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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");
1510 // cosine acceleration is only supported in leap-frog
1511 if (ir->cos_accel != 0.0 && ir->eI != eiMD)
1513 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1517 /* interpret a number of doubles from a string and put them in an array,
1518 after allocating space for them.
1519 str = the input string
1520 n = the (pre-allocated) number of doubles read
1521 r = the output array of doubles. */
1522 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1524 auto values = gmx::splitString(str);
1528 for (int i = 0; i < *n; i++)
1532 (*r)[i] = gmx::fromString<real>(values[i]);
1534 catch (gmx::GromacsException&)
1536 warning_error(wi, "Invalid value " + values[i]
1537 + " in string in mdp file. Expected a real number.");
1543 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1546 int i, j, max_n_lambda, nweights, nfep[efptNR];
1547 t_lambda* fep = ir->fepvals;
1548 t_expanded* expand = ir->expandedvals;
1549 real** count_fep_lambdas;
1550 bool bOneLambda = TRUE;
1552 snew(count_fep_lambdas, efptNR);
1554 /* FEP input processing */
1555 /* first, identify the number of lambda values for each type.
1556 All that are nonzero must have the same number */
1558 for (i = 0; i < efptNR; i++)
1560 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1563 /* now, determine the number of components. All must be either zero, or equal. */
1566 for (i = 0; i < efptNR; i++)
1568 if (nfep[i] > max_n_lambda)
1570 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1571 must have the same number if its not zero.*/
1576 for (i = 0; i < efptNR; i++)
1580 ir->fepvals->separate_dvdl[i] = FALSE;
1582 else if (nfep[i] == max_n_lambda)
1584 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1585 the derivative with respect to the temperature currently */
1587 ir->fepvals->separate_dvdl[i] = TRUE;
1593 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1595 nfep[i], efpt_names[i], max_n_lambda);
1598 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1599 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1601 /* the number of lambdas is the number we've read in, which is either zero
1602 or the same for all */
1603 fep->n_lambda = max_n_lambda;
1605 /* allocate space for the array of lambda values */
1606 snew(fep->all_lambda, efptNR);
1607 /* if init_lambda is defined, we need to set lambda */
1608 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1610 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1612 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1613 for (i = 0; i < efptNR; i++)
1615 snew(fep->all_lambda[i], fep->n_lambda);
1616 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1619 for (j = 0; j < fep->n_lambda; j++)
1621 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1623 sfree(count_fep_lambdas[i]);
1626 sfree(count_fep_lambdas);
1628 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1629 internal bookkeeping -- for now, init_lambda */
1631 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1633 for (i = 0; i < fep->n_lambda; i++)
1635 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1639 /* check to see if only a single component lambda is defined, and soft core is defined.
1640 In this case, turn on coulomb soft core */
1642 if (max_n_lambda == 0)
1648 for (i = 0; i < efptNR; i++)
1650 if ((nfep[i] != 0) && (i != efptFEP))
1656 if ((bOneLambda) && (fep->sc_alpha > 0))
1658 fep->bScCoul = TRUE;
1661 /* Fill in the others with the efptFEP if they are not explicitly
1662 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1663 they are all zero. */
1665 for (i = 0; i < efptNR; i++)
1667 if ((nfep[i] == 0) && (i != efptFEP))
1669 for (j = 0; j < fep->n_lambda; j++)
1671 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1677 /* now read in the weights */
1678 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1681 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1683 else if (nweights != fep->n_lambda)
1685 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1686 nweights, fep->n_lambda);
1688 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1690 expand->nstexpanded = fep->nstdhdl;
1691 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1696 static void do_simtemp_params(t_inputrec* ir)
1699 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1700 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1703 template<typename T>
1704 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1707 for (const auto& input : inputs)
1711 outputs[i] = gmx::fromStdString<T>(input);
1713 catch (gmx::GromacsException&)
1715 auto message = gmx::formatString(
1716 "Invalid value for mdp option %s. %s should only consist of integers separated "
1719 warning_error(wi, message);
1725 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1728 for (const auto& input : inputs)
1732 outputs[i] = gmx::fromString<real>(input);
1734 catch (gmx::GromacsException&)
1736 auto message = gmx::formatString(
1737 "Invalid value for mdp option %s. %s should only consist of real numbers "
1738 "separated by spaces.",
1740 warning_error(wi, message);
1746 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1749 for (const auto& input : inputs)
1753 outputs[i][d] = gmx::fromString<real>(input);
1755 catch (gmx::GromacsException&)
1757 auto message = gmx::formatString(
1758 "Invalid value for mdp option %s. %s should only consist of real numbers "
1759 "separated by spaces.",
1761 warning_error(wi, message);
1772 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1774 opts->wall_atomtype[0] = nullptr;
1775 opts->wall_atomtype[1] = nullptr;
1777 ir->wall_atomtype[0] = -1;
1778 ir->wall_atomtype[1] = -1;
1779 ir->wall_density[0] = 0;
1780 ir->wall_density[1] = 0;
1784 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1785 if (wallAtomTypes.size() != size_t(ir->nwall))
1787 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1788 wallAtomTypes.size());
1790 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1791 for (int i = 0; i < ir->nwall; i++)
1793 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1796 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1798 auto wallDensity = gmx::splitString(wall_density);
1799 if (wallDensity.size() != size_t(ir->nwall))
1801 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1802 wallDensity.size());
1804 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1805 for (int i = 0; i < ir->nwall; i++)
1807 if (ir->wall_density[i] <= 0)
1809 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1816 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1820 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1821 for (int i = 0; i < nwall; i++)
1823 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1824 grps->emplace_back(groups->groupNames.size() - 1);
1829 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1831 /* read expanded ensemble parameters */
1832 printStringNewline(inp, "expanded ensemble variables");
1833 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1834 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1835 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1836 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1837 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1838 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1839 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1840 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1841 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1842 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1843 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1844 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1845 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1846 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1847 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1848 expand->bSymmetrizedTMatrix =
1849 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1850 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1851 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1852 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1853 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1854 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1855 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1856 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1859 /*! \brief Return whether an end state with the given coupling-lambda
1860 * value describes fully-interacting VDW.
1862 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1863 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1865 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1867 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1873 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1876 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1878 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1880 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1883 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1884 std::string message = gmx::formatExceptionMessageToString(*ex);
1885 warning_error(wi_, message.c_str());
1890 std::string getOptionName(const gmx::KeyValueTreePath& context)
1892 if (mapping_ != nullptr)
1894 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1895 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1898 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1903 const gmx::IKeyValueTreeBackMapping* mapping_;
1908 void get_ir(const char* mdparin,
1909 const char* mdparout,
1910 gmx::MDModules* mdModules,
1913 WriteMdpHeader writeMdpHeader,
1917 double dumdub[2][6];
1919 char warn_buf[STRLEN];
1920 t_lambda* fep = ir->fepvals;
1921 t_expanded* expand = ir->expandedvals;
1923 const char* no_names[] = { "no", nullptr };
1925 init_inputrec_strings();
1926 gmx::TextInputFile stream(mdparin);
1927 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1929 snew(dumstr[0], STRLEN);
1930 snew(dumstr[1], STRLEN);
1932 /* ignore the following deprecated commands */
1933 replace_inp_entry(inp, "title", nullptr);
1934 replace_inp_entry(inp, "cpp", nullptr);
1935 replace_inp_entry(inp, "domain-decomposition", nullptr);
1936 replace_inp_entry(inp, "andersen-seed", nullptr);
1937 replace_inp_entry(inp, "dihre", nullptr);
1938 replace_inp_entry(inp, "dihre-fc", nullptr);
1939 replace_inp_entry(inp, "dihre-tau", nullptr);
1940 replace_inp_entry(inp, "nstdihreout", nullptr);
1941 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1942 replace_inp_entry(inp, "optimize-fft", nullptr);
1943 replace_inp_entry(inp, "adress_type", nullptr);
1944 replace_inp_entry(inp, "adress_const_wf", nullptr);
1945 replace_inp_entry(inp, "adress_ex_width", nullptr);
1946 replace_inp_entry(inp, "adress_hy_width", nullptr);
1947 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1948 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1949 replace_inp_entry(inp, "adress_site", nullptr);
1950 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1951 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1952 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1953 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1954 replace_inp_entry(inp, "rlistlong", nullptr);
1955 replace_inp_entry(inp, "nstcalclr", nullptr);
1956 replace_inp_entry(inp, "pull-print-com2", nullptr);
1957 replace_inp_entry(inp, "gb-algorithm", nullptr);
1958 replace_inp_entry(inp, "nstgbradii", nullptr);
1959 replace_inp_entry(inp, "rgbradii", nullptr);
1960 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1961 replace_inp_entry(inp, "gb-saltconc", nullptr);
1962 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1963 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1964 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1965 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1966 replace_inp_entry(inp, "sa-algorithm", nullptr);
1967 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1968 replace_inp_entry(inp, "ns-type", nullptr);
1970 /* replace the following commands with the clearer new versions*/
1971 replace_inp_entry(inp, "unconstrained-start", "continuation");
1972 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1973 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1974 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1975 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1976 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1977 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1979 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1980 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1981 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1982 setStringEntry(&inp, "include", opts->include, nullptr);
1983 printStringNoNewline(
1984 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1985 setStringEntry(&inp, "define", opts->define, nullptr);
1987 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1988 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1989 printStringNoNewline(&inp, "Start time and timestep in ps");
1990 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1991 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1992 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1993 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1994 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1995 printStringNoNewline(
1996 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1997 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1998 printStringNoNewline(&inp, "Multiple time-stepping");
1999 ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
2002 opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
2003 ir->mtsLevels.resize(2);
2004 gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
2005 opts->mtsLevel2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
2006 mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
2008 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2009 if (!EI_DYNAMICS(ir->eI))
2012 ir->mtsLevels.clear();
2015 printStringNoNewline(&inp, "mode for center of mass motion removal");
2016 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
2017 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2018 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2019 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2020 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2022 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2023 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2024 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2025 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2028 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2029 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2030 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2031 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2032 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2033 ir->niter = get_eint(&inp, "niter", 20, wi);
2034 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2035 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2036 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2037 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2038 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2040 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2041 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2043 /* Output options */
2044 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2045 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2046 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2047 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2048 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2049 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2050 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2051 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2052 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2053 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2054 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2055 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2056 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2057 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2058 printStringNoNewline(&inp, "default, all atoms will be written.");
2059 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2060 printStringNoNewline(&inp, "Selection of energy groups");
2061 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2063 /* Neighbor searching */
2064 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2065 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2066 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
2067 printStringNoNewline(&inp, "nblist update frequency");
2068 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2069 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2070 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2071 std::vector<const char*> pbcTypesNamesChar;
2072 for (const auto& pbcTypeName : c_pbcTypeNames)
2074 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2076 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2077 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
2078 printStringNoNewline(&inp,
2079 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2080 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2081 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2082 printStringNoNewline(&inp, "nblist cut-off");
2083 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2084 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2086 /* Electrostatics */
2087 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2088 printStringNoNewline(&inp, "Method for doing electrostatics");
2089 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
2090 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
2091 printStringNoNewline(&inp, "cut-off lengths");
2092 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2093 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2094 printStringNoNewline(&inp,
2095 "Relative dielectric constant for the medium and the reaction field");
2096 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2097 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2098 printStringNoNewline(&inp, "Method for doing Van der Waals");
2099 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
2100 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
2101 printStringNoNewline(&inp, "cut-off lengths");
2102 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2103 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2104 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2105 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
2106 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2107 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2108 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2109 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2110 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2111 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2112 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2113 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2114 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2115 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2116 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2117 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2118 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2119 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2120 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2121 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2122 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2124 /* Implicit solvation is no longer supported, but we need grompp
2125 to be able to refuse old .mdp files that would have built a tpr
2126 to run it. Thus, only "no" is accepted. */
2127 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2129 /* Coupling stuff */
2130 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2131 printStringNoNewline(&inp, "Temperature coupling");
2132 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2133 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2134 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2135 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2136 printStringNoNewline(&inp, "Groups to couple separately");
2137 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2138 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2139 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2140 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2141 printStringNoNewline(&inp, "pressure coupling");
2142 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2143 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2144 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2145 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2146 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2147 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2148 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2149 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2150 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2153 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2154 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2155 printStringNoNewline(&inp, "Groups treated with MiMiC");
2156 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2158 /* Simulated annealing */
2159 printStringNewline(&inp, "SIMULATED ANNEALING");
2160 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2161 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2162 printStringNoNewline(&inp,
2163 "Number of time points to use for specifying annealing in each group");
2164 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2165 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2166 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2167 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2168 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2171 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2172 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2173 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2174 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2177 printStringNewline(&inp, "OPTIONS FOR BONDS");
2178 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2179 printStringNoNewline(&inp, "Type of constraint algorithm");
2180 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2181 printStringNoNewline(&inp, "Do not constrain the start configuration");
2182 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2183 printStringNoNewline(&inp,
2184 "Use successive overrelaxation to reduce the number of shake iterations");
2185 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2186 printStringNoNewline(&inp, "Relative tolerance of shake");
2187 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2188 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2189 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2190 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2191 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2192 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2193 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2194 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2195 printStringNoNewline(&inp, "rotates over more degrees than");
2196 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2197 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2198 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2200 /* Energy group exclusions */
2201 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2202 printStringNoNewline(
2203 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2204 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2207 printStringNewline(&inp, "WALLS");
2208 printStringNoNewline(
2209 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2210 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2211 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2212 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2213 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2214 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2215 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2218 printStringNewline(&inp, "COM PULLING");
2219 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2222 ir->pull = std::make_unique<pull_params_t>();
2223 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2227 for (int c = 0; c < ir->pull->ncoord; c++)
2229 if (ir->pull->coord[c].eType == epullCONSTRAINT)
2232 "Constraint COM pulling is not supported in combination with "
2233 "multiple time stepping");
2241 NOTE: needs COM pulling or free energy input */
2242 printStringNewline(&inp, "AWH biasing");
2243 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2246 ir->awhParams = gmx::readAwhParams(&inp, wi);
2249 /* Enforced rotation */
2250 printStringNewline(&inp, "ENFORCED ROTATION");
2251 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2252 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2256 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2259 /* Interactive MD */
2261 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2262 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2263 if (inputrecStrings->imd_grp[0] != '\0')
2270 printStringNewline(&inp, "NMR refinement stuff");
2271 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2272 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2273 printStringNoNewline(
2274 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2275 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2276 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2277 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2278 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2279 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2280 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2281 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2282 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2283 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2284 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2285 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2286 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2287 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2288 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2289 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2291 /* free energy variables */
2292 printStringNewline(&inp, "Free energy variables");
2293 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2294 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2295 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2296 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2297 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2299 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2301 it was not entered */
2302 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2303 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2304 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2305 setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
2306 setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
2307 setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
2308 setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
2309 setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
2310 setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
2311 setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
2312 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2313 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2314 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2315 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2316 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2317 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2318 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2319 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2320 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2321 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2322 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2323 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2324 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2325 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2327 /* Non-equilibrium MD stuff */
2328 printStringNewline(&inp, "Non-equilibrium MD stuff");
2329 setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
2330 setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
2331 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2332 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2333 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2334 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2336 /* simulated tempering variables */
2337 printStringNewline(&inp, "simulated tempering variables");
2338 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2339 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2340 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2341 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2343 /* expanded ensemble variables */
2344 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2346 read_expandedparams(&inp, expand, wi);
2349 /* Electric fields */
2351 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2352 gmx::KeyValueTreeTransformer transform;
2353 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2354 mdModules->initMdpTransform(transform.rules());
2355 for (const auto& path : transform.mappedPaths())
2357 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2358 mark_einp_set(inp, path[0].c_str());
2360 MdpErrorHandler errorHandler(wi);
2361 auto result = transform.transform(convertedValues, &errorHandler);
2362 ir->params = new gmx::KeyValueTreeObject(result.object());
2363 mdModules->adjustInputrecBasedOnModules(ir);
2364 errorHandler.setBackMapping(result.backMapping());
2365 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2368 /* Ion/water position swapping ("computational electrophysiology") */
2369 printStringNewline(&inp,
2370 "Ion/water position swapping for computational electrophysiology setups");
2371 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2372 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2373 if (ir->eSwapCoords != eswapNO)
2380 printStringNoNewline(&inp, "Swap attempt frequency");
2381 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2382 printStringNoNewline(&inp, "Number of ion types to be controlled");
2383 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2386 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2388 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2389 snew(ir->swap->grp, ir->swap->ngrp);
2390 for (i = 0; i < ir->swap->ngrp; i++)
2392 snew(ir->swap->grp[i].molname, STRLEN);
2394 printStringNoNewline(&inp,
2395 "Two index groups that contain the compartment-partitioning atoms");
2396 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2397 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2398 printStringNoNewline(&inp,
2399 "Use center of mass of split groups (yes/no), otherwise center of "
2400 "geometry is used");
2401 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2402 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2404 printStringNoNewline(&inp, "Name of solvent molecules");
2405 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2407 printStringNoNewline(&inp,
2408 "Split cylinder: radius, upper and lower extension (nm) (this will "
2409 "define the channels)");
2410 printStringNoNewline(&inp,
2411 "Note that the split cylinder settings do not have an influence on "
2412 "the swapping protocol,");
2413 printStringNoNewline(
2415 "however, if correctly defined, the permeation events are recorded per channel");
2416 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2417 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2418 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2419 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2420 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2421 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2423 printStringNoNewline(
2425 "Average the number of ions per compartment over these many swap attempt steps");
2426 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2428 printStringNoNewline(
2429 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2430 printStringNoNewline(
2431 &inp, "and the requested number of ions of this type in compartments A and B");
2432 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2433 for (i = 0; i < nIonTypes; i++)
2435 int ig = eSwapFixedGrpNR + i;
2437 sprintf(buf, "iontype%d-name", i);
2438 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2439 sprintf(buf, "iontype%d-in-A", i);
2440 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2441 sprintf(buf, "iontype%d-in-B", i);
2442 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2445 printStringNoNewline(
2447 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2448 printStringNoNewline(
2450 "at maximum distance (= bulk concentration) to the split group layers. However,");
2451 printStringNoNewline(&inp,
2452 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2453 "layer from the middle at 0.0");
2454 printStringNoNewline(&inp,
2455 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2456 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2457 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2458 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2459 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2461 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2464 printStringNoNewline(
2465 &inp, "Start to swap ions if threshold difference to requested count is reached");
2466 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2469 /* AdResS is no longer supported, but we need grompp to be able to
2470 refuse to process old .mdp files that used it. */
2471 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2473 /* User defined thingies */
2474 printStringNewline(&inp, "User defined thingies");
2475 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2476 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2477 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2478 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2479 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2480 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2481 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2482 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2483 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2484 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2488 gmx::TextOutputFile stream(mdparout);
2489 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2491 // Transform module data into a flat key-value tree for output.
2492 gmx::KeyValueTreeBuilder builder;
2493 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2494 mdModules->buildMdpOutput(&builderObject);
2496 gmx::TextWriter writer(&stream);
2497 writeKeyValueTreeAsMdp(&writer, builder.build());
2502 /* Process options if necessary */
2503 for (m = 0; m < 2; m++)
2505 for (i = 0; i < 2 * DIM; i++)
2514 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2518 "Pressure coupling incorrect number of values (I need exactly 1)");
2520 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2522 case epctSEMIISOTROPIC:
2523 case epctSURFACETENSION:
2524 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2528 "Pressure coupling incorrect number of values (I need exactly 2)");
2530 dumdub[m][YY] = dumdub[m][XX];
2532 case epctANISOTROPIC:
2533 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2534 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2539 "Pressure coupling incorrect number of values (I need exactly 6)");
2543 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2544 epcoupltype_names[ir->epct]);
2548 clear_mat(ir->ref_p);
2549 clear_mat(ir->compress);
2550 for (i = 0; i < DIM; i++)
2552 ir->ref_p[i][i] = dumdub[1][i];
2553 ir->compress[i][i] = dumdub[0][i];
2555 if (ir->epct == epctANISOTROPIC)
2557 ir->ref_p[XX][YY] = dumdub[1][3];
2558 ir->ref_p[XX][ZZ] = dumdub[1][4];
2559 ir->ref_p[YY][ZZ] = dumdub[1][5];
2560 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2563 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2564 "apply a threefold shear stress?\n");
2566 ir->compress[XX][YY] = dumdub[0][3];
2567 ir->compress[XX][ZZ] = dumdub[0][4];
2568 ir->compress[YY][ZZ] = dumdub[0][5];
2569 for (i = 0; i < DIM; i++)
2571 for (m = 0; m < i; m++)
2573 ir->ref_p[i][m] = ir->ref_p[m][i];
2574 ir->compress[i][m] = ir->compress[m][i];
2579 if (ir->comm_mode == ecmNO)
2584 opts->couple_moltype = nullptr;
2585 if (strlen(inputrecStrings->couple_moltype) > 0)
2587 if (ir->efep != efepNO)
2589 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2590 if (opts->couple_lam0 == opts->couple_lam1)
2592 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2594 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2598 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2605 "Free energy is turned off, so we will not decouple the molecule listed "
2609 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2610 if (ir->efep != efepNO)
2612 if (fep->delta_lambda != 0)
2614 ir->efep = efepSLOWGROWTH;
2618 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2620 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2622 "Old option for dhdl-print-energy given: "
2623 "changing \"yes\" to \"total\"\n");
2626 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2628 /* always print out the energy to dhdl if we are doing
2629 expanded ensemble, since we need the total energy for
2630 analysis if the temperature is changing. In some
2631 conditions one may only want the potential energy, so
2632 we will allow that if the appropriate mdp setting has
2633 been enabled. Otherwise, total it is:
2635 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2638 if ((ir->efep != efepNO) || ir->bSimTemp)
2640 ir->bExpanded = FALSE;
2641 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2643 ir->bExpanded = TRUE;
2645 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2646 if (ir->bSimTemp) /* done after fep params */
2648 do_simtemp_params(ir);
2651 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2652 * setup and not on the old way of specifying the free-energy setup,
2653 * we should check for using soft-core when not needed, since that
2654 * can complicate the sampling significantly.
2655 * Note that we only check for the automated coupling setup.
2656 * If the (advanced) user does FEP through manual topology changes,
2657 * this check will not be triggered.
2659 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2660 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2663 "You are using soft-core interactions while the Van der Waals interactions are "
2664 "not decoupled (note that the sc-coul option is only active when using lambda "
2665 "states). Although this will not lead to errors, you will need much more "
2666 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2671 ir->fepvals->n_lambda = 0;
2674 /* WALL PARAMETERS */
2676 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2678 /* ORIENTATION RESTRAINT PARAMETERS */
2680 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2682 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2685 /* DEFORMATION PARAMETERS */
2687 clear_mat(ir->deform);
2688 for (i = 0; i < 6; i++)
2693 double gmx_unused canary;
2694 int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
2695 &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
2696 &(dumdub[0][5]), &canary);
2698 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2702 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2703 inputrecStrings->deform)
2706 for (i = 0; i < 3; i++)
2708 ir->deform[i][i] = dumdub[0][i];
2710 ir->deform[YY][XX] = dumdub[0][3];
2711 ir->deform[ZZ][XX] = dumdub[0][4];
2712 ir->deform[ZZ][YY] = dumdub[0][5];
2713 if (ir->epc != epcNO)
2715 for (i = 0; i < 3; i++)
2717 for (j = 0; j <= i; j++)
2719 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2721 warning_error(wi, "A box element has deform set and compressibility > 0");
2725 for (i = 0; i < 3; i++)
2727 for (j = 0; j < i; j++)
2729 if (ir->deform[i][j] != 0)
2731 for (m = j; m < DIM; m++)
2733 if (ir->compress[m][j] != 0)
2736 "An off-diagonal box element has deform set while "
2737 "compressibility > 0 for the same component of another box "
2738 "vector, this might lead to spurious periodicity effects.");
2739 warning(wi, warn_buf);
2747 /* Ion/water position swapping checks */
2748 if (ir->eSwapCoords != eswapNO)
2750 if (ir->swap->nstswap < 1)
2752 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2754 if (ir->swap->nAverage < 1)
2756 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2758 if (ir->swap->threshold < 1.0)
2760 warning_error(wi, "Ion count threshold must be at least 1.\n");
2764 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2767 setupMtsLevels(ir->mtsLevels, *ir, *opts, wi);
2772 gmx::checkAwhParams(ir->awhParams, ir, wi);
2779 /* We would like gn to be const as well, but C doesn't allow this */
2780 /* TODO this is utility functionality (search for the index of a
2781 string in a collection), so should be refactored and located more
2783 int search_string(const char* s, int ng, char* gn[])
2787 for (i = 0; (i < ng); i++)
2789 if (gmx_strcasecmp(s, gn[i]) == 0)
2796 "Group %s referenced in the .mdp file was not found in the index file.\n"
2797 "Group names must match either [moleculetype] names or custom index group\n"
2798 "names, in which case you must supply an index file to the '-n' option\n"
2803 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2805 /* Now go over the atoms in the group */
2806 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2808 int aj = block.a[j];
2810 /* Range checking */
2811 if ((aj < 0) || (aj >= natoms))
2813 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2818 static void do_numbering(int natoms,
2819 SimulationGroups* groups,
2820 gmx::ArrayRef<std::string> groupsFromMdpFile,
2823 SimulationAtomGroupType gtype,
2829 unsigned short* cbuf;
2830 AtomGroupIndices* grps = &(groups->groups[gtype]);
2833 char warn_buf[STRLEN];
2835 title = shortName(gtype);
2838 /* Mark all id's as not set */
2839 for (int i = 0; (i < natoms); i++)
2844 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2846 /* Lookup the group name in the block structure */
2847 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2848 if ((grptp != egrptpONE) || (i == 0))
2850 grps->emplace_back(gid);
2852 GMX_ASSERT(block, "Can't have a nullptr block");
2853 atomGroupRangeValidation(natoms, gid, *block);
2854 /* Now go over the atoms in the group */
2855 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2857 const int aj = block->a[j];
2858 /* Lookup up the old group number */
2859 const int ognr = cbuf[aj];
2862 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2867 /* Store the group number in buffer */
2868 if (grptp == egrptpONE)
2881 /* Now check whether we have done all atoms */
2884 if (grptp == egrptpALL)
2886 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2888 else if (grptp == egrptpPART)
2890 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2891 warning_note(wi, warn_buf);
2893 /* Assign all atoms currently unassigned to a rest group */
2894 for (int j = 0; (j < natoms); j++)
2896 if (cbuf[j] == NOGID)
2898 cbuf[j] = grps->size();
2901 if (grptp != egrptpPART)
2905 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2908 /* Add group name "rest" */
2909 grps->emplace_back(restnm);
2911 /* Assign the rest name to all atoms not currently assigned to a group */
2912 for (int j = 0; (j < natoms); j++)
2914 if (cbuf[j] == NOGID)
2916 // group size was not updated before this here, so need to use -1.
2917 cbuf[j] = grps->size() - 1;
2923 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2925 /* All atoms are part of one (or no) group, no index required */
2926 groups->groupNumbers[gtype].clear();
2930 for (int j = 0; (j < natoms); j++)
2932 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2939 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2942 pull_params_t* pull;
2943 int natoms, imin, jmin;
2944 int * nrdf2, *na_vcm, na_tot;
2945 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2950 * First calc 3xnr-atoms for each group
2951 * then subtract half a degree of freedom for each constraint
2953 * Only atoms and nuclei contribute to the degrees of freedom...
2958 const SimulationGroups& groups = mtop->groups;
2959 natoms = mtop->natoms;
2961 /* Allocate one more for a possible rest group */
2962 /* We need to sum degrees of freedom into doubles,
2963 * since floats give too low nrdf's above 3 million atoms.
2965 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2966 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2967 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2968 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2969 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2971 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2975 for (gmx::index i = 0;
2976 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2979 clear_ivec(dof_vcm[i]);
2981 nrdf_vcm_sub[i] = 0;
2983 snew(nrdf2, natoms);
2984 for (const AtomProxy atomP : AtomRange(*mtop))
2986 const t_atom& local = atomP.atom();
2987 int i = atomP.globalAtomNumber();
2989 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2991 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2992 for (int d = 0; d < DIM; d++)
2994 if (opts->nFreeze[g][d] == 0)
2996 /* Add one DOF for particle i (counted as 2*1) */
2998 /* VCM group i has dim d as a DOF */
2999 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3003 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3005 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3011 for (const gmx_molblock_t& molb : mtop->molblock)
3013 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3014 const t_atom* atom = molt.atoms.atom;
3015 for (int mol = 0; mol < molb.nmol; mol++)
3017 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3019 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3020 for (int i = 0; i < molt.ilist[ftype].size();)
3022 /* Subtract degrees of freedom for the constraints,
3023 * if the particles still have degrees of freedom left.
3024 * If one of the particles is a vsite or a shell, then all
3025 * constraint motion will go there, but since they do not
3026 * contribute to the constraints the degrees of freedom do not
3029 int ai = as + ia[i + 1];
3030 int aj = as + ia[i + 2];
3031 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
3032 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
3050 imin = std::min(imin, nrdf2[ai]);
3051 jmin = std::min(jmin, nrdf2[aj]);
3054 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3056 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3058 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3060 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3063 i += interaction_function[ftype].nratoms + 1;
3066 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3067 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3069 /* Subtract 1 dof from every atom in the SETTLE */
3070 for (int j = 0; j < 3; j++)
3072 int ai = as + ia[i + 1 + j];
3073 imin = std::min(2, nrdf2[ai]);
3075 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3077 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3082 as += molt.atoms.nr;
3088 /* Correct nrdf for the COM constraints.
3089 * We correct using the TC and VCM group of the first atom
3090 * in the reference and pull group. If atoms in one pull group
3091 * belong to different TC or VCM groups it is anyhow difficult
3092 * to determine the optimal nrdf assignment.
3094 pull = ir->pull.get();
3096 for (int i = 0; i < pull->ncoord; i++)
3098 if (pull->coord[i].eType != epullCONSTRAINT)
3105 for (int j = 0; j < 2; j++)
3107 const t_pull_group* pgrp;
3109 pgrp = &pull->group[pull->coord[i].group[j]];
3111 if (!pgrp->ind.empty())
3113 /* Subtract 1/2 dof from each group */
3114 int ai = pgrp->ind[0];
3115 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3117 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3119 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3122 "Center of mass pulling constraints caused the number of degrees "
3123 "of freedom for temperature coupling group %s to be negative",
3124 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3125 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3130 /* We need to subtract the whole DOF from group j=1 */
3137 if (ir->nstcomm != 0)
3139 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3140 "Expect at least one group when removing COM motion");
3142 /* We remove COM motion up to dim ndof_com() */
3143 const int ndim_rm_vcm = ndof_com(ir);
3145 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3146 * the number of degrees of freedom in each vcm group when COM
3147 * translation is removed and 6 when rotation is removed as well.
3148 * Note that we do not and should not include the rest group here.
3150 for (gmx::index j = 0;
3151 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3153 switch (ir->comm_mode)
3156 case ecmLINEAR_ACCELERATION_CORRECTION:
3157 nrdf_vcm_sub[j] = 0;
3158 for (int d = 0; d < ndim_rm_vcm; d++)
3166 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3167 default: gmx_incons("Checking comm_mode");
3171 for (gmx::index i = 0;
3172 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3174 /* Count the number of atoms of TC group i for every VCM group */
3175 for (gmx::index j = 0;
3176 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3181 for (int ai = 0; ai < natoms; ai++)
3183 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3185 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3189 /* Correct for VCM removal according to the fraction of each VCM
3190 * group present in this TC group.
3192 nrdf_uc = nrdf_tc[i];
3194 for (gmx::index j = 0;
3195 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3197 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3199 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3200 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3205 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3207 opts->nrdf[i] = nrdf_tc[i];
3208 if (opts->nrdf[i] < 0)
3212 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3213 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3221 sfree(nrdf_vcm_sub);
3224 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3226 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3227 * But since this is much larger than STRLEN, such a line can not be parsed.
3228 * The real maximum is the number of names that fit in a string: STRLEN/2.
3230 #define EGP_MAX (STRLEN / 2)
3234 auto names = gmx::splitString(val);
3235 if (names.size() % 2 != 0)
3237 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3239 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3241 for (size_t i = 0; i < names.size() / 2; i++)
3243 // TODO this needs to be replaced by a solution using std::find_if
3247 names[2 * i].c_str(),
3248 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3254 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3259 names[2 * i + 1].c_str(),
3260 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3266 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3268 if ((j < nr) && (k < nr))
3270 ir->opts.egp_flags[nr * j + k] |= flag;
3271 ir->opts.egp_flags[nr * k + j] |= flag;
3280 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3282 int ig = -1, i = 0, gind;
3286 /* Just a quick check here, more thorough checks are in mdrun */
3287 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3289 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3292 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3293 for (ig = 0; ig < swap->ngrp; ig++)
3295 swapg = &swap->grp[ig];
3296 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3297 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3301 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3302 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3303 snew(swapg->ind, swapg->nat);
3304 for (i = 0; i < swapg->nat; i++)
3306 swapg->ind[i] = grps->a[grps->index[gind] + i];
3311 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3317 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3322 ig = search_string(IMDgname, grps->nr, gnames);
3323 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3325 if (IMDgroup->nat > 0)
3328 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3330 IMDgname, IMDgroup->nat);
3331 snew(IMDgroup->ind, IMDgroup->nat);
3332 for (i = 0; i < IMDgroup->nat; i++)
3334 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3339 /* Checks whether atoms are both part of a COM removal group and frozen.
3340 * If a fully frozen atom is part of a COM removal group, it is removed
3341 * from the COM removal group. A note is issued if such atoms are present.
3342 * A warning is issued for atom with one or two dimensions frozen that
3343 * are part of a COM removal group (mdrun would need to compute COM mass
3344 * per dimension to handle this correctly).
3345 * Also issues a warning when non-frozen atoms are not part of a COM
3346 * removal group while COM removal is active.
3348 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3350 const t_grpopts& opts,
3353 const int vcmRestGroup =
3354 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3356 int numFullyFrozenVcmAtoms = 0;
3357 int numPartiallyFrozenVcmAtoms = 0;
3358 int numNonVcmAtoms = 0;
3359 for (int a = 0; a < numAtoms; a++)
3361 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3362 int numFrozenDims = 0;
3363 for (int d = 0; d < DIM; d++)
3365 numFrozenDims += opts.nFreeze[freezeGroup][d];
3368 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3369 if (vcmGroup < vcmRestGroup)
3371 if (numFrozenDims == DIM)
3373 /* Do not remove COM motion for this fully frozen atom */
3374 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3376 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3379 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3380 numFullyFrozenVcmAtoms++;
3382 else if (numFrozenDims > 0)
3384 numPartiallyFrozenVcmAtoms++;
3387 else if (numFrozenDims < DIM)
3393 if (numFullyFrozenVcmAtoms > 0)
3395 std::string warningText = gmx::formatString(
3396 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3397 "removing these atoms from the COMM removal group(s)",
3398 numFullyFrozenVcmAtoms);
3399 warning_note(wi, warningText.c_str());
3401 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3403 std::string warningText = gmx::formatString(
3404 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3405 "removal group(s), due to limitations in the code these still contribute to the "
3406 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3408 numPartiallyFrozenVcmAtoms, DIM);
3409 warning(wi, warningText.c_str());
3411 if (numNonVcmAtoms > 0)
3413 std::string warningText = gmx::formatString(
3414 "%d atoms are not part of any center of mass motion removal group.\n"
3415 "This may lead to artifacts.\n"
3416 "In most cases one should use one group for the whole system.",
3418 warning(wi, warningText.c_str());
3422 void do_index(const char* mdparin,
3426 const gmx::MdModulesNotifier& notifier,
3430 t_blocka* defaultIndexGroups;
3438 int i, j, k, restnm;
3439 bool bExcl, bTable, bAnneal;
3440 char warn_buf[STRLEN];
3444 fprintf(stderr, "processing index file...\n");
3448 snew(defaultIndexGroups, 1);
3449 snew(defaultIndexGroups->index, 1);
3451 atoms_all = gmx_mtop_global_atoms(mtop);
3452 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3453 done_atom(&atoms_all);
3457 defaultIndexGroups = init_index(ndx, &gnames);
3460 SimulationGroups* groups = &mtop->groups;
3461 natoms = mtop->natoms;
3462 symtab = &mtop->symtab;
3464 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3466 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3468 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3469 restnm = groups->groupNames.size() - 1;
3470 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3471 srenew(gnames, defaultIndexGroups->nr + 1);
3472 gnames[restnm] = *(groups->groupNames.back());
3474 set_warning_line(wi, mdparin, -1);
3476 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3477 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3478 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3479 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3480 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3483 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3485 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3486 temperatureCouplingTauValues.size());
3489 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3490 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3491 SimulationAtomGroupType::TemperatureCoupling, restnm,
3492 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3493 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3495 snew(ir->opts.nrdf, nr);
3496 snew(ir->opts.tau_t, nr);
3497 snew(ir->opts.ref_t, nr);
3498 if (ir->eI == eiBD && ir->bd_fric == 0)
3500 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3503 if (useReferenceTemperature)
3505 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3507 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3511 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3512 for (i = 0; (i < nr); i++)
3514 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3516 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3517 warning_error(wi, warn_buf);
3520 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3524 "tau-t = -1 is the value to signal that a group should not have "
3525 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3528 if (ir->opts.tau_t[i] >= 0)
3530 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3533 if (ir->etc != etcNO && ir->nsttcouple == -1)
3535 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3540 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3543 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3544 "md-vv; use either vrescale temperature with berendsen pressure or "
3545 "Nose-Hoover temperature with MTTK pressure");
3547 if (ir->epc == epcMTTK)
3549 if (ir->etc != etcNOSEHOOVER)
3552 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3557 if (ir->nstpcouple != ir->nsttcouple)
3559 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3560 ir->nstpcouple = ir->nsttcouple = mincouple;
3562 "for current Trotter decomposition methods with vv, nsttcouple and "
3563 "nstpcouple must be equal. Both have been reset to "
3564 "min(nsttcouple,nstpcouple) = %d",
3566 warning_note(wi, warn_buf);
3571 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3572 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3574 if (ETC_ANDERSEN(ir->etc))
3576 if (ir->nsttcouple != 1)
3580 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3581 "need for larger nsttcouple > 1, since no global parameters are computed. "
3582 "nsttcouple has been reset to 1");
3583 warning_note(wi, warn_buf);
3586 nstcmin = tcouple_min_integration_steps(ir->etc);
3589 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3592 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3593 "least %d times larger than nsttcouple*dt (%g)",
3594 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3595 warning(wi, warn_buf);
3598 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3599 for (i = 0; (i < nr); i++)
3601 if (ir->opts.ref_t[i] < 0)
3603 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3606 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3607 if we are in this conditional) if mc_temp is negative */
3608 if (ir->expandedvals->mc_temp < 0)
3610 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3614 /* Simulated annealing for each group. There are nr groups */
3615 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3616 if (simulatedAnnealingGroupNames.size() == 1
3617 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3619 simulatedAnnealingGroupNames.resize(0);
3621 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3623 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3624 simulatedAnnealingGroupNames.size(), nr);
3628 snew(ir->opts.annealing, nr);
3629 snew(ir->opts.anneal_npoints, nr);
3630 snew(ir->opts.anneal_time, nr);
3631 snew(ir->opts.anneal_temp, nr);
3632 for (i = 0; i < nr; i++)
3634 ir->opts.annealing[i] = eannNO;
3635 ir->opts.anneal_npoints[i] = 0;
3636 ir->opts.anneal_time[i] = nullptr;
3637 ir->opts.anneal_temp[i] = nullptr;
3639 if (!simulatedAnnealingGroupNames.empty())
3642 for (i = 0; i < nr; i++)
3644 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3646 ir->opts.annealing[i] = eannNO;
3648 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3650 ir->opts.annealing[i] = eannSINGLE;
3653 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3655 ir->opts.annealing[i] = eannPERIODIC;
3661 /* Read the other fields too */
3662 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3663 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3665 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3666 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3668 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3669 size_t numSimulatedAnnealingFields = 0;
3670 for (i = 0; i < nr; i++)
3672 if (ir->opts.anneal_npoints[i] == 1)
3676 "Please specify at least a start and an end point for annealing\n");
3678 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3679 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3680 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3683 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3685 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3687 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3688 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3690 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3691 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3693 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3694 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3697 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3698 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3699 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3700 allSimulatedAnnealingTimes.data());
3701 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3702 allSimulatedAnnealingTemperatures.data());
3703 for (i = 0, k = 0; i < nr; i++)
3705 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3707 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3708 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3711 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3713 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3719 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3722 "Annealing timepoints out of order: t=%f comes after "
3724 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3727 if (ir->opts.anneal_temp[i][j] < 0)
3729 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3730 ir->opts.anneal_temp[i][j]);
3735 /* Print out some summary information, to make sure we got it right */
3736 for (i = 0; i < nr; i++)
3738 if (ir->opts.annealing[i] != eannNO)
3740 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3741 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3742 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3743 ir->opts.anneal_npoints[i]);
3744 fprintf(stderr, "Time (ps) Temperature (K)\n");
3745 /* All terms except the last one */
3746 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3748 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3749 ir->opts.anneal_temp[i][j]);
3752 /* Finally the last one */
3753 j = ir->opts.anneal_npoints[i] - 1;
3754 if (ir->opts.annealing[i] == eannSINGLE)
3756 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3757 ir->opts.anneal_temp[i][j]);
3761 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3762 ir->opts.anneal_temp[i][j]);
3763 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3766 "There is a temperature jump when your annealing "
3778 for (int i = 1; i < ir->pull->ngroup; i++)
3780 const int gid = search_string(inputrecStrings->pullGroupNames[i].c_str(),
3781 defaultIndexGroups->nr, gnames);
3782 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3783 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3786 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3788 checkPullCoords(ir->pull->group, ir->pull->coord);
3793 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3796 if (ir->eSwapCoords != eswapNO)
3798 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3801 /* Make indices for IMD session */
3804 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3807 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3808 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3809 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3811 auto accelerations = gmx::splitString(inputrecStrings->acc);
3812 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
3813 if (accelerationGroupNames.size() * DIM != accelerations.size())
3815 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3816 accelerationGroupNames.size(), accelerations.size());
3818 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3819 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3820 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3821 snew(ir->opts.acc, nr);
3822 ir->opts.ngacc = nr;
3824 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3826 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3827 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3828 if (freezeDims.size() != DIM * freezeGroupNames.size())
3830 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3831 freezeGroupNames.size(), freezeDims.size());
3833 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3834 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3835 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3836 ir->opts.ngfrz = nr;
3837 snew(ir->opts.nFreeze, nr);
3838 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3840 for (j = 0; (j < DIM); j++, k++)
3842 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3843 if (!ir->opts.nFreeze[i][j])
3845 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3848 "Please use Y(ES) or N(O) for freezedim only "
3850 freezeDims[k].c_str());
3851 warning(wi, warn_buf);
3856 for (; (i < nr); i++)
3858 for (j = 0; (j < DIM); j++)
3860 ir->opts.nFreeze[i][j] = 0;
3864 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3865 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3866 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3867 add_wall_energrps(groups, ir->nwall, symtab);
3868 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3869 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3870 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3871 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3872 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3874 if (ir->comm_mode != ecmNO)
3876 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3879 /* Now we have filled the freeze struct, so we can calculate NRDF */
3880 calc_nrdf(mtop, ir, gnames);
3882 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3883 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3884 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3885 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3886 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3887 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3888 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3889 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3890 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3891 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3892 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3893 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3896 /* MiMiC QMMM input processing */
3897 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3898 if (qmGroupNames.size() > 1)
3900 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3902 /* group rest, if any, is always MM! */
3903 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3904 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3905 ir->opts.ngQM = qmGroupNames.size();
3907 /* end of MiMiC QMMM input */
3911 for (auto group : gmx::keysOf(groups->groups))
3913 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3914 for (const auto& entry : groups->groups[group])
3916 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3918 fprintf(stderr, "\n");
3922 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3923 snew(ir->opts.egp_flags, nr * nr);
3925 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
3926 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3928 warning_error(wi, "Energy group exclusions are currently not supported");
3930 if (bExcl && EEL_FULL(ir->coulombtype))
3932 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3935 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
3936 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3937 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3940 "Can only have energy group pair tables in combination with user tables for VdW "
3944 /* final check before going out of scope if simulated tempering variables
3945 * need to be set to default values.
3947 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3949 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3950 warning(wi, gmx::formatString(
3951 "the value for nstexpanded was not specified for "
3952 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3953 "by default, but it is recommended to set it to an explicit value!",
3954 ir->expandedvals->nstexpanded));
3956 for (i = 0; (i < defaultIndexGroups->nr); i++)
3961 done_blocka(defaultIndexGroups);
3962 sfree(defaultIndexGroups);
3966 static void check_disre(const gmx_mtop_t* mtop)
3968 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3970 const gmx_ffparams_t& ffparams = mtop->ffparams;
3973 for (int i = 0; i < ffparams.numTypes(); i++)
3975 int ftype = ffparams.functype[i];
3976 if (ftype == F_DISRES)
3978 int label = ffparams.iparams[i].disres.label;
3979 if (label == old_label)
3981 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3990 "Found %d double distance restraint indices,\n"
3991 "probably the parameters for multiple pairs in one restraint "
3992 "are not identical\n",
3998 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
4001 gmx_mtop_ilistloop_t iloop;
4003 const t_iparams* pr;
4010 for (d = 0; d < DIM; d++)
4012 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
4014 /* Check for freeze groups */
4015 for (g = 0; g < ir->opts.ngfrz; g++)
4017 for (d = 0; d < DIM; d++)
4019 if (ir->opts.nFreeze[g][d] != 0)
4027 /* Check for position restraints */
4028 iloop = gmx_mtop_ilistloop_init(sys);
4029 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4031 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4033 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4035 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4036 for (d = 0; d < DIM; d++)
4038 if (pr->posres.fcA[d] != 0)
4044 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4046 /* Check for flat-bottom posres */
4047 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4048 if (pr->fbposres.k != 0)
4050 switch (pr->fbposres.geom)
4052 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4053 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4054 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4055 case efbposresCYLINDER:
4056 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4057 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4058 case efbposresX: /* d=XX */
4059 case efbposresY: /* d=YY */
4060 case efbposresZ: /* d=ZZ */
4061 d = pr->fbposres.geom - efbposresX;
4066 " Invalid geometry for flat-bottom position restraint.\n"
4067 "Expected nr between 1 and %d. Found %d\n",
4068 efbposresNR - 1, pr->fbposres.geom);
4075 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4078 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4080 bool* bC6ParametersWorkWithGeometricRules,
4081 bool* bC6ParametersWorkWithLBRules,
4082 bool* bLBRulesPossible)
4084 int ntypes, tpi, tpj;
4087 double c6i, c6j, c12i, c12j;
4088 double c6, c6_geometric, c6_LB;
4089 double sigmai, sigmaj, epsi, epsj;
4090 bool bCanDoLBRules, bCanDoGeometricRules;
4093 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4094 * force-field floating point parameters.
4097 ptr = getenv("GMX_LJCOMB_TOL");
4101 double gmx_unused canary;
4103 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4106 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4111 *bC6ParametersWorkWithLBRules = TRUE;
4112 *bC6ParametersWorkWithGeometricRules = TRUE;
4113 bCanDoLBRules = TRUE;
4114 ntypes = mtop->ffparams.atnr;
4115 snew(typecount, ntypes);
4116 gmx_mtop_count_atomtypes(mtop, state, typecount);
4117 *bLBRulesPossible = TRUE;
4118 for (tpi = 0; tpi < ntypes; ++tpi)
4120 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4121 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4122 for (tpj = tpi; tpj < ntypes; ++tpj)
4124 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4125 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4126 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4127 c6_geometric = std::sqrt(c6i * c6j);
4128 if (!gmx_numzero(c6_geometric))
4130 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4132 sigmai = gmx::sixthroot(c12i / c6i);
4133 sigmaj = gmx::sixthroot(c12j / c6j);
4134 epsi = c6i * c6i / (4.0 * c12i);
4135 epsj = c6j * c6j / (4.0 * c12j);
4136 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4140 *bLBRulesPossible = FALSE;
4141 c6_LB = c6_geometric;
4143 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4148 *bC6ParametersWorkWithLBRules = FALSE;
4151 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4153 if (!bCanDoGeometricRules)
4155 *bC6ParametersWorkWithGeometricRules = FALSE;
4162 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4164 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4166 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4167 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4168 if (ir->ljpme_combination_rule == eljpmeLB)
4170 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4173 "You are using arithmetic-geometric combination rules "
4174 "in LJ-PME, but your non-bonded C6 parameters do not "
4175 "follow these rules.");
4180 if (!bC6ParametersWorkWithGeometricRules)
4182 if (ir->eDispCorr != edispcNO)
4185 "You are using geometric combination rules in "
4186 "LJ-PME, but your non-bonded C6 parameters do "
4187 "not follow these rules. "
4188 "This will introduce very small errors in the forces and energies in "
4189 "your simulations. Dispersion correction will correct total energy "
4190 "and/or pressure for isotropic systems, but not forces or surface "
4196 "You are using geometric combination rules in "
4197 "LJ-PME, but your non-bonded C6 parameters do "
4198 "not follow these rules. "
4199 "This will introduce very small errors in the forces and energies in "
4200 "your simulations. If your system is homogeneous, consider using "
4201 "dispersion correction "
4202 "for the total energy and pressure.");
4208 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4210 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4211 gmx::assertMtsRequirements(*ir);
4213 char err_buf[STRLEN];
4218 gmx_mtop_atomloop_block_t aloopb;
4220 char warn_buf[STRLEN];
4222 set_warning_line(wi, mdparin, -1);
4224 if (absolute_reference(ir, sys, false, AbsRef))
4227 "Removing center of mass motion in the presence of position restraints might "
4228 "cause artifacts. When you are using position restraints to equilibrate a "
4229 "macro-molecule, the artifacts are usually negligible.");
4232 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4233 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4235 /* Check if a too small Verlet buffer might potentially
4236 * cause more drift than the thermostat can couple off.
4238 /* Temperature error fraction for warning and suggestion */
4239 const real T_error_warn = 0.002;
4240 const real T_error_suggest = 0.001;
4241 /* For safety: 2 DOF per atom (typical with constraints) */
4242 const real nrdf_at = 2;
4243 real T, tau, max_T_error;
4248 for (i = 0; i < ir->opts.ngtc; i++)
4250 T = std::max(T, ir->opts.ref_t[i]);
4251 tau = std::max(tau, ir->opts.tau_t[i]);
4255 /* This is a worst case estimate of the temperature error,
4256 * assuming perfect buffer estimation and no cancelation
4257 * of errors. The factor 0.5 is because energy distributes
4258 * equally over Ekin and Epot.
4260 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4261 if (max_T_error > T_error_warn)
4264 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4265 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4266 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4267 "%.0e or decrease tau_t.",
4268 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4269 ir->verletbuf_tol * T_error_suggest / max_T_error);
4270 warning(wi, warn_buf);
4275 if (ETC_ANDERSEN(ir->etc))
4279 for (i = 0; i < ir->opts.ngtc; i++)
4282 "all tau_t must currently be equal using Andersen temperature control, "
4283 "violated for group %d",
4285 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4287 "all tau_t must be positive using Andersen temperature control, "
4289 i, ir->opts.tau_t[i]);
4290 CHECK(ir->opts.tau_t[i] < 0);
4293 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4295 for (i = 0; i < ir->opts.ngtc; i++)
4297 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4299 "tau_t/delta_t for group %d for temperature control method %s must be a "
4300 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4301 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4303 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4304 CHECK(nsteps % ir->nstcomm != 0);
4309 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4310 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4313 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4314 "rounding errors can lead to build up of kinetic energy of the center of mass");
4317 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4320 for (int g = 0; g < ir->opts.ngtc; g++)
4322 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4324 if (ir->tau_p < 1.9 * tau_t_max)
4326 std::string message = gmx::formatString(
4327 "With %s T-coupling and %s p-coupling, "
4328 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4329 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4331 warning(wi, message.c_str());
4335 /* Check for pressure coupling with absolute position restraints */
4336 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4338 absolute_reference(ir, sys, TRUE, AbsRef);
4340 for (m = 0; m < DIM; m++)
4342 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4345 "You are using pressure coupling with absolute position restraints, "
4346 "this will give artifacts. Use the refcoord_scaling option.");
4354 aloopb = gmx_mtop_atomloop_block_init(sys);
4356 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4358 if (atom->q != 0 || atom->qB != 0)
4366 if (EEL_FULL(ir->coulombtype))
4369 "You are using full electrostatics treatment %s for a system without charges.\n"
4370 "This costs a lot of performance for just processing zeros, consider using %s "
4372 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4373 warning(wi, err_buf);
4378 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4381 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4382 "You might want to consider using %s electrostatics.\n",
4384 warning_note(wi, err_buf);
4388 /* Check if combination rules used in LJ-PME are the same as in the force field */
4389 if (EVDW_PME(ir->vdwtype))
4391 check_combination_rules(ir, sys, wi);
4394 /* Generalized reaction field */
4395 if (ir->coulombtype == eelGRF_NOTUSED)
4398 "Generalized reaction-field electrostatics is no longer supported. "
4399 "You can use normal reaction-field instead and compute the reaction-field "
4400 "constant by hand.");
4404 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4406 for (m = 0; (m < DIM); m++)
4408 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4417 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4418 for (const AtomProxy atomP : AtomRange(*sys))
4420 const t_atom& local = atomP.atom();
4421 int i = atomP.globalAtomNumber();
4422 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4425 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4427 for (m = 0; (m < DIM); m++)
4429 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4433 for (m = 0; (m < DIM); m++)
4435 if (fabs(acc[m]) > 1e-6)
4437 const char* dim[DIM] = { "X", "Y", "Z" };
4438 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4439 ir->nstcomm != 0 ? "" : "not");
4440 if (ir->nstcomm != 0 && m < ndof_com(ir))
4444 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4446 ir->opts.acc[i][m] -= acc[m];
4454 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4455 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4457 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4465 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4467 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4469 absolute_reference(ir, sys, FALSE, AbsRef);
4470 for (m = 0; m < DIM; m++)
4472 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4475 "You are using an absolute reference for pulling, but the rest of "
4476 "the system does not have an absolute reference. This will lead to "
4485 for (i = 0; i < 3; i++)
4487 for (m = 0; m <= i; m++)
4489 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4491 for (c = 0; c < ir->pull->ncoord; c++)
4493 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4496 "Can not have dynamic box while using pull geometry '%s' "
4498 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4509 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4511 char warn_buf[STRLEN];
4514 ptr = check_box(ir->pbcType, box);
4517 warning_error(wi, ptr);
4520 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4522 if (ir->shake_tol <= 0.0)
4524 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4525 warning_error(wi, warn_buf);
4529 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4531 /* If we have Lincs constraints: */
4532 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4535 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4536 warning_note(wi, warn_buf);
4539 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4542 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4544 warning_note(wi, warn_buf);
4546 if (ir->epc == epcMTTK)
4548 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4552 if (bHasAnyConstraints && ir->epc == epcMTTK)
4554 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4557 if (ir->LincsWarnAngle > 90.0)
4559 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4560 warning(wi, warn_buf);
4561 ir->LincsWarnAngle = 90.0;
4564 if (ir->pbcType != PbcType::No)
4566 if (ir->nstlist == 0)
4569 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4570 "atoms might cause the simulation to crash.");
4572 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4575 "ERROR: The cut-off length is longer than half the shortest box vector or "
4576 "longer than the smallest box diagonal element. Increase the box size or "
4577 "decrease rlist.\n");
4578 warning_error(wi, warn_buf);