling incorrect number of values (I need exactly 6)");
2538 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2539 epcoupltype_names[ir->epct]);
2543 clear_mat(ir->ref_p);
2544 clear_mat(ir->compress);
2545 for (i = 0; i < DIM; i++)
2547 ir->ref_p[i][i] = dumdub[1][i];
2548 ir->compress[i][i] = dumdub[0][i];
2550 if (ir->epct == epctANISOTROPIC)
2552 ir->ref_p[XX][YY] = dumdub[1][3];
2553 ir->ref_p[XX][ZZ] = dumdub[1][4];
2554 ir->ref_p[YY][ZZ] = dumdub[1][5];
2555 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2558 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2559 "apply a threefold shear stress?\n");
2561 ir->compress[XX][YY] = dumdub[0][3];
2562 ir->compress[XX][ZZ] = dumdub[0][4];
2563 ir->compress[YY][ZZ] = dumdub[0][5];
2564 for (i = 0; i < DIM; i++)
2566 for (m = 0; m < i; m++)
2568 ir->ref_p[i][m] = ir->ref_p[m][i];
2569 ir->compress[i][m] = ir->compress[m][i];
2574 if (ir->comm_mode == ecmNO)
2579 opts->couple_moltype = nullptr;
2580 if (strlen(inputrecStrings->couple_moltype) > 0)
2582 if (ir->efep != efepNO)
2584 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2585 if (opts->couple_lam0 == opts->couple_lam1)
2587 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2589 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2593 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2600 "Free energy is turned off, so we will not decouple the molecule listed "
2604 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2605 if (ir->efep != efepNO)
2607 if (fep->delta_lambda != 0)
2609 ir->efep = efepSLOWGROWTH;
2613 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2615 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2617 "Old option for dhdl-print-energy given: "
2618 "changing \"yes\" to \"total\"\n");
2621 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2623 /* always print out the energy to dhdl if we are doing
2624 expanded ensemble, since we need the total energy for
2625 analysis if the temperature is changing. In some
2626 conditions one may only want the potential energy, so
2627 we will allow that if the appropriate mdp setting has
2628 been enabled. Otherwise, total it is:
2630 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2633 if ((ir->efep != efepNO) || ir->bSimTemp)
2635 ir->bExpanded = FALSE;
2636 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2638 ir->bExpanded = TRUE;
2640 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2641 if (ir->bSimTemp) /* done after fep params */
2643 do_simtemp_params(ir);
2646 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2647 * setup and not on the old way of specifying the free-energy setup,
2648 * we should check for using soft-core when not needed, since that
2649 * can complicate the sampling significantly.
2650 * Note that we only check for the automated coupling setup.
2651 * If the (advanced) user does FEP through manual topology changes,
2652 * this check will not be triggered.
2654 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2655 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2658 "You are using soft-core interactions while the Van der Waals interactions are "
2659 "not decoupled (note that the sc-coul option is only active when using lambda "
2660 "states). Although this will not lead to errors, you will need much more "
2661 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2666 ir->fepvals->n_lambda = 0;
2669 /* WALL PARAMETERS */
2671 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2673 /* ORIENTATION RESTRAINT PARAMETERS */
2675 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2677 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2680 /* DEFORMATION PARAMETERS */
2682 clear_mat(ir->deform);
2683 for (i = 0; i < 6; i++)
2688 double gmx_unused canary;
2689 int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
2690 &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
2691 &(dumdub[0][5]), &canary);
2693 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2697 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2698 inputrecStrings->deform)
2701 for (i = 0; i < 3; i++)
2703 ir->deform[i][i] = dumdub[0][i];
2705 ir->deform[YY][XX] = dumdub[0][3];
2706 ir->deform[ZZ][XX] = dumdub[0][4];
2707 ir->deform[ZZ][YY] = dumdub[0][5];
2708 if (ir->epc != epcNO)
2710 for (i = 0; i < 3; i++)
2712 for (j = 0; j <= i; j++)
2714 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2716 warning_error(wi, "A box element has deform set and compressibility > 0");
2720 for (i = 0; i < 3; i++)
2722 for (j = 0; j < i; j++)
2724 if (ir->deform[i][j] != 0)
2726 for (m = j; m < DIM; m++)
2728 if (ir->compress[m][j] != 0)
2731 "An off-diagonal box element has deform set while "
2732 "compressibility > 0 for the same component of another box "
2733 "vector, this might lead to spurious periodicity effects.");
2734 warning(wi, warn_buf);
2742 /* Ion/water position swapping checks */
2743 if (ir->eSwapCoords != eswapNO)
2745 if (ir->swap->nstswap < 1)
2747 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2749 if (ir->swap->nAverage < 1)
2751 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2753 if (ir->swap->threshold < 1.0)
2755 warning_error(wi, "Ion count threshold must be at least 1.\n");
2759 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2762 setupMtsLevels(ir->mtsLevels, *ir, *opts, wi);
2767 gmx::checkAwhParams(ir->awhParams, ir, wi);
2774 /* We would like gn to be const as well, but C doesn't allow this */
2775 /* TODO this is utility functionality (search for the index of a
2776 string in a collection), so should be refactored and located more
2778 int search_string(const char* s, int ng, char* gn[])
2782 for (i = 0; (i < ng); i++)
2784 if (gmx_strcasecmp(s, gn[i]) == 0)
2791 "Group %s referenced in the .mdp file was not found in the index file.\n"
2792 "Group names must match either [moleculetype] names or custom index group\n"
2793 "names, in which case you must supply an index file to the '-n' option\n"
2798 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2800 /* Now go over the atoms in the group */
2801 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2803 int aj = block.a[j];
2805 /* Range checking */
2806 if ((aj < 0) || (aj >= natoms))
2808 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2813 static void do_numbering(int natoms,
2814 SimulationGroups* groups,
2815 gmx::ArrayRef<std::string> groupsFromMdpFile,
2818 SimulationAtomGroupType gtype,
2824 unsigned short* cbuf;
2825 AtomGroupIndices* grps = &(groups->groups[gtype]);
2828 char warn_buf[STRLEN];
2830 title = shortName(gtype);
2833 /* Mark all id's as not set */
2834 for (int i = 0; (i < natoms); i++)
2839 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2841 /* Lookup the group name in the block structure */
2842 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2843 if ((grptp != egrptpONE) || (i == 0))
2845 grps->emplace_back(gid);
2847 GMX_ASSERT(block, "Can't have a nullptr block");
2848 atomGroupRangeValidation(natoms, gid, *block);
2849 /* Now go over the atoms in the group */
2850 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2852 const int aj = block->a[j];
2853 /* Lookup up the old group number */
2854 const int ognr = cbuf[aj];
2857 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2862 /* Store the group number in buffer */
2863 if (grptp == egrptpONE)
2876 /* Now check whether we have done all atoms */
2879 if (grptp == egrptpALL)
2881 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2883 else if (grptp == egrptpPART)
2885 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2886 warning_note(wi, warn_buf);
2888 /* Assign all atoms currently unassigned to a rest group */
2889 for (int j = 0; (j < natoms); j++)
2891 if (cbuf[j] == NOGID)
2893 cbuf[j] = grps->size();
2896 if (grptp != egrptpPART)
2900 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2903 /* Add group name "rest" */
2904 grps->emplace_back(restnm);
2906 /* Assign the rest name to all atoms not currently assigned to a group */
2907 for (int j = 0; (j < natoms); j++)
2909 if (cbuf[j] == NOGID)
2911 // group size was not updated before this here, so need to use -1.
2912 cbuf[j] = grps->size() - 1;
2918 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2920 /* All atoms are part of one (or no) group, no index required */
2921 groups->groupNumbers[gtype].clear();
2925 for (int j = 0; (j < natoms); j++)
2927 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2934 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2937 pull_params_t* pull;
2938 int natoms, imin, jmin;
2939 int * nrdf2, *na_vcm, na_tot;
2940 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2945 * First calc 3xnr-atoms for each group
2946 * then subtract half a degree of freedom for each constraint
2948 * Only atoms and nuclei contribute to the degrees of freedom...
2953 const SimulationGroups& groups = mtop->groups;
2954 natoms = mtop->natoms;
2956 /* Allocate one more for a possible rest group */
2957 /* We need to sum degrees of freedom into doubles,
2958 * since floats give too low nrdf's above 3 million atoms.
2960 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2961 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2962 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2963 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2964 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2966 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2970 for (gmx::index i = 0;
2971 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2974 clear_ivec(dof_vcm[i]);
2976 nrdf_vcm_sub[i] = 0;
2978 snew(nrdf2, natoms);
2979 for (const AtomProxy atomP : AtomRange(*mtop))
2981 const t_atom& local = atomP.atom();
2982 int i = atomP.globalAtomNumber();
2984 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2986 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2987 for (int d = 0; d < DIM; d++)
2989 if (opts->nFreeze[g][d] == 0)
2991 /* Add one DOF for particle i (counted as 2*1) */
2993 /* VCM group i has dim d as a DOF */
2994 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2998 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3000 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3006 for (const gmx_molblock_t& molb : mtop->molblock)
3008 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3009 const t_atom* atom = molt.atoms.atom;
3010 for (int mol = 0; mol < molb.nmol; mol++)
3012 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3014 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3015 for (int i = 0; i < molt.ilist[ftype].size();)
3017 /* Subtract degrees of freedom for the constraints,
3018 * if the particles still have degrees of freedom left.
3019 * If one of the particles is a vsite or a shell, then all
3020 * constraint motion will go there, but since they do not
3021 * contribute to the constraints the degrees of freedom do not
3024 int ai = as + ia[i + 1];
3025 int aj = as + ia[i + 2];
3026 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
3027 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
3045 imin = std::min(imin, nrdf2[ai]);
3046 jmin = std::min(jmin, nrdf2[aj]);
3049 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3051 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3053 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3055 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3058 i += interaction_function[ftype].nratoms + 1;
3061 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3062 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3064 /* Subtract 1 dof from every atom in the SETTLE */
3065 for (int j = 0; j < 3; j++)
3067 int ai = as + ia[i + 1 + j];
3068 imin = std::min(2, nrdf2[ai]);
3070 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3072 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3077 as += molt.atoms.nr;
3083 /* Correct nrdf for the COM constraints.
3084 * We correct using the TC and VCM group of the first atom
3085 * in the reference and pull group. If atoms in one pull group
3086 * belong to different TC or VCM groups it is anyhow difficult
3087 * to determine the optimal nrdf assignment.
3089 pull = ir->pull.get();
3091 for (int i = 0; i < pull->ncoord; i++)
3093 if (pull->coord[i].eType != epullCONSTRAINT)
3100 for (int j = 0; j < 2; j++)
3102 const t_pull_group* pgrp;
3104 pgrp = &pull->group[pull->coord[i].group[j]];
3106 if (!pgrp->ind.empty())
3108 /* Subtract 1/2 dof from each group */
3109 int ai = pgrp->ind[0];
3110 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3112 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3114 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3117 "Center of mass pulling constraints caused the number of degrees "
3118 "of freedom for temperature coupling group %s to be negative",
3119 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3120 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3125 /* We need to subtract the whole DOF from group j=1 */
3132 if (ir->nstcomm != 0)
3134 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3135 "Expect at least one group when removing COM motion");
3137 /* We remove COM motion up to dim ndof_com() */
3138 const int ndim_rm_vcm = ndof_com(ir);
3140 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3141 * the number of degrees of freedom in each vcm group when COM
3142 * translation is removed and 6 when rotation is removed as well.
3143 * Note that we do not and should not include the rest group here.
3145 for (gmx::index j = 0;
3146 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3148 switch (ir->comm_mode)
3151 case ecmLINEAR_ACCELERATION_CORRECTION:
3152 nrdf_vcm_sub[j] = 0;
3153 for (int d = 0; d < ndim_rm_vcm; d++)
3161 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3162 default: gmx_incons("Checking comm_mode");
3166 for (gmx::index i = 0;
3167 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3169 /* Count the number of atoms of TC group i for every VCM group */
3170 for (gmx::index j = 0;
3171 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3176 for (int ai = 0; ai < natoms; ai++)
3178 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3180 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3184 /* Correct for VCM removal according to the fraction of each VCM
3185 * group present in this TC group.
3187 nrdf_uc = nrdf_tc[i];
3189 for (gmx::index j = 0;
3190 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3192 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3194 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3195 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3200 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3202 opts->nrdf[i] = nrdf_tc[i];
3203 if (opts->nrdf[i] < 0)
3207 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3208 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3216 sfree(nrdf_vcm_sub);
3219 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3221 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3222 * But since this is much larger than STRLEN, such a line can not be parsed.
3223 * The real maximum is the number of names that fit in a string: STRLEN/2.
3225 #define EGP_MAX (STRLEN / 2)
3229 auto names = gmx::splitString(val);
3230 if (names.size() % 2 != 0)
3232 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3234 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3236 for (size_t i = 0; i < names.size() / 2; i++)
3238 // TODO this needs to be replaced by a solution using std::find_if
3242 names[2 * i].c_str(),
3243 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3249 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3254 names[2 * i + 1].c_str(),
3255 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3261 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3263 if ((j < nr) && (k < nr))
3265 ir->opts.egp_flags[nr * j + k] |= flag;
3266 ir->opts.egp_flags[nr * k + j] |= flag;
3275 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3277 int ig = -1, i = 0, gind;
3281 /* Just a quick check here, more thorough checks are in mdrun */
3282 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3284 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3287 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3288 for (ig = 0; ig < swap->ngrp; ig++)
3290 swapg = &swap->grp[ig];
3291 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3292 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3296 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3297 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3298 snew(swapg->ind, swapg->nat);
3299 for (i = 0; i < swapg->nat; i++)
3301 swapg->ind[i] = grps->a[grps->index[gind] + i];
3306 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3312 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3317 ig = search_string(IMDgname, grps->nr, gnames);
3318 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3320 if (IMDgroup->nat > 0)
3323 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3325 IMDgname, IMDgroup->nat);
3326 snew(IMDgroup->ind, IMDgroup->nat);
3327 for (i = 0; i < IMDgroup->nat; i++)
3329 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3334 /* Checks whether atoms are both part of a COM removal group and frozen.
3335 * If a fully frozen atom is part of a COM removal group, it is removed
3336 * from the COM removal group. A note is issued if such atoms are present.
3337 * A warning is issued for atom with one or two dimensions frozen that
3338 * are part of a COM removal group (mdrun would need to compute COM mass
3339 * per dimension to handle this correctly).
3340 * Also issues a warning when non-frozen atoms are not part of a COM
3341 * removal group while COM removal is active.
3343 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3345 const t_grpopts& opts,
3348 const int vcmRestGroup =
3349 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3351 int numFullyFrozenVcmAtoms = 0;
3352 int numPartiallyFrozenVcmAtoms = 0;
3353 int numNonVcmAtoms = 0;
3354 for (int a = 0; a < numAtoms; a++)
3356 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3357 int numFrozenDims = 0;
3358 for (int d = 0; d < DIM; d++)
3360 numFrozenDims += opts.nFreeze[freezeGroup][d];
3363 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3364 if (vcmGroup < vcmRestGroup)
3366 if (numFrozenDims == DIM)
3368 /* Do not remove COM motion for this fully frozen atom */
3369 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3371 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3374 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3375 numFullyFrozenVcmAtoms++;
3377 else if (numFrozenDims > 0)
3379 numPartiallyFrozenVcmAtoms++;
3382 else if (numFrozenDims < DIM)
3388 if (numFullyFrozenVcmAtoms > 0)
3390 std::string warningText = gmx::formatString(
3391 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3392 "removing these atoms from the COMM removal group(s)",
3393 numFullyFrozenVcmAtoms);
3394 warning_note(wi, warningText.c_str());
3396 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3398 std::string warningText = gmx::formatString(
3399 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3400 "removal group(s), due to limitations in the code these still contribute to the "
3401 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3403 numPartiallyFrozenVcmAtoms, DIM);
3404 warning(wi, warningText.c_str());
3406 if (numNonVcmAtoms > 0)
3408 std::string warningText = gmx::formatString(
3409 "%d atoms are not part of any center of mass motion removal group.\n"
3410 "This may lead to artifacts.\n"
3411 "In most cases one should use one group for the whole system.",
3413 warning(wi, warningText.c_str());
3417 void do_index(const char* mdparin,
3421 const gmx::MdModulesNotifier& notifier,
3425 t_blocka* defaultIndexGroups;
3433 int i, j, k, restnm;
3434 bool bExcl, bTable, bAnneal;
3435 char warn_buf[STRLEN];
3439 fprintf(stderr, "processing index file...\n");
3443 snew(defaultIndexGroups, 1);
3444 snew(defaultIndexGroups->index, 1);
3446 atoms_all = gmx_mtop_global_atoms(mtop);
3447 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3448 done_atom(&atoms_all);
3452 defaultIndexGroups = init_index(ndx, &gnames);
3455 SimulationGroups* groups = &mtop->groups;
3456 natoms = mtop->natoms;
3457 symtab = &mtop->symtab;
3459 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3461 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3463 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3464 restnm = groups->groupNames.size() - 1;
3465 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3466 srenew(gnames, defaultIndexGroups->nr + 1);
3467 gnames[restnm] = *(groups->groupNames.back());
3469 set_warning_line(wi, mdparin, -1);
3471 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3472 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3473 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3474 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3475 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3478 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3480 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3481 temperatureCouplingTauValues.size());
3484 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3485 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3486 SimulationAtomGroupType::TemperatureCoupling, restnm,
3487 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3488 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3490 snew(ir->opts.nrdf, nr);
3491 snew(ir->opts.tau_t, nr);
3492 snew(ir->opts.ref_t, nr);
3493 if (ir->eI == eiBD && ir->bd_fric == 0)
3495 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3498 if (useReferenceTemperature)
3500 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3502 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3506 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3507 for (i = 0; (i < nr); i++)
3509 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3511 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3512 warning_error(wi, warn_buf);
3515 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3519 "tau-t = -1 is the value to signal that a group should not have "
3520 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3523 if (ir->opts.tau_t[i] >= 0)
3525 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3528 if (ir->etc != etcNO && ir->nsttcouple == -1)
3530 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3535 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3538 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3539 "md-vv; use either vrescale temperature with berendsen pressure or "
3540 "Nose-Hoover temperature with MTTK pressure");
3542 if (ir->epc == epcMTTK)
3544 if (ir->etc != etcNOSEHOOVER)
3547 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3552 if (ir->nstpcouple != ir->nsttcouple)
3554 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3555 ir->nstpcouple = ir->nsttcouple = mincouple;
3557 "for current Trotter decomposition methods with vv, nsttcouple and "
3558 "nstpcouple must be equal. Both have been reset to "
3559 "min(nsttcouple,nstpcouple) = %d",
3561 warning_note(wi, warn_buf);
3566 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3567 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3569 if (ETC_ANDERSEN(ir->etc))
3571 if (ir->nsttcouple != 1)
3575 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3576 "need for larger nsttcouple > 1, since no global parameters are computed. "
3577 "nsttcouple has been reset to 1");
3578 warning_note(wi, warn_buf);
3581 nstcmin = tcouple_min_integration_steps(ir->etc);
3584 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3587 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3588 "least %d times larger than nsttcouple*dt (%g)",
3589 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3590 warning(wi, warn_buf);
3593 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3594 for (i = 0; (i < nr); i++)
3596 if (ir->opts.ref_t[i] < 0)
3598 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3601 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3602 if we are in this conditional) if mc_temp is negative */
3603 if (ir->expandedvals->mc_temp < 0)
3605 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3609 /* Simulated annealing for each group. There are nr groups */
3610 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3611 if (simulatedAnnealingGroupNames.size() == 1
3612 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3614 simulatedAnnealingGroupNames.resize(0);
3616 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3618 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3619 simulatedAnnealingGroupNames.size(), nr);
3623 snew(ir->opts.annealing, nr);
3624 snew(ir->opts.anneal_npoints, nr);
3625 snew(ir->opts.anneal_time, nr);
3626 snew(ir->opts.anneal_temp, nr);
3627 for (i = 0; i < nr; i++)
3629 ir->opts.annealing[i] = eannNO;
3630 ir->opts.anneal_npoints[i] = 0;
3631 ir->opts.anneal_time[i] = nullptr;
3632 ir->opts.anneal_temp[i] = nullptr;
3634 if (!simulatedAnnealingGroupNames.empty())
3637 for (i = 0; i < nr; i++)
3639 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3641 ir->opts.annealing[i] = eannNO;
3643 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3645 ir->opts.annealing[i] = eannSINGLE;
3648 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3650 ir->opts.annealing[i] = eannPERIODIC;
3656 /* Read the other fields too */
3657 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3658 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3660 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3661 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3663 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3664 size_t numSimulatedAnnealingFields = 0;
3665 for (i = 0; i < nr; i++)
3667 if (ir->opts.anneal_npoints[i] == 1)
3671 "Please specify at least a start and an end point for annealing\n");
3673 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3674 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3675 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3678 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3680 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3682 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3683 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3685 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3686 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3688 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3689 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3692 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3693 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3694 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3695 allSimulatedAnnealingTimes.data());
3696 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3697 allSimulatedAnnealingTemperatures.data());
3698 for (i = 0, k = 0; i < nr; i++)
3700 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3702 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3703 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3706 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3708 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3714 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3717 "Annealing timepoints out of order: t=%f comes after "
3719 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3722 if (ir->opts.anneal_temp[i][j] < 0)
3724 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3725 ir->opts.anneal_temp[i][j]);
3730 /* Print out some summary information, to make sure we got it right */
3731 for (i = 0; i < nr; i++)
3733 if (ir->opts.annealing[i] != eannNO)
3735 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3736 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3737 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3738 ir->opts.anneal_npoints[i]);
3739 fprintf(stderr, "Time (ps) Temperature (K)\n");
3740 /* All terms except the last one */
3741 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3743 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3744 ir->opts.anneal_temp[i][j]);
3747 /* Finally the last one */
3748 j = ir->opts.anneal_npoints[i] - 1;
3749 if (ir->opts.annealing[i] == eannSINGLE)
3751 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3752 ir->opts.anneal_temp[i][j]);
3756 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3757 ir->opts.anneal_temp[i][j]);
3758 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3761 "There is a temperature jump when your annealing "
3773 for (int i = 1; i < ir->pull->ngroup; i++)
3775 const int gid = search_string(inputrecStrings->pullGroupNames[i].c_str(),
3776 defaultIndexGroups->nr, gnames);
3777 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3778 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3781 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3783 checkPullCoords(ir->pull->group, ir->pull->coord);
3788 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3791 if (ir->eSwapCoords != eswapNO)
3793 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3796 /* Make indices for IMD session */
3799 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3802 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3803 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3804 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3806 auto accelerations = gmx::splitString(inputrecStrings->acc);
3807 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
3808 if (accelerationGroupNames.size() * DIM != accelerations.size())
3810 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3811 accelerationGroupNames.size(), accelerations.size());
3813 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3814 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3815 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3816 snew(ir->opts.acc, nr);
3817 ir->opts.ngacc = nr;
3819 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3821 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3822 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3823 if (freezeDims.size() != DIM * freezeGroupNames.size())
3825 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3826 freezeGroupNames.size(), freezeDims.size());
3828 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3829 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3830 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3831 ir->opts.ngfrz = nr;
3832 snew(ir->opts.nFreeze, nr);
3833 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3835 for (j = 0; (j < DIM); j++, k++)
3837 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3838 if (!ir->opts.nFreeze[i][j])
3840 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3843 "Please use Y(ES) or N(O) for freezedim only "
3845 freezeDims[k].c_str());
3846 warning(wi, warn_buf);
3851 for (; (i < nr); i++)
3853 for (j = 0; (j < DIM); j++)
3855 ir->opts.nFreeze[i][j] = 0;
3859 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3860 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3861 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3862 add_wall_energrps(groups, ir->nwall, symtab);
3863 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3864 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3865 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3866 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3867 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3869 if (ir->comm_mode != ecmNO)
3871 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3874 /* Now we have filled the freeze struct, so we can calculate NRDF */
3875 calc_nrdf(mtop, ir, gnames);
3877 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3878 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3879 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3880 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3881 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3882 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3883 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3884 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3885 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3886 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3887 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3888 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3891 /* MiMiC QMMM input processing */
3892 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3893 if (qmGroupNames.size() > 1)
3895 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3897 /* group rest, if any, is always MM! */
3898 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3899 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3900 ir->opts.ngQM = qmGroupNames.size();
3902 /* end of MiMiC QMMM input */
3906 for (auto group : gmx::keysOf(groups->groups))
3908 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3909 for (const auto& entry : groups->groups[group])
3911 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3913 fprintf(stderr, "\n");
3917 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3918 snew(ir->opts.egp_flags, nr * nr);
3920 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
3921 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3923 warning_error(wi, "Energy group exclusions are currently not supported");
3925 if (bExcl && EEL_FULL(ir->coulombtype))
3927 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3930 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
3931 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3932 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3935 "Can only have energy group pair tables in combination with user tables for VdW "
3939 /* final check before going out of scope if simulated tempering variables
3940 * need to be set to default values.
3942 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3944 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3945 warning(wi, gmx::formatString(
3946 "the value for nstexpanded was not specified for "
3947 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3948 "by default, but it is recommended to set it to an explicit value!",
3949 ir->expandedvals->nstexpanded));
3951 for (i = 0; (i < defaultIndexGroups->nr); i++)
3956 done_blocka(defaultIndexGroups);
3957 sfree(defaultIndexGroups);
3961 static void check_disre(const gmx_mtop_t* mtop)
3963 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3965 const gmx_ffparams_t& ffparams = mtop->ffparams;
3968 for (int i = 0; i < ffparams.numTypes(); i++)
3970 int ftype = ffparams.functype[i];
3971 if (ftype == F_DISRES)
3973 int label = ffparams.iparams[i].disres.label;
3974 if (label == old_label)
3976 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3985 "Found %d double distance restraint indices,\n"
3986 "probably the parameters for multiple pairs in one restraint "
3987 "are not identical\n",
3993 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3996 gmx_mtop_ilistloop_t iloop;
3998 const t_iparams* pr;
4005 for (d = 0; d < DIM; d++)
4007 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
4009 /* Check for freeze groups */
4010 for (g = 0; g < ir->opts.ngfrz; g++)
4012 for (d = 0; d < DIM; d++)
4014 if (ir->opts.nFreeze[g][d] != 0)
4022 /* Check for position restraints */
4023 iloop = gmx_mtop_ilistloop_init(sys);
4024 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4026 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4028 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4030 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4031 for (d = 0; d < DIM; d++)
4033 if (pr->posres.fcA[d] != 0)
4039 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4041 /* Check for flat-bottom posres */
4042 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4043 if (pr->fbposres.k != 0)
4045 switch (pr->fbposres.geom)
4047 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4048 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4049 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4050 case efbposresCYLINDER:
4051 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4052 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4053 case efbposresX: /* d=XX */
4054 case efbposresY: /* d=YY */
4055 case efbposresZ: /* d=ZZ */
4056 d = pr->fbposres.geom - efbposresX;
4061 " Invalid geometry for flat-bottom position restraint.\n"
4062 "Expected nr between 1 and %d. Found %d\n",
4063 efbposresNR - 1, pr->fbposres.geom);
4070 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4073 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4075 bool* bC6ParametersWorkWithGeometricRules,
4076 bool* bC6ParametersWorkWithLBRules,
4077 bool* bLBRulesPossible)
4079 int ntypes, tpi, tpj;
4082 double c6i, c6j, c12i, c12j;
4083 double c6, c6_geometric, c6_LB;
4084 double sigmai, sigmaj, epsi, epsj;
4085 bool bCanDoLBRules, bCanDoGeometricRules;
4088 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4089 * force-field floating point parameters.
4092 ptr = getenv("GMX_LJCOMB_TOL");
4096 double gmx_unused canary;
4098 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4101 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4106 *bC6ParametersWorkWithLBRules = TRUE;
4107 *bC6ParametersWorkWithGeometricRules = TRUE;
4108 bCanDoLBRules = TRUE;
4109 ntypes = mtop->ffparams.atnr;
4110 snew(typecount, ntypes);
4111 gmx_mtop_count_atomtypes(mtop, state, typecount);
4112 *bLBRulesPossible = TRUE;
4113 for (tpi = 0; tpi < ntypes; ++tpi)
4115 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4116 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4117 for (tpj = tpi; tpj < ntypes; ++tpj)
4119 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4120 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4121 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4122 c6_geometric = std::sqrt(c6i * c6j);
4123 if (!gmx_numzero(c6_geometric))
4125 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4127 sigmai = gmx::sixthroot(c12i / c6i);
4128 sigmaj = gmx::sixthroot(c12j / c6j);
4129 epsi = c6i * c6i / (4.0 * c12i);
4130 epsj = c6j * c6j / (4.0 * c12j);
4131 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4135 *bLBRulesPossible = FALSE;
4136 c6_LB = c6_geometric;
4138 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4143 *bC6ParametersWorkWithLBRules = FALSE;
4146 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4148 if (!bCanDoGeometricRules)
4150 *bC6ParametersWorkWithGeometricRules = FALSE;
4157 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4159 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4161 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4162 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4163 if (ir->ljpme_combination_rule == eljpmeLB)
4165 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4168 "You are using arithmetic-geometric combination rules "
4169 "in LJ-PME, but your non-bonded C6 parameters do not "
4170 "follow these rules.");
4175 if (!bC6ParametersWorkWithGeometricRules)
4177 if (ir->eDispCorr != edispcNO)
4180 "You are using geometric combination rules in "
4181 "LJ-PME, but your non-bonded C6 parameters do "
4182 "not follow these rules. "
4183 "This will introduce very small errors in the forces and energies in "
4184 "your simulations. Dispersion correction will correct total energy "
4185 "and/or pressure for isotropic systems, but not forces or surface "
4191 "You are using geometric combination rules in "
4192 "LJ-PME, but your non-bonded C6 parameters do "
4193 "not follow these rules. "
4194 "This will introduce very small errors in the forces and energies in "
4195 "your simulations. If your system is homogeneous, consider using "
4196 "dispersion correction "
4197 "for the total energy and pressure.");
4203 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4205 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4206 gmx::assertMtsRequirements(*ir);
4208 char err_buf[STRLEN];
4213 gmx_mtop_atomloop_block_t aloopb;
4215 char warn_buf[STRLEN];
4217 set_warning_line(wi, mdparin, -1);
4219 if (absolute_reference(ir, sys, false, AbsRef))
4222 "Removing center of mass motion in the presence of position restraints might "
4223 "cause artifacts. When you are using position restraints to equilibrate a "
4224 "macro-molecule, the artifacts are usually negligible.");
4227 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4228 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4230 /* Check if a too small Verlet buffer might potentially
4231 * cause more drift than the thermostat can couple off.
4233 /* Temperature error fraction for warning and suggestion */
4234 const real T_error_warn = 0.002;
4235 const real T_error_suggest = 0.001;
4236 /* For safety: 2 DOF per atom (typical with constraints) */
4237 const real nrdf_at = 2;
4238 real T, tau, max_T_error;
4243 for (i = 0; i < ir->opts.ngtc; i++)
4245 T = std::max(T, ir->opts.ref_t[i]);
4246 tau = std::max(tau, ir->opts.tau_t[i]);
4250 /* This is a worst case estimate of the temperature error,
4251 * assuming perfect buffer estimation and no cancelation
4252 * of errors. The factor 0.5 is because energy distributes
4253 * equally over Ekin and Epot.
4255 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4256 if (max_T_error > T_error_warn)
4259 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4260 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4261 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4262 "%.0e or decrease tau_t.",
4263 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4264 ir->verletbuf_tol * T_error_suggest / max_T_error);
4265 warning(wi, warn_buf);
4270 if (ETC_ANDERSEN(ir->etc))
4274 for (i = 0; i < ir->opts.ngtc; i++)
4277 "all tau_t must currently be equal using Andersen temperature control, "
4278 "violated for group %d",
4280 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4282 "all tau_t must be positive using Andersen temperature control, "
4284 i, ir->opts.tau_t[i]);
4285 CHECK(ir->opts.tau_t[i] < 0);
4288 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4290 for (i = 0; i < ir->opts.ngtc; i++)
4292 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4294 "tau_t/delta_t for group %d for temperature control method %s must be a "
4295 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4296 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4298 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4299 CHECK(nsteps % ir->nstcomm != 0);
4304 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4305 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4308 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4309 "rounding errors can lead to build up of kinetic energy of the center of mass");
4312 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4315 for (int g = 0; g < ir->opts.ngtc; g++)
4317 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4319 if (ir->tau_p < 1.9 * tau_t_max)
4321 std::string message = gmx::formatString(
4322 "With %s T-coupling and %s p-coupling, "
4323 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4324 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4326 warning(wi, message.c_str());
4330 /* Check for pressure coupling with absolute position restraints */
4331 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4333 absolute_reference(ir, sys, TRUE, AbsRef);
4335 for (m = 0; m < DIM; m++)
4337 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4340 "You are using pressure coupling with absolute position restraints, "
4341 "this will give artifacts. Use the refcoord_scaling option.");
4349 aloopb = gmx_mtop_atomloop_block_init(sys);
4351 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4353 if (atom->q != 0 || atom->qB != 0)
4361 if (EEL_FULL(ir->coulombtype))
4364 "You are using full electrostatics treatment %s for a system without charges.\n"
4365 "This costs a lot of performance for just processing zeros, consider using %s "
4367 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4368 warning(wi, err_buf);
4373 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4376 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4377 "You might want to consider using %s electrostatics.\n",
4379 warning_note(wi, err_buf);
4383 /* Check if combination rules used in LJ-PME are the same as in the force field */
4384 if (EVDW_PME(ir->vdwtype))
4386 check_combination_rules(ir, sys, wi);
4389 /* Generalized reaction field */
4390 if (ir->coulombtype == eelGRF_NOTUSED)
4393 "Generalized reaction-field electrostatics is no longer supported. "
4394 "You can use normal reaction-field instead and compute the reaction-field "
4395 "constant by hand.");
4399 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4401 for (m = 0; (m < DIM); m++)
4403 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4412 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4413 for (const AtomProxy atomP : AtomRange(*sys))
4415 const t_atom& local = atomP.atom();
4416 int i = atomP.globalAtomNumber();
4417 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4420 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4422 for (m = 0; (m < DIM); m++)
4424 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4428 for (m = 0; (m < DIM); m++)
4430 if (fabs(acc[m]) > 1e-6)
4432 const char* dim[DIM] = { "X", "Y", "Z" };
4433 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4434 ir->nstcomm != 0 ? "" : "not");
4435 if (ir->nstcomm != 0 && m < ndof_com(ir))
4439 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4441 ir->opts.acc[i][m] -= acc[m];
4449 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4450 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4452 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4460 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4462 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4464 absolute_reference(ir, sys, FALSE, AbsRef);
4465 for (m = 0; m < DIM; m++)
4467 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4470 "You are using an absolute reference for pulling, but the rest of "
4471 "the system does not have an absolute reference. This will lead to "
4480 for (i = 0; i < 3; i++)
4482 for (m = 0; m <= i; m++)
4484 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4486 for (c = 0; c < ir->pull->ncoord; c++)
4488 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4491 "Can not have dynamic box while using pull geometry '%s' "
4493 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4504 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4506 char warn_buf[STRLEN];
4509 ptr = check_box(ir->pbcType, box);
4512 warning_error(wi, ptr);
4515 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4517 if (ir->shake_tol <= 0.0)
4519 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4520 warning_error(wi, warn_buf);
4524 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4526 /* If we have Lincs constraints: */
4527 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4530 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4531 warning_note(wi, warn_buf);
4534 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4537 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4539 warning_note(wi, warn_buf);
4541 if (ir->epc == epcMTTK)
4543 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4547 if (bHasAnyConstraints && ir->epc == epcMTTK)
4549 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4552 if (ir->LincsWarnAngle > 90.0)
4554 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4555 warning(wi, warn_buf);
4556 ir->LincsWarnAngle = 90.0;
4559 if (ir->pbcType != PbcType::No)
4561 if (ir->nstlist == 0)
4564 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4565 "atoms might cause the simulation to crash.");
4567 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4570 "ERROR: The cut-off length is longer than half the shortest box vector or "
4571 "longer than the smallest box diagonal element. Increase the box size or "
4572 "decrease rlist.\n");
4573 warning_error(wi, warn_buf);