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50 #include "gromacs/applied_forces/awh/read_params.h"
51 #include "gromacs/fileio/readinp.h"
52 #include "gromacs/fileio/warninp.h"
53 #include "gromacs/gmxlib/network.h"
54 #include "gromacs/gmxpreprocess/toputil.h"
55 #include "gromacs/math/functions.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/calc_verletbuf.h"
59 #include "gromacs/mdrun/mdmodules.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/mdtypes/multipletimestepping.h"
63 #include "gromacs/mdtypes/pull_params.h"
64 #include "gromacs/options/options.h"
65 #include "gromacs/options/treesupport.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/selection/indexutil.h"
68 #include "gromacs/topology/block.h"
69 #include "gromacs/topology/ifunc.h"
70 #include "gromacs/topology/index.h"
71 #include "gromacs/topology/mtop_util.h"
72 #include "gromacs/topology/symtab.h"
73 #include "gromacs/topology/topology.h"
74 #include "gromacs/utility/cstringutil.h"
75 #include "gromacs/utility/exceptions.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/filestream.h"
78 #include "gromacs/utility/gmxassert.h"
79 #include "gromacs/utility/ikeyvaluetreeerror.h"
80 #include "gromacs/utility/keyvaluetree.h"
81 #include "gromacs/utility/keyvaluetreebuilder.h"
82 #include "gromacs/utility/keyvaluetreemdpwriter.h"
83 #include "gromacs/utility/keyvaluetreetransform.h"
84 #include "gromacs/utility/mdmodulenotification.h"
85 #include "gromacs/utility/smalloc.h"
86 #include "gromacs/utility/strconvert.h"
87 #include "gromacs/utility/stringcompare.h"
88 #include "gromacs/utility/stringutil.h"
89 #include "gromacs/utility/textwriter.h"
94 /* Resource parameters
95 * Do not change any of these until you read the instruction
96 * in readinp.h. Some cpp's do not take spaces after the backslash
97 * (like the c-shell), which will give you a very weird compiler
101 struct gmx_inputrec_strings
103 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
104 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
105 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
106 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
107 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
108 char fep_lambda[efptNR][STRLEN];
109 char lambda_weights[STRLEN];
110 std::vector<std::string> pullGroupNames;
111 std::vector<std::string> rotateGroupNames;
112 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
113 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
114 CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[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 if (!(ir.eI == eiMD || ir.eI == eiSD1))
255 auto message = gmx::formatString(
256 "Multiple time stepping is only supported with integrators %s and %s",
257 ei_names[eiMD], ei_names[eiSD1]);
258 warning_error(wi, message.c_str());
260 if (opts.numMtsLevels != 2)
262 warning_error(wi, "Only mts-levels = 2 is supported");
266 const std::vector<std::string> inputForceGroups = gmx::splitString(opts.mtsLevel2Forces);
267 auto& forceGroups = mtsLevels[1].forceGroups;
268 for (const auto& inputForceGroup : inputForceGroups)
272 for (const auto& forceGroupName : gmx::mtsForceGroupNames)
274 if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
276 forceGroups.set(nameIndex);
284 gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str());
285 warning_error(wi, message.c_str());
289 if (mtsLevels[1].stepFactor <= 1)
291 gmx_fatal(FARGS, "mts-factor should be larger than 1");
294 // Make the level 0 use the complement of the force groups of group 1
295 mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
296 mtsLevels[0].stepFactor = 1;
298 if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
299 && !mtsLevels[1].forceGroups[static_cast<int>(gmx::MtsForceGroups::LongrangeNonbonded)])
302 "With long-range electrostatics and/or LJ treatment, the long-range part "
303 "has to be part of the mts-level2-forces");
306 if (ir.nstcalcenergy > 0)
308 checkMtsRequirement(ir, "nstcalcenergy", ir.nstcalcenergy, wi);
310 checkMtsRequirement(ir, "nstenergy", ir.nstenergy, wi);
311 checkMtsRequirement(ir, "nstlog", ir.nstlog, wi);
312 if (ir.efep != efepNO)
314 checkMtsRequirement(ir, "nstdhdl", ir.fepvals->nstdhdl, wi);
319 void check_ir(const char* mdparin,
320 const gmx::MdModulesNotifier& mdModulesNotifier,
324 /* Check internal consistency.
325 * NOTE: index groups are not set here yet, don't check things
326 * like temperature coupling group options here, but in triple_check
329 /* Strange macro: first one fills the err_buf, and then one can check
330 * the condition, which will print the message and increase the error
333 #define CHECK(b) _low_check(b, err_buf, wi)
334 char err_buf[256], warn_buf[STRLEN];
337 t_lambda* fep = ir->fepvals;
338 t_expanded* expand = ir->expandedvals;
340 set_warning_line(wi, mdparin, -1);
342 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
344 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
345 warning_error(wi, warn_buf);
348 /* BASIC CUT-OFF STUFF */
349 if (ir->rcoulomb < 0)
351 warning_error(wi, "rcoulomb should be >= 0");
355 warning_error(wi, "rvdw should be >= 0");
357 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
359 warning_error(wi, "rlist should be >= 0");
362 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
363 "neighbour-list update scheme for efficient buffering for improved energy "
364 "conservation, please use the Verlet cut-off scheme instead.)");
365 CHECK(ir->nstlist < 0);
367 process_interaction_modifier(&ir->coulomb_modifier);
368 process_interaction_modifier(&ir->vdw_modifier);
370 if (ir->cutoff_scheme == ecutsGROUP)
373 "The group cutoff scheme has been removed since GROMACS 2020. "
374 "Please use the Verlet cutoff scheme.");
376 if (ir->cutoff_scheme == ecutsVERLET)
380 /* Normal Verlet type neighbor-list, currently only limited feature support */
381 if (inputrec2nboundeddim(ir) < 3)
383 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
386 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
387 if (ir->rcoulomb != ir->rvdw)
389 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
390 // for PME load balancing, we can support this exception.
391 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
392 && ir->rcoulomb > ir->rvdw);
393 if (!bUsesPmeTwinRangeKernel)
396 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
397 "rcoulomb>rvdw with PME electrostatics)");
401 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
403 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
405 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
408 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
410 evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
411 warning_note(wi, warn_buf);
413 ir->vdwtype = evdwCUT;
417 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
418 evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
419 warning_error(wi, warn_buf);
423 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
426 "With Verlet lists only cut-off and PME LJ interactions are supported");
428 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
429 || ir->coulombtype == eelEWALD))
432 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
433 "electrostatics are supported");
435 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
437 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
438 warning_error(wi, warn_buf);
441 if (EEL_USER(ir->coulombtype))
443 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
444 eel_names[ir->coulombtype]);
445 warning_error(wi, warn_buf);
448 if (ir->nstlist <= 0)
450 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
453 if (ir->nstlist < 10)
456 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
457 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
461 rc_max = std::max(ir->rvdw, ir->rcoulomb);
465 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
466 ir->verletbuf_tol = 0;
469 else if (ir->verletbuf_tol <= 0)
471 if (ir->verletbuf_tol == 0)
473 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
476 if (ir->rlist < rc_max)
479 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
482 if (ir->rlist == rc_max && ir->nstlist > 1)
486 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
487 "buffer. The cluster pair list does have a buffering effect, but choosing "
488 "a larger rlist might be necessary for good energy conservation.");
493 if (ir->rlist > rc_max)
496 "You have set rlist larger than the interaction cut-off, but you also "
497 "have verlet-buffer-tolerance > 0. Will set rlist using "
498 "verlet-buffer-tolerance.");
501 if (ir->nstlist == 1)
503 /* No buffer required */
508 if (EI_DYNAMICS(ir->eI))
510 if (inputrec2nboundeddim(ir) < 3)
513 "The box volume is required for calculating rlist from the "
514 "energy drift with verlet-buffer-tolerance > 0. You are "
515 "using at least one unbounded dimension, so no volume can be "
516 "computed. Either use a finite box, or set rlist yourself "
517 "together with verlet-buffer-tolerance = -1.");
519 /* Set rlist temporarily so we can continue processing */
524 /* Set the buffer to 5% of the cut-off */
525 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
531 /* GENERAL INTEGRATOR STUFF */
534 if (ir->etc != etcNO)
536 if (EI_RANDOM(ir->eI))
539 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
540 "implicitly. See the documentation for more information on which "
541 "parameters affect temperature for %s.",
542 etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
547 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
549 etcoupl_names[ir->etc], ei_names[ir->eI]);
551 warning_note(wi, warn_buf);
555 if (ir->eI == eiVVAK)
558 "Integrator method %s is implemented primarily for validation purposes; for "
559 "molecular dynamics, you should probably be using %s or %s",
560 ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
561 warning_note(wi, warn_buf);
563 if (!EI_DYNAMICS(ir->eI))
565 if (ir->epc != epcNO)
568 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
569 epcoupl_names[ir->epc], ei_names[ir->eI]);
570 warning_note(wi, warn_buf);
574 if (EI_DYNAMICS(ir->eI))
576 if (ir->nstcalcenergy < 0)
578 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
579 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
581 /* nstcalcenergy larger than nstener does not make sense.
582 * We ideally want nstcalcenergy=nstener.
586 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
590 ir->nstcalcenergy = ir->nstenergy;
594 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
595 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
596 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
599 const char* nsten = "nstenergy";
600 const char* nstdh = "nstdhdl";
601 const char* min_name = nsten;
602 int min_nst = ir->nstenergy;
604 /* find the smallest of ( nstenergy, nstdhdl ) */
605 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
606 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
608 min_nst = ir->fepvals->nstdhdl;
611 /* If the user sets nstenergy small, we should respect that */
612 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
614 warning_note(wi, warn_buf);
615 ir->nstcalcenergy = min_nst;
618 if (ir->epc != epcNO)
620 if (ir->nstpcouple < 0)
622 ir->nstpcouple = ir_optimal_nstpcouple(ir);
624 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
627 "With multiple time stepping, nstpcouple should be a mutiple of "
632 if (ir->nstcalcenergy > 0)
634 if (ir->efep != efepNO)
636 /* nstdhdl should be a multiple of nstcalcenergy */
637 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
641 /* nstexpanded should be a multiple of nstcalcenergy */
642 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
643 &ir->expandedvals->nstexpanded, wi);
645 /* for storing exact averages nstenergy should be
646 * a multiple of nstcalcenergy
648 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
651 // Inquire all MdModules, if their parameters match with the energy
652 // calculation frequency
653 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
654 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
656 // Emit all errors from the energy calculation frequency checks
657 for (const std::string& energyFrequencyErrorMessage :
658 energyCalculationFrequencyErrors.errorMessages())
660 warning_error(wi, energyFrequencyErrorMessage);
664 if (ir->nsteps == 0 && !ir->bContinuation)
667 "For a correct single-point energy evaluation with nsteps = 0, use "
668 "continuation = yes to avoid constraining the input coordinates.");
672 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
675 "You are doing a continuation with SD or BD, make sure that ld_seed is "
676 "different from the previous run (using ld_seed=-1 will ensure this)");
682 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
683 CHECK(ir->pbcType != PbcType::Xyz);
684 sprintf(err_buf, "with TPI nstlist should be larger than zero");
685 CHECK(ir->nstlist <= 0);
686 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
687 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
691 if ((opts->nshake > 0) && (opts->bMorse))
693 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
694 warning(wi, warn_buf);
697 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
700 "You are doing a continuation with SD or BD, make sure that ld_seed is "
701 "different from the previous run (using ld_seed=-1 will ensure this)");
703 /* verify simulated tempering options */
707 bool bAllTempZero = TRUE;
708 for (i = 0; i < fep->n_lambda; i++)
710 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
711 efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
712 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
713 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
715 bAllTempZero = FALSE;
718 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
719 CHECK(bAllTempZero == TRUE);
721 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
722 CHECK(ir->eI != eiVV);
724 /* check compatability of the temperature coupling with simulated tempering */
726 if (ir->etc == etcNOSEHOOVER)
729 "Nose-Hoover based temperature control such as [%s] my not be "
730 "entirelyconsistent with simulated tempering",
731 etcoupl_names[ir->etc]);
732 warning_note(wi, warn_buf);
735 /* check that the temperatures make sense */
738 "Higher simulated tempering temperature (%g) must be >= than the simulated "
739 "tempering lower temperature (%g)",
740 ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
741 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
743 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
744 ir->simtempvals->simtemp_high);
745 CHECK(ir->simtempvals->simtemp_high <= 0);
747 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
748 ir->simtempvals->simtemp_low);
749 CHECK(ir->simtempvals->simtemp_low <= 0);
752 /* verify free energy options */
754 if (ir->efep != efepNO)
757 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
758 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
761 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
763 static_cast<int>(fep->sc_r_power));
764 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
767 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
770 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
772 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
774 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
776 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
777 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
779 sprintf(err_buf, "Free-energy not implemented for Ewald");
780 CHECK(ir->coulombtype == eelEWALD);
782 /* check validty of lambda inputs */
783 if (fep->n_lambda == 0)
785 /* Clear output in case of no states:*/
786 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
787 fep->init_fep_state);
788 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
792 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
793 fep->init_fep_state, fep->n_lambda - 1);
794 CHECK((fep->init_fep_state >= fep->n_lambda));
798 "Lambda state must be set, either with init-lambda-state or with init-lambda");
799 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
802 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
803 "init-lambda-state or with init-lambda, but not both",
804 fep->init_lambda, fep->init_fep_state);
805 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
808 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
812 for (i = 0; i < efptNR; i++)
814 if (fep->separate_dvdl[i])
819 if (n_lambda_terms > 1)
822 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
823 "use init-lambda to set lambda state (except for slow growth). Use "
824 "init-lambda-state instead.");
825 warning(wi, warn_buf);
828 if (n_lambda_terms < 2 && fep->n_lambda > 0)
831 "init-lambda is deprecated for setting lambda state (except for slow "
832 "growth). Use init-lambda-state instead.");
836 for (j = 0; j < efptNR; j++)
838 for (i = 0; i < fep->n_lambda; i++)
840 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
841 efpt_names[j], fep->all_lambda[j][i]);
842 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
846 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
848 for (i = 0; i < fep->n_lambda; i++)
851 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
852 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
853 "crashes, and is not supported.",
854 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
855 CHECK((fep->sc_alpha > 0)
856 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
857 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
861 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
863 real sigma, lambda, r_sc;
866 /* Maximum estimate for A and B charges equal with lambda power 1 */
868 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
869 1.0 / fep->sc_r_power);
871 "With PME there is a minor soft core effect present at the cut-off, "
872 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
873 "energy conservation, but usually other effects dominate. With a common sigma "
874 "value of %g nm the fraction of the particle-particle potential at the cut-off "
875 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
876 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
877 warning_note(wi, warn_buf);
880 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
881 be treated differently, but that's the next step */
883 for (i = 0; i < efptNR; i++)
885 for (j = 0; j < fep->n_lambda; j++)
887 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
888 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
893 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
897 /* checking equilibration of weights inputs for validity */
900 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
902 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
903 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
906 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
908 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
909 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
912 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
913 expand->equil_steps, elmceq_names[elmceqSTEPS]);
914 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
917 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
918 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
919 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
922 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
923 expand->equil_ratio, elmceq_names[elmceqRATIO]);
924 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
927 "weight-equil-number-all-lambda (%d) must be a positive integer if "
928 "lmc-weights-equil=%s",
929 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
930 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
933 "weight-equil-number-samples (%d) must be a positive integer if "
934 "lmc-weights-equil=%s",
935 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
936 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
939 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
940 expand->equil_steps, elmceq_names[elmceqSTEPS]);
941 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
943 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
944 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
945 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
947 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
948 expand->equil_ratio, elmceq_names[elmceqRATIO]);
949 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
951 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
952 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
953 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
955 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
956 CHECK((expand->lmc_repeats <= 0));
957 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
958 CHECK((expand->minvarmin <= 0));
959 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
960 CHECK((expand->c_range < 0));
962 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
964 fep->init_fep_state, expand->lmc_forced_nstart);
965 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
966 && (expand->elmcmove != elmcmoveNO));
967 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
968 CHECK((expand->lmc_forced_nstart < 0));
969 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
970 fep->init_fep_state);
971 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
973 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
974 CHECK((expand->init_wl_delta < 0));
975 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
976 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
977 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
978 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
980 /* if there is no temperature control, we need to specify an MC temperature */
981 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
982 && (expand->mc_temp <= 0.0))
985 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
986 "to a positive number");
987 warning_error(wi, err_buf);
989 if (expand->nstTij > 0)
991 sprintf(err_buf, "nstlog must be non-zero");
992 CHECK(ir->nstlog == 0);
993 // Avoid modulus by zero in the case that already triggered an error exit.
997 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
998 expand->nstTij, ir->nstlog);
999 CHECK((expand->nstTij % ir->nstlog) != 0);
1005 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
1006 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
1009 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
1011 if (ir->pbcType == PbcType::No)
1013 if (ir->epc != epcNO)
1015 warning(wi, "Turning off pressure coupling for vacuum system");
1021 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
1022 c_pbcTypeNames[ir->pbcType].c_str());
1023 CHECK(ir->epc != epcNO);
1025 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1026 CHECK(EEL_FULL(ir->coulombtype));
1028 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
1029 c_pbcTypeNames[ir->pbcType].c_str());
1030 CHECK(ir->eDispCorr != edispcNO);
1033 if (ir->rlist == 0.0)
1036 "can only have neighborlist cut-off zero (=infinite)\n"
1037 "with coulombtype = %s or coulombtype = %s\n"
1038 "without periodic boundary conditions (pbc = %s) and\n"
1039 "rcoulomb and rvdw set to zero",
1040 eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
1041 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
1042 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1044 if (ir->nstlist > 0)
1047 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1048 "nstype=simple and only one MPI rank");
1053 if (ir->nstcomm == 0)
1055 // TODO Change this behaviour. There should be exactly one way
1056 // to turn off an algorithm.
1057 ir->comm_mode = ecmNO;
1059 if (ir->comm_mode != ecmNO)
1061 if (ir->nstcomm < 0)
1063 // TODO Such input was once valid. Now that we've been
1064 // helpful for a few years, we should reject such input,
1065 // lest we have to support every historical decision
1068 "If you want to remove the rotation around the center of mass, you should set "
1069 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1070 "its absolute value");
1071 ir->nstcomm = abs(ir->nstcomm);
1074 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1077 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1078 "nstcomm to nstcalcenergy");
1079 ir->nstcomm = ir->nstcalcenergy;
1082 if (ir->comm_mode == ecmANGULAR)
1085 "Can not remove the rotation around the center of mass with periodic "
1087 CHECK(ir->bPeriodicMols);
1088 if (ir->pbcType != PbcType::No)
1091 "Removing the rotation around the center of mass in a periodic system, "
1092 "this can lead to artifacts. Only use this on a single (cluster of) "
1093 "molecules. This cluster should not cross periodic boundaries.");
1098 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
1101 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1102 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1105 warning_note(wi, warn_buf);
1108 /* TEMPERATURE COUPLING */
1109 if (ir->etc == etcYES)
1111 ir->etc = etcBERENDSEN;
1113 "Old option for temperature coupling given: "
1114 "changing \"yes\" to \"Berendsen\"\n");
1117 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1119 if (ir->opts.nhchainlength < 1)
1122 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1124 ir->opts.nhchainlength);
1125 ir->opts.nhchainlength = 1;
1126 warning(wi, warn_buf);
1129 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1133 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1134 ir->opts.nhchainlength = 1;
1139 ir->opts.nhchainlength = 0;
1142 if (ir->eI == eiVVAK)
1145 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1148 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1151 if (ETC_ANDERSEN(ir->etc))
1153 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1154 etcoupl_names[ir->etc], ei_names[ir->eI]);
1155 CHECK(!(EI_VV(ir->eI)));
1157 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1160 "Center of mass removal not necessary for %s. All velocities of coupled "
1161 "groups are rerandomized periodically, so flying ice cube errors will not "
1163 etcoupl_names[ir->etc]);
1164 warning_note(wi, warn_buf);
1168 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1169 "randomized every time step",
1170 ir->nstcomm, etcoupl_names[ir->etc]);
1171 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1174 if (ir->etc == etcBERENDSEN)
1177 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1178 "might want to consider using the %s thermostat.",
1179 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1180 warning_note(wi, warn_buf);
1183 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1186 "Using Berendsen pressure coupling invalidates the "
1187 "true ensemble for the thermostat");
1188 warning(wi, warn_buf);
1191 /* PRESSURE COUPLING */
1192 if (ir->epc == epcISOTROPIC)
1194 ir->epc = epcBERENDSEN;
1196 "Old option for pressure coupling given: "
1197 "changing \"Isotropic\" to \"Berendsen\"\n");
1200 if (ir->epc != epcNO)
1202 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1204 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1205 CHECK(ir->tau_p <= 0);
1207 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1210 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1211 "times larger than nstpcouple*dt (%g)",
1212 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1213 warning(wi, warn_buf);
1217 "compressibility must be > 0 when using pressure"
1219 EPCOUPLTYPE(ir->epc));
1220 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1221 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1222 && ir->compress[ZZ][YY] <= 0));
1224 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1227 "You are generating velocities so I am assuming you "
1228 "are equilibrating a system. You are using "
1229 "%s pressure coupling, but this can be "
1230 "unstable for equilibration. If your system crashes, try "
1231 "equilibrating first with Berendsen pressure coupling. If "
1232 "you are not equilibrating the system, you can probably "
1233 "ignore this warning.",
1234 epcoupl_names[ir->epc]);
1235 warning(wi, warn_buf);
1241 if (ir->epc == epcMTTK)
1243 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1247 /* ELECTROSTATICS */
1248 /* More checks are in triple check (grompp.c) */
1250 if (ir->coulombtype == eelSWITCH)
1253 "coulombtype = %s is only for testing purposes and can lead to serious "
1254 "artifacts, advice: use coulombtype = %s",
1255 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1256 warning(wi, warn_buf);
1259 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1262 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1263 "format and exchanging epsilon-r and epsilon-rf",
1265 warning(wi, warn_buf);
1266 ir->epsilon_rf = ir->epsilon_r;
1267 ir->epsilon_r = 1.0;
1270 if (ir->epsilon_r == 0)
1273 "It is pointless to use long-range electrostatics with infinite relative "
1275 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1277 CHECK(EEL_FULL(ir->coulombtype));
1280 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1282 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1283 CHECK(ir->epsilon_r < 0);
1286 if (EEL_RF(ir->coulombtype))
1288 /* reaction field (at the cut-off) */
1290 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1293 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1294 eel_names[ir->coulombtype]);
1295 warning(wi, warn_buf);
1296 ir->epsilon_rf = 0.0;
1299 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1300 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1301 if (ir->epsilon_rf == ir->epsilon_r)
1303 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1304 eel_names[ir->coulombtype]);
1305 warning(wi, warn_buf);
1308 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1309 * means the interaction is zero outside rcoulomb, but it helps to
1310 * provide accurate energy conservation.
1312 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1314 if (ir_coulomb_switched(ir))
1317 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1318 "potential modifier options!",
1319 eel_names[ir->coulombtype]);
1320 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1324 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1327 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1328 "secondary coulomb-modifier.");
1329 CHECK(ir->coulomb_modifier != eintmodNONE);
1331 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1334 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1335 "secondary vdw-modifier.");
1336 CHECK(ir->vdw_modifier != eintmodNONE);
1339 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1340 || ir->vdwtype == evdwSHIFT)
1343 "The switch/shift interaction settings are just for compatibility; you will get "
1345 "performance from applying potential modifiers to your interactions!\n");
1346 warning_note(wi, warn_buf);
1349 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1351 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1353 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1355 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1356 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1357 "will be good regardless, since ewald_rtol = %g.",
1358 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1359 warning(wi, warn_buf);
1363 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1365 if (ir->rvdw_switch == 0)
1368 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1369 "potential. This suggests it was not set in the mdp, which can lead to large "
1370 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1371 "switching range.");
1372 warning(wi, warn_buf);
1376 if (EEL_FULL(ir->coulombtype))
1378 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1379 || ir->coulombtype == eelPMEUSERSWITCH)
1381 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1382 eel_names[ir->coulombtype]);
1383 CHECK(ir->rcoulomb > ir->rlist);
1387 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1389 // TODO: Move these checks into the ewald module with the options class
1391 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1393 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1395 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1396 eel_names[ir->coulombtype], orderMin, orderMax);
1397 warning_error(wi, warn_buf);
1401 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1403 if (ir->ewald_geometry == eewg3D)
1405 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1406 c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
1407 warning(wi, warn_buf);
1409 /* This check avoids extra pbc coding for exclusion corrections */
1410 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1411 CHECK(ir->wall_ewald_zfac < 2);
1413 if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
1415 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1416 eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
1417 warning(wi, warn_buf);
1419 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1421 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1422 CHECK(ir->bPeriodicMols);
1423 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1424 warning_note(wi, warn_buf);
1426 "With epsilon_surface > 0 you can only use domain decomposition "
1427 "when there are only small molecules with all bonds constrained (mdrun will check "
1429 warning_note(wi, warn_buf);
1432 if (ir_vdw_switched(ir))
1434 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1435 CHECK(ir->rvdw_switch >= ir->rvdw);
1437 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1440 "You are applying a switch function to vdw forces or potentials from %g to %g "
1441 "nm, which is more than half the interaction range, whereas switch functions "
1442 "are intended to act only close to the cut-off.",
1443 ir->rvdw_switch, ir->rvdw);
1444 warning_note(wi, warn_buf);
1448 if (ir->vdwtype == evdwPME)
1450 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1452 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1453 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1454 warning_error(wi, err_buf);
1458 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1461 "You have selected user tables with dispersion correction, the dispersion "
1462 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1463 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1464 "really want dispersion correction to -C6/r^6.");
1467 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1469 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1472 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1474 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1477 /* IMPLICIT SOLVENT */
1478 if (ir->coulombtype == eelGB_NOTUSED)
1480 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1481 warning_error(wi, warn_buf);
1486 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1491 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1495 /* interpret a number of doubles from a string and put them in an array,
1496 after allocating space for them.
1497 str = the input string
1498 n = the (pre-allocated) number of doubles read
1499 r = the output array of doubles. */
1500 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1502 auto values = gmx::splitString(str);
1506 for (int i = 0; i < *n; i++)
1510 (*r)[i] = gmx::fromString<real>(values[i]);
1512 catch (gmx::GromacsException&)
1514 warning_error(wi, "Invalid value " + values[i]
1515 + " in string in mdp file. Expected a real number.");
1521 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1524 int i, j, max_n_lambda, nweights, nfep[efptNR];
1525 t_lambda* fep = ir->fepvals;
1526 t_expanded* expand = ir->expandedvals;
1527 real** count_fep_lambdas;
1528 bool bOneLambda = TRUE;
1530 snew(count_fep_lambdas, efptNR);
1532 /* FEP input processing */
1533 /* first, identify the number of lambda values for each type.
1534 All that are nonzero must have the same number */
1536 for (i = 0; i < efptNR; i++)
1538 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1541 /* now, determine the number of components. All must be either zero, or equal. */
1544 for (i = 0; i < efptNR; i++)
1546 if (nfep[i] > max_n_lambda)
1548 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1549 must have the same number if its not zero.*/
1554 for (i = 0; i < efptNR; i++)
1558 ir->fepvals->separate_dvdl[i] = FALSE;
1560 else if (nfep[i] == max_n_lambda)
1562 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1563 the derivative with respect to the temperature currently */
1565 ir->fepvals->separate_dvdl[i] = TRUE;
1571 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1573 nfep[i], efpt_names[i], max_n_lambda);
1576 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1577 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1579 /* the number of lambdas is the number we've read in, which is either zero
1580 or the same for all */
1581 fep->n_lambda = max_n_lambda;
1583 /* allocate space for the array of lambda values */
1584 snew(fep->all_lambda, efptNR);
1585 /* if init_lambda is defined, we need to set lambda */
1586 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1588 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1590 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1591 for (i = 0; i < efptNR; i++)
1593 snew(fep->all_lambda[i], fep->n_lambda);
1594 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1597 for (j = 0; j < fep->n_lambda; j++)
1599 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1601 sfree(count_fep_lambdas[i]);
1604 sfree(count_fep_lambdas);
1606 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1607 internal bookkeeping -- for now, init_lambda */
1609 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1611 for (i = 0; i < fep->n_lambda; i++)
1613 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1617 /* check to see if only a single component lambda is defined, and soft core is defined.
1618 In this case, turn on coulomb soft core */
1620 if (max_n_lambda == 0)
1626 for (i = 0; i < efptNR; i++)
1628 if ((nfep[i] != 0) && (i != efptFEP))
1634 if ((bOneLambda) && (fep->sc_alpha > 0))
1636 fep->bScCoul = TRUE;
1639 /* Fill in the others with the efptFEP if they are not explicitly
1640 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1641 they are all zero. */
1643 for (i = 0; i < efptNR; i++)
1645 if ((nfep[i] == 0) && (i != efptFEP))
1647 for (j = 0; j < fep->n_lambda; j++)
1649 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1655 /* now read in the weights */
1656 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1659 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1661 else if (nweights != fep->n_lambda)
1663 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1664 nweights, fep->n_lambda);
1666 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1668 expand->nstexpanded = fep->nstdhdl;
1669 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1674 static void do_simtemp_params(t_inputrec* ir)
1677 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1678 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1681 template<typename T>
1682 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1685 for (const auto& input : inputs)
1689 outputs[i] = gmx::fromStdString<T>(input);
1691 catch (gmx::GromacsException&)
1693 auto message = gmx::formatString(
1694 "Invalid value for mdp option %s. %s should only consist of integers separated "
1697 warning_error(wi, message);
1703 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1706 for (const auto& input : inputs)
1710 outputs[i] = gmx::fromString<real>(input);
1712 catch (gmx::GromacsException&)
1714 auto message = gmx::formatString(
1715 "Invalid value for mdp option %s. %s should only consist of real numbers "
1716 "separated by spaces.",
1718 warning_error(wi, message);
1724 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1727 for (const auto& input : inputs)
1731 outputs[i][d] = gmx::fromString<real>(input);
1733 catch (gmx::GromacsException&)
1735 auto message = gmx::formatString(
1736 "Invalid value for mdp option %s. %s should only consist of real numbers "
1737 "separated by spaces.",
1739 warning_error(wi, message);
1750 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1752 opts->wall_atomtype[0] = nullptr;
1753 opts->wall_atomtype[1] = nullptr;
1755 ir->wall_atomtype[0] = -1;
1756 ir->wall_atomtype[1] = -1;
1757 ir->wall_density[0] = 0;
1758 ir->wall_density[1] = 0;
1762 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1763 if (wallAtomTypes.size() != size_t(ir->nwall))
1765 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1766 wallAtomTypes.size());
1768 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1769 for (int i = 0; i < ir->nwall; i++)
1771 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1774 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1776 auto wallDensity = gmx::splitString(wall_density);
1777 if (wallDensity.size() != size_t(ir->nwall))
1779 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1780 wallDensity.size());
1782 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1783 for (int i = 0; i < ir->nwall; i++)
1785 if (ir->wall_density[i] <= 0)
1787 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1794 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1798 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1799 for (int i = 0; i < nwall; i++)
1801 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1802 grps->emplace_back(groups->groupNames.size() - 1);
1807 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1809 /* read expanded ensemble parameters */
1810 printStringNewline(inp, "expanded ensemble variables");
1811 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1812 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1813 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1814 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1815 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1816 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1817 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1818 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1819 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1820 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1821 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1822 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1823 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1824 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1825 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1826 expand->bSymmetrizedTMatrix =
1827 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1828 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1829 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1830 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1831 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1832 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1833 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1834 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1837 /*! \brief Return whether an end state with the given coupling-lambda
1838 * value describes fully-interacting VDW.
1840 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1841 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1843 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1845 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1851 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1854 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1856 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1858 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1861 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1862 std::string message = gmx::formatExceptionMessageToString(*ex);
1863 warning_error(wi_, message.c_str());
1868 std::string getOptionName(const gmx::KeyValueTreePath& context)
1870 if (mapping_ != nullptr)
1872 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1873 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1876 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1881 const gmx::IKeyValueTreeBackMapping* mapping_;
1886 void get_ir(const char* mdparin,
1887 const char* mdparout,
1888 gmx::MDModules* mdModules,
1891 WriteMdpHeader writeMdpHeader,
1895 double dumdub[2][6];
1897 char warn_buf[STRLEN];
1898 t_lambda* fep = ir->fepvals;
1899 t_expanded* expand = ir->expandedvals;
1901 const char* no_names[] = { "no", nullptr };
1903 init_inputrec_strings();
1904 gmx::TextInputFile stream(mdparin);
1905 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1907 snew(dumstr[0], STRLEN);
1908 snew(dumstr[1], STRLEN);
1910 /* ignore the following deprecated commands */
1911 replace_inp_entry(inp, "title", nullptr);
1912 replace_inp_entry(inp, "cpp", nullptr);
1913 replace_inp_entry(inp, "domain-decomposition", nullptr);
1914 replace_inp_entry(inp, "andersen-seed", nullptr);
1915 replace_inp_entry(inp, "dihre", nullptr);
1916 replace_inp_entry(inp, "dihre-fc", nullptr);
1917 replace_inp_entry(inp, "dihre-tau", nullptr);
1918 replace_inp_entry(inp, "nstdihreout", nullptr);
1919 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1920 replace_inp_entry(inp, "optimize-fft", nullptr);
1921 replace_inp_entry(inp, "adress_type", nullptr);
1922 replace_inp_entry(inp, "adress_const_wf", nullptr);
1923 replace_inp_entry(inp, "adress_ex_width", nullptr);
1924 replace_inp_entry(inp, "adress_hy_width", nullptr);
1925 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1926 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1927 replace_inp_entry(inp, "adress_site", nullptr);
1928 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1929 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1930 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1931 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1932 replace_inp_entry(inp, "rlistlong", nullptr);
1933 replace_inp_entry(inp, "nstcalclr", nullptr);
1934 replace_inp_entry(inp, "pull-print-com2", nullptr);
1935 replace_inp_entry(inp, "gb-algorithm", nullptr);
1936 replace_inp_entry(inp, "nstgbradii", nullptr);
1937 replace_inp_entry(inp, "rgbradii", nullptr);
1938 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1939 replace_inp_entry(inp, "gb-saltconc", nullptr);
1940 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1941 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1942 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1943 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1944 replace_inp_entry(inp, "sa-algorithm", nullptr);
1945 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1946 replace_inp_entry(inp, "ns-type", nullptr);
1948 /* replace the following commands with the clearer new versions*/
1949 replace_inp_entry(inp, "unconstrained-start", "continuation");
1950 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1951 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1952 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1953 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1954 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1955 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1957 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1958 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1959 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1960 setStringEntry(&inp, "include", opts->include, nullptr);
1961 printStringNoNewline(
1962 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1963 setStringEntry(&inp, "define", opts->define, nullptr);
1965 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1966 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1967 printStringNoNewline(&inp, "Start time and timestep in ps");
1968 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1969 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1970 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1971 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1972 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1973 printStringNoNewline(
1974 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1975 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1976 printStringNoNewline(&inp, "Multiple time-stepping");
1977 ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
1980 opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
1981 ir->mtsLevels.resize(2);
1982 gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
1983 setStringEntry(&inp, "mts-level2-forces", opts->mtsLevel2Forces,
1984 "longrange-nonbonded nonbonded pair dihedral");
1985 mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
1987 // We clear after reading without dynamics to not force the user to remove MTS mdp options
1988 if (!EI_DYNAMICS(ir->eI))
1991 ir->mtsLevels.clear();
1994 printStringNoNewline(&inp, "mode for center of mass motion removal");
1995 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1996 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1997 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1998 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1999 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2001 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2002 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2003 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2004 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2007 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2008 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2009 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2010 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2011 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2012 ir->niter = get_eint(&inp, "niter", 20, wi);
2013 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2014 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2015 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2016 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2017 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2019 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2020 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2022 /* Output options */
2023 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2024 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2025 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2026 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2027 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2028 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2029 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2030 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2031 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2032 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2033 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2034 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2035 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2036 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2037 printStringNoNewline(&inp, "default, all atoms will be written.");
2038 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2039 printStringNoNewline(&inp, "Selection of energy groups");
2040 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2042 /* Neighbor searching */
2043 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2044 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2045 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
2046 printStringNoNewline(&inp, "nblist update frequency");
2047 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2048 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2049 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2050 std::vector<const char*> pbcTypesNamesChar;
2051 for (const auto& pbcTypeName : c_pbcTypeNames)
2053 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2055 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2056 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
2057 printStringNoNewline(&inp,
2058 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2059 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2060 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2061 printStringNoNewline(&inp, "nblist cut-off");
2062 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2063 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2065 /* Electrostatics */
2066 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2067 printStringNoNewline(&inp, "Method for doing electrostatics");
2068 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
2069 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
2070 printStringNoNewline(&inp, "cut-off lengths");
2071 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2072 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2073 printStringNoNewline(&inp,
2074 "Relative dielectric constant for the medium and the reaction field");
2075 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2076 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2077 printStringNoNewline(&inp, "Method for doing Van der Waals");
2078 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
2079 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
2080 printStringNoNewline(&inp, "cut-off lengths");
2081 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2082 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2083 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2084 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
2085 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2086 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2087 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2088 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2089 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2090 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2091 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2092 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2093 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2094 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2095 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2096 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2097 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2098 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2099 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2100 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2101 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2103 /* Implicit solvation is no longer supported, but we need grompp
2104 to be able to refuse old .mdp files that would have built a tpr
2105 to run it. Thus, only "no" is accepted. */
2106 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2108 /* Coupling stuff */
2109 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2110 printStringNoNewline(&inp, "Temperature coupling");
2111 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2112 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2113 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2114 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2115 printStringNoNewline(&inp, "Groups to couple separately");
2116 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2117 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2118 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2119 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2120 printStringNoNewline(&inp, "pressure coupling");
2121 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2122 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2123 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2124 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2125 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2126 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2127 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2128 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2129 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2132 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2133 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2134 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2135 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2136 printStringNoNewline(&inp, "QM method");
2137 setStringEntry(&inp, "QMmethod", inputrecStrings->QMmethod, nullptr);
2138 printStringNoNewline(&inp, "QMMM scheme");
2139 const char* noQMMMSchemeName = "normal";
2140 get_eeenum(&inp, "QMMMscheme", &noQMMMSchemeName, wi);
2141 printStringNoNewline(&inp, "QM basisset");
2142 setStringEntry(&inp, "QMbasis", inputrecStrings->QMbasis, nullptr);
2143 printStringNoNewline(&inp, "QM charge");
2144 setStringEntry(&inp, "QMcharge", inputrecStrings->QMcharge, nullptr);
2145 printStringNoNewline(&inp, "QM multiplicity");
2146 setStringEntry(&inp, "QMmult", inputrecStrings->QMmult, nullptr);
2147 printStringNoNewline(&inp, "Surface Hopping");
2148 setStringEntry(&inp, "SH", inputrecStrings->bSH, nullptr);
2149 printStringNoNewline(&inp, "CAS space options");
2150 setStringEntry(&inp, "CASorbitals", inputrecStrings->CASorbitals, nullptr);
2151 setStringEntry(&inp, "CASelectrons", inputrecStrings->CASelectrons, nullptr);
2152 setStringEntry(&inp, "SAon", inputrecStrings->SAon, nullptr);
2153 setStringEntry(&inp, "SAoff", inputrecStrings->SAoff, nullptr);
2154 setStringEntry(&inp, "SAsteps", inputrecStrings->SAsteps, nullptr);
2155 printStringNoNewline(&inp, "Scale factor for MM charges");
2156 get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
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);
2223 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull, 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 do_numbering(int natoms,
2804 SimulationGroups* groups,
2805 gmx::ArrayRef<std::string> groupsFromMdpFile,
2808 SimulationAtomGroupType gtype,
2814 unsigned short* cbuf;
2815 AtomGroupIndices* grps = &(groups->groups[gtype]);
2816 int j, gid, aj, ognr, ntot = 0;
2818 char warn_buf[STRLEN];
2820 title = shortName(gtype);
2823 /* Mark all id's as not set */
2824 for (int i = 0; (i < natoms); i++)
2829 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2831 /* Lookup the group name in the block structure */
2832 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2833 if ((grptp != egrptpONE) || (i == 0))
2835 grps->emplace_back(gid);
2838 /* Now go over the atoms in the group */
2839 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2844 /* Range checking */
2845 if ((aj < 0) || (aj >= natoms))
2847 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2849 /* Lookup up the old group number */
2853 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2858 /* Store the group number in buffer */
2859 if (grptp == egrptpONE)
2872 /* Now check whether we have done all atoms */
2875 if (grptp == egrptpALL)
2877 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2879 else if (grptp == egrptpPART)
2881 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2882 warning_note(wi, warn_buf);
2884 /* Assign all atoms currently unassigned to a rest group */
2885 for (j = 0; (j < natoms); j++)
2887 if (cbuf[j] == NOGID)
2889 cbuf[j] = grps->size();
2892 if (grptp != egrptpPART)
2896 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2899 /* Add group name "rest" */
2900 grps->emplace_back(restnm);
2902 /* Assign the rest name to all atoms not currently assigned to a group */
2903 for (j = 0; (j < natoms); j++)
2905 if (cbuf[j] == NOGID)
2907 // group size was not updated before this here, so need to use -1.
2908 cbuf[j] = grps->size() - 1;
2914 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2916 /* All atoms are part of one (or no) group, no index required */
2917 groups->groupNumbers[gtype].clear();
2921 for (int j = 0; (j < natoms); j++)
2923 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2930 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2933 pull_params_t* pull;
2934 int natoms, imin, jmin;
2935 int * nrdf2, *na_vcm, na_tot;
2936 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2941 * First calc 3xnr-atoms for each group
2942 * then subtract half a degree of freedom for each constraint
2944 * Only atoms and nuclei contribute to the degrees of freedom...
2949 const SimulationGroups& groups = mtop->groups;
2950 natoms = mtop->natoms;
2952 /* Allocate one more for a possible rest group */
2953 /* We need to sum degrees of freedom into doubles,
2954 * since floats give too low nrdf's above 3 million atoms.
2956 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2957 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2958 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2959 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2960 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2962 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2966 for (gmx::index i = 0;
2967 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2970 clear_ivec(dof_vcm[i]);
2972 nrdf_vcm_sub[i] = 0;
2974 snew(nrdf2, natoms);
2975 for (const AtomProxy atomP : AtomRange(*mtop))
2977 const t_atom& local = atomP.atom();
2978 int i = atomP.globalAtomNumber();
2980 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2982 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2983 for (int d = 0; d < DIM; d++)
2985 if (opts->nFreeze[g][d] == 0)
2987 /* Add one DOF for particle i (counted as 2*1) */
2989 /* VCM group i has dim d as a DOF */
2990 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2994 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2996 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3002 for (const gmx_molblock_t& molb : mtop->molblock)
3004 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3005 const t_atom* atom = molt.atoms.atom;
3006 for (int mol = 0; mol < molb.nmol; mol++)
3008 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3010 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3011 for (int i = 0; i < molt.ilist[ftype].size();)
3013 /* Subtract degrees of freedom for the constraints,
3014 * if the particles still have degrees of freedom left.
3015 * If one of the particles is a vsite or a shell, then all
3016 * constraint motion will go there, but since they do not
3017 * contribute to the constraints the degrees of freedom do not
3020 int ai = as + ia[i + 1];
3021 int aj = as + ia[i + 2];
3022 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
3023 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
3041 imin = std::min(imin, nrdf2[ai]);
3042 jmin = std::min(jmin, nrdf2[aj]);
3045 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3047 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3049 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3051 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3054 i += interaction_function[ftype].nratoms + 1;
3057 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3058 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3060 /* Subtract 1 dof from every atom in the SETTLE */
3061 for (int j = 0; j < 3; j++)
3063 int ai = as + ia[i + 1 + j];
3064 imin = std::min(2, nrdf2[ai]);
3066 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3068 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3073 as += molt.atoms.nr;
3079 /* Correct nrdf for the COM constraints.
3080 * We correct using the TC and VCM group of the first atom
3081 * in the reference and pull group. If atoms in one pull group
3082 * belong to different TC or VCM groups it is anyhow difficult
3083 * to determine the optimal nrdf assignment.
3087 for (int i = 0; i < pull->ncoord; i++)
3089 if (pull->coord[i].eType != epullCONSTRAINT)
3096 for (int j = 0; j < 2; j++)
3098 const t_pull_group* pgrp;
3100 pgrp = &pull->group[pull->coord[i].group[j]];
3104 /* Subtract 1/2 dof from each group */
3105 int ai = pgrp->ind[0];
3106 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3108 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3110 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3113 "Center of mass pulling constraints caused the number of degrees "
3114 "of freedom for temperature coupling group %s to be negative",
3115 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3116 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3121 /* We need to subtract the whole DOF from group j=1 */
3128 if (ir->nstcomm != 0)
3130 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3131 "Expect at least one group when removing COM motion");
3133 /* We remove COM motion up to dim ndof_com() */
3134 const int ndim_rm_vcm = ndof_com(ir);
3136 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3137 * the number of degrees of freedom in each vcm group when COM
3138 * translation is removed and 6 when rotation is removed as well.
3139 * Note that we do not and should not include the rest group here.
3141 for (gmx::index j = 0;
3142 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3144 switch (ir->comm_mode)
3147 case ecmLINEAR_ACCELERATION_CORRECTION:
3148 nrdf_vcm_sub[j] = 0;
3149 for (int d = 0; d < ndim_rm_vcm; d++)
3157 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3158 default: gmx_incons("Checking comm_mode");
3162 for (gmx::index i = 0;
3163 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3165 /* Count the number of atoms of TC group i for every VCM group */
3166 for (gmx::index j = 0;
3167 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3172 for (int ai = 0; ai < natoms; ai++)
3174 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3176 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3180 /* Correct for VCM removal according to the fraction of each VCM
3181 * group present in this TC group.
3183 nrdf_uc = nrdf_tc[i];
3185 for (gmx::index j = 0;
3186 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3188 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3190 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3191 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3196 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3198 opts->nrdf[i] = nrdf_tc[i];
3199 if (opts->nrdf[i] < 0)
3203 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3204 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3212 sfree(nrdf_vcm_sub);
3215 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3217 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3218 * But since this is much larger than STRLEN, such a line can not be parsed.
3219 * The real maximum is the number of names that fit in a string: STRLEN/2.
3221 #define EGP_MAX (STRLEN / 2)
3225 auto names = gmx::splitString(val);
3226 if (names.size() % 2 != 0)
3228 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3230 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3232 for (size_t i = 0; i < names.size() / 2; i++)
3234 // TODO this needs to be replaced by a solution using std::find_if
3238 names[2 * i].c_str(),
3239 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3245 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3250 names[2 * i + 1].c_str(),
3251 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3257 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3259 if ((j < nr) && (k < nr))
3261 ir->opts.egp_flags[nr * j + k] |= flag;
3262 ir->opts.egp_flags[nr * k + j] |= flag;
3271 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3273 int ig = -1, i = 0, gind;
3277 /* Just a quick check here, more thorough checks are in mdrun */
3278 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3280 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3283 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3284 for (ig = 0; ig < swap->ngrp; ig++)
3286 swapg = &swap->grp[ig];
3287 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3288 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3292 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3293 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3294 snew(swapg->ind, swapg->nat);
3295 for (i = 0; i < swapg->nat; i++)
3297 swapg->ind[i] = grps->a[grps->index[gind] + i];
3302 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3308 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3313 ig = search_string(IMDgname, grps->nr, gnames);
3314 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3316 if (IMDgroup->nat > 0)
3319 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3321 IMDgname, IMDgroup->nat);
3322 snew(IMDgroup->ind, IMDgroup->nat);
3323 for (i = 0; i < IMDgroup->nat; i++)
3325 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3330 /* Checks whether atoms are both part of a COM removal group and frozen.
3331 * If a fully frozen atom is part of a COM removal group, it is removed
3332 * from the COM removal group. A note is issued if such atoms are present.
3333 * A warning is issued for atom with one or two dimensions frozen that
3334 * are part of a COM removal group (mdrun would need to compute COM mass
3335 * per dimension to handle this correctly).
3336 * Also issues a warning when non-frozen atoms are not part of a COM
3337 * removal group while COM removal is active.
3339 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3341 const t_grpopts& opts,
3344 const int vcmRestGroup =
3345 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3347 int numFullyFrozenVcmAtoms = 0;
3348 int numPartiallyFrozenVcmAtoms = 0;
3349 int numNonVcmAtoms = 0;
3350 for (int a = 0; a < numAtoms; a++)
3352 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3353 int numFrozenDims = 0;
3354 for (int d = 0; d < DIM; d++)
3356 numFrozenDims += opts.nFreeze[freezeGroup][d];
3359 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3360 if (vcmGroup < vcmRestGroup)
3362 if (numFrozenDims == DIM)
3364 /* Do not remove COM motion for this fully frozen atom */
3365 if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3367 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
3369 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3370 numFullyFrozenVcmAtoms++;
3372 else if (numFrozenDims > 0)
3374 numPartiallyFrozenVcmAtoms++;
3377 else if (numFrozenDims < DIM)
3383 if (numFullyFrozenVcmAtoms > 0)
3385 std::string warningText = gmx::formatString(
3386 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3387 "removing these atoms from the COMM removal group(s)",
3388 numFullyFrozenVcmAtoms);
3389 warning_note(wi, warningText.c_str());
3391 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3393 std::string warningText = gmx::formatString(
3394 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3395 "removal group(s), due to limitations in the code these still contribute to the "
3396 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3398 numPartiallyFrozenVcmAtoms, DIM);
3399 warning(wi, warningText.c_str());
3401 if (numNonVcmAtoms > 0)
3403 std::string warningText = gmx::formatString(
3404 "%d atoms are not part of any center of mass motion removal group.\n"
3405 "This may lead to artifacts.\n"
3406 "In most cases one should use one group for the whole system.",
3408 warning(wi, warningText.c_str());
3412 void do_index(const char* mdparin,
3416 const gmx::MdModulesNotifier& notifier,
3420 t_blocka* defaultIndexGroups;
3428 int i, j, k, restnm;
3429 bool bExcl, bTable, bAnneal;
3430 char warn_buf[STRLEN];
3434 fprintf(stderr, "processing index file...\n");
3438 snew(defaultIndexGroups, 1);
3439 snew(defaultIndexGroups->index, 1);
3441 atoms_all = gmx_mtop_global_atoms(mtop);
3442 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3443 done_atom(&atoms_all);
3447 defaultIndexGroups = init_index(ndx, &gnames);
3450 SimulationGroups* groups = &mtop->groups;
3451 natoms = mtop->natoms;
3452 symtab = &mtop->symtab;
3454 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3456 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3458 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3459 restnm = groups->groupNames.size() - 1;
3460 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3461 srenew(gnames, defaultIndexGroups->nr + 1);
3462 gnames[restnm] = *(groups->groupNames.back());
3464 set_warning_line(wi, mdparin, -1);
3466 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3467 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3468 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3469 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3470 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3473 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3475 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3476 temperatureCouplingTauValues.size());
3479 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3480 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3481 SimulationAtomGroupType::TemperatureCoupling, restnm,
3482 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3483 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3485 snew(ir->opts.nrdf, nr);
3486 snew(ir->opts.tau_t, nr);
3487 snew(ir->opts.ref_t, nr);
3488 if (ir->eI == eiBD && ir->bd_fric == 0)
3490 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3493 if (useReferenceTemperature)
3495 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3497 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3501 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3502 for (i = 0; (i < nr); i++)
3504 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3506 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3507 warning_error(wi, warn_buf);
3510 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3514 "tau-t = -1 is the value to signal that a group should not have "
3515 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3518 if (ir->opts.tau_t[i] >= 0)
3520 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3523 if (ir->etc != etcNO && ir->nsttcouple == -1)
3525 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3530 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3533 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3534 "md-vv; use either vrescale temperature with berendsen pressure or "
3535 "Nose-Hoover temperature with MTTK pressure");
3537 if (ir->epc == epcMTTK)
3539 if (ir->etc != etcNOSEHOOVER)
3542 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3547 if (ir->nstpcouple != ir->nsttcouple)
3549 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3550 ir->nstpcouple = ir->nsttcouple = mincouple;
3552 "for current Trotter decomposition methods with vv, nsttcouple and "
3553 "nstpcouple must be equal. Both have been reset to "
3554 "min(nsttcouple,nstpcouple) = %d",
3556 warning_note(wi, warn_buf);
3561 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3562 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3564 if (ETC_ANDERSEN(ir->etc))
3566 if (ir->nsttcouple != 1)
3570 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3571 "need for larger nsttcouple > 1, since no global parameters are computed. "
3572 "nsttcouple has been reset to 1");
3573 warning_note(wi, warn_buf);
3576 nstcmin = tcouple_min_integration_steps(ir->etc);
3579 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3582 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3583 "least %d times larger than nsttcouple*dt (%g)",
3584 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3585 warning(wi, warn_buf);
3588 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3589 for (i = 0; (i < nr); i++)
3591 if (ir->opts.ref_t[i] < 0)
3593 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3596 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3597 if we are in this conditional) if mc_temp is negative */
3598 if (ir->expandedvals->mc_temp < 0)
3600 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3604 /* Simulated annealing for each group. There are nr groups */
3605 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3606 if (simulatedAnnealingGroupNames.size() == 1
3607 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3609 simulatedAnnealingGroupNames.resize(0);
3611 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3613 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3614 simulatedAnnealingGroupNames.size(), nr);
3618 snew(ir->opts.annealing, nr);
3619 snew(ir->opts.anneal_npoints, nr);
3620 snew(ir->opts.anneal_time, nr);
3621 snew(ir->opts.anneal_temp, nr);
3622 for (i = 0; i < nr; i++)
3624 ir->opts.annealing[i] = eannNO;
3625 ir->opts.anneal_npoints[i] = 0;
3626 ir->opts.anneal_time[i] = nullptr;
3627 ir->opts.anneal_temp[i] = nullptr;
3629 if (!simulatedAnnealingGroupNames.empty())
3632 for (i = 0; i < nr; i++)
3634 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3636 ir->opts.annealing[i] = eannNO;
3638 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3640 ir->opts.annealing[i] = eannSINGLE;
3643 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3645 ir->opts.annealing[i] = eannPERIODIC;
3651 /* Read the other fields too */
3652 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3653 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3655 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3656 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3658 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3659 size_t numSimulatedAnnealingFields = 0;
3660 for (i = 0; i < nr; i++)
3662 if (ir->opts.anneal_npoints[i] == 1)
3666 "Please specify at least a start and an end point for annealing\n");
3668 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3669 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3670 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3673 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3675 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3677 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3678 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3680 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3681 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3683 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3684 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3687 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3688 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3689 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3690 allSimulatedAnnealingTimes.data());
3691 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3692 allSimulatedAnnealingTemperatures.data());
3693 for (i = 0, k = 0; i < nr; i++)
3695 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3697 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3698 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3701 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3703 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3709 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3712 "Annealing timepoints out of order: t=%f comes after "
3714 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3717 if (ir->opts.anneal_temp[i][j] < 0)
3719 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3720 ir->opts.anneal_temp[i][j]);
3725 /* Print out some summary information, to make sure we got it right */
3726 for (i = 0; i < nr; i++)
3728 if (ir->opts.annealing[i] != eannNO)
3730 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3731 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3732 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3733 ir->opts.anneal_npoints[i]);
3734 fprintf(stderr, "Time (ps) Temperature (K)\n");
3735 /* All terms except the last one */
3736 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3738 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3739 ir->opts.anneal_temp[i][j]);
3742 /* Finally the last one */
3743 j = ir->opts.anneal_npoints[i] - 1;
3744 if (ir->opts.annealing[i] == eannSINGLE)
3746 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3747 ir->opts.anneal_temp[i][j]);
3751 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3752 ir->opts.anneal_temp[i][j]);
3753 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3756 "There is a temperature jump when your annealing "
3768 make_pull_groups(ir->pull, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3770 make_pull_coords(ir->pull);
3775 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3778 if (ir->eSwapCoords != eswapNO)
3780 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3783 /* Make indices for IMD session */
3786 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3789 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3790 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3791 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3793 auto accelerations = gmx::splitString(inputrecStrings->acc);
3794 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
3795 if (accelerationGroupNames.size() * DIM != accelerations.size())
3797 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3798 accelerationGroupNames.size(), accelerations.size());
3800 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3801 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3802 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3803 snew(ir->opts.acc, nr);
3804 ir->opts.ngacc = nr;
3806 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3808 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3809 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3810 if (freezeDims.size() != DIM * freezeGroupNames.size())
3812 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3813 freezeGroupNames.size(), freezeDims.size());
3815 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3816 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3817 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3818 ir->opts.ngfrz = nr;
3819 snew(ir->opts.nFreeze, nr);
3820 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3822 for (j = 0; (j < DIM); j++, k++)
3824 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3825 if (!ir->opts.nFreeze[i][j])
3827 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3830 "Please use Y(ES) or N(O) for freezedim only "
3832 freezeDims[k].c_str());
3833 warning(wi, warn_buf);
3838 for (; (i < nr); i++)
3840 for (j = 0; (j < DIM); j++)
3842 ir->opts.nFreeze[i][j] = 0;
3846 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3847 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3848 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3849 add_wall_energrps(groups, ir->nwall, symtab);
3850 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3851 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3852 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3853 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3854 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3856 if (ir->comm_mode != ecmNO)
3858 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3861 /* Now we have filled the freeze struct, so we can calculate NRDF */
3862 calc_nrdf(mtop, ir, gnames);
3864 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3865 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3866 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3867 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3868 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3869 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3870 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3871 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3872 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3873 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3874 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3875 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3878 /* MiMiC QMMM input processing */
3879 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3880 if (qmGroupNames.size() > 1)
3882 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3884 /* group rest, if any, is always MM! */
3885 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3886 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3887 ir->opts.ngQM = qmGroupNames.size();
3889 /* end of MiMiC QMMM input */
3893 for (auto group : gmx::keysOf(groups->groups))
3895 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3896 for (const auto& entry : groups->groups[group])
3898 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3900 fprintf(stderr, "\n");
3904 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3905 snew(ir->opts.egp_flags, nr * nr);
3907 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
3908 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3910 warning_error(wi, "Energy group exclusions are currently not supported");
3912 if (bExcl && EEL_FULL(ir->coulombtype))
3914 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3917 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
3918 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3919 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3922 "Can only have energy group pair tables in combination with user tables for VdW "
3926 /* final check before going out of scope if simulated tempering variables
3927 * need to be set to default values.
3929 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3931 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3932 warning(wi, gmx::formatString(
3933 "the value for nstexpanded was not specified for "
3934 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3935 "by default, but it is recommended to set it to an explicit value!",
3936 ir->expandedvals->nstexpanded));
3938 for (i = 0; (i < defaultIndexGroups->nr); i++)
3943 done_blocka(defaultIndexGroups);
3944 sfree(defaultIndexGroups);
3948 static void check_disre(const gmx_mtop_t* mtop)
3950 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3952 const gmx_ffparams_t& ffparams = mtop->ffparams;
3955 for (int i = 0; i < ffparams.numTypes(); i++)
3957 int ftype = ffparams.functype[i];
3958 if (ftype == F_DISRES)
3960 int label = ffparams.iparams[i].disres.label;
3961 if (label == old_label)
3963 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3972 "Found %d double distance restraint indices,\n"
3973 "probably the parameters for multiple pairs in one restraint "
3974 "are not identical\n",
3980 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3983 gmx_mtop_ilistloop_t iloop;
3985 const t_iparams* pr;
3992 for (d = 0; d < DIM; d++)
3994 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3996 /* Check for freeze groups */
3997 for (g = 0; g < ir->opts.ngfrz; g++)
3999 for (d = 0; d < DIM; d++)
4001 if (ir->opts.nFreeze[g][d] != 0)
4009 /* Check for position restraints */
4010 iloop = gmx_mtop_ilistloop_init(sys);
4011 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4013 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4015 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4017 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4018 for (d = 0; d < DIM; d++)
4020 if (pr->posres.fcA[d] != 0)
4026 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4028 /* Check for flat-bottom posres */
4029 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4030 if (pr->fbposres.k != 0)
4032 switch (pr->fbposres.geom)
4034 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4035 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4036 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4037 case efbposresCYLINDER:
4038 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4039 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4040 case efbposresX: /* d=XX */
4041 case efbposresY: /* d=YY */
4042 case efbposresZ: /* d=ZZ */
4043 d = pr->fbposres.geom - efbposresX;
4048 " Invalid geometry for flat-bottom position restraint.\n"
4049 "Expected nr between 1 and %d. Found %d\n",
4050 efbposresNR - 1, pr->fbposres.geom);
4057 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4060 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4062 bool* bC6ParametersWorkWithGeometricRules,
4063 bool* bC6ParametersWorkWithLBRules,
4064 bool* bLBRulesPossible)
4066 int ntypes, tpi, tpj;
4069 double c6i, c6j, c12i, c12j;
4070 double c6, c6_geometric, c6_LB;
4071 double sigmai, sigmaj, epsi, epsj;
4072 bool bCanDoLBRules, bCanDoGeometricRules;
4075 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4076 * force-field floating point parameters.
4079 ptr = getenv("GMX_LJCOMB_TOL");
4083 double gmx_unused canary;
4085 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4088 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4093 *bC6ParametersWorkWithLBRules = TRUE;
4094 *bC6ParametersWorkWithGeometricRules = TRUE;
4095 bCanDoLBRules = TRUE;
4096 ntypes = mtop->ffparams.atnr;
4097 snew(typecount, ntypes);
4098 gmx_mtop_count_atomtypes(mtop, state, typecount);
4099 *bLBRulesPossible = TRUE;
4100 for (tpi = 0; tpi < ntypes; ++tpi)
4102 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4103 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4104 for (tpj = tpi; tpj < ntypes; ++tpj)
4106 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4107 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4108 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4109 c6_geometric = std::sqrt(c6i * c6j);
4110 if (!gmx_numzero(c6_geometric))
4112 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4114 sigmai = gmx::sixthroot(c12i / c6i);
4115 sigmaj = gmx::sixthroot(c12j / c6j);
4116 epsi = c6i * c6i / (4.0 * c12i);
4117 epsj = c6j * c6j / (4.0 * c12j);
4118 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4122 *bLBRulesPossible = FALSE;
4123 c6_LB = c6_geometric;
4125 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4130 *bC6ParametersWorkWithLBRules = FALSE;
4133 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4135 if (!bCanDoGeometricRules)
4137 *bC6ParametersWorkWithGeometricRules = FALSE;
4144 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4146 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4148 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4149 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4150 if (ir->ljpme_combination_rule == eljpmeLB)
4152 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4155 "You are using arithmetic-geometric combination rules "
4156 "in LJ-PME, but your non-bonded C6 parameters do not "
4157 "follow these rules.");
4162 if (!bC6ParametersWorkWithGeometricRules)
4164 if (ir->eDispCorr != edispcNO)
4167 "You are using geometric combination rules in "
4168 "LJ-PME, but your non-bonded C6 parameters do "
4169 "not follow these rules. "
4170 "This will introduce very small errors in the forces and energies in "
4171 "your simulations. Dispersion correction will correct total energy "
4172 "and/or pressure for isotropic systems, but not forces or surface "
4178 "You are using geometric combination rules in "
4179 "LJ-PME, but your non-bonded C6 parameters do "
4180 "not follow these rules. "
4181 "This will introduce very small errors in the forces and energies in "
4182 "your simulations. If your system is homogeneous, consider using "
4183 "dispersion correction "
4184 "for the total energy and pressure.");
4190 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4192 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4193 gmx::assertMtsRequirements(*ir);
4195 char err_buf[STRLEN];
4200 gmx_mtop_atomloop_block_t aloopb;
4202 char warn_buf[STRLEN];
4204 set_warning_line(wi, mdparin, -1);
4206 if (absolute_reference(ir, sys, false, AbsRef))
4209 "Removing center of mass motion in the presence of position restraints might "
4210 "cause artifacts. When you are using position restraints to equilibrate a "
4211 "macro-molecule, the artifacts are usually negligible.");
4214 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4215 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4217 /* Check if a too small Verlet buffer might potentially
4218 * cause more drift than the thermostat can couple off.
4220 /* Temperature error fraction for warning and suggestion */
4221 const real T_error_warn = 0.002;
4222 const real T_error_suggest = 0.001;
4223 /* For safety: 2 DOF per atom (typical with constraints) */
4224 const real nrdf_at = 2;
4225 real T, tau, max_T_error;
4230 for (i = 0; i < ir->opts.ngtc; i++)
4232 T = std::max(T, ir->opts.ref_t[i]);
4233 tau = std::max(tau, ir->opts.tau_t[i]);
4237 /* This is a worst case estimate of the temperature error,
4238 * assuming perfect buffer estimation and no cancelation
4239 * of errors. The factor 0.5 is because energy distributes
4240 * equally over Ekin and Epot.
4242 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4243 if (max_T_error > T_error_warn)
4246 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4247 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4248 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4249 "%.0e or decrease tau_t.",
4250 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4251 ir->verletbuf_tol * T_error_suggest / max_T_error);
4252 warning(wi, warn_buf);
4257 if (ETC_ANDERSEN(ir->etc))
4261 for (i = 0; i < ir->opts.ngtc; i++)
4264 "all tau_t must currently be equal using Andersen temperature control, "
4265 "violated for group %d",
4267 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4269 "all tau_t must be positive using Andersen temperature control, "
4271 i, ir->opts.tau_t[i]);
4272 CHECK(ir->opts.tau_t[i] < 0);
4275 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4277 for (i = 0; i < ir->opts.ngtc; i++)
4279 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4281 "tau_t/delta_t for group %d for temperature control method %s must be a "
4282 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4283 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4285 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4286 CHECK(nsteps % ir->nstcomm != 0);
4291 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4292 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4295 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4296 "rounding errors can lead to build up of kinetic energy of the center of mass");
4299 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4302 for (int g = 0; g < ir->opts.ngtc; g++)
4304 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4306 if (ir->tau_p < 1.9 * tau_t_max)
4308 std::string message = gmx::formatString(
4309 "With %s T-coupling and %s p-coupling, "
4310 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4311 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4313 warning(wi, message.c_str());
4317 /* Check for pressure coupling with absolute position restraints */
4318 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4320 absolute_reference(ir, sys, TRUE, AbsRef);
4322 for (m = 0; m < DIM; m++)
4324 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4327 "You are using pressure coupling with absolute position restraints, "
4328 "this will give artifacts. Use the refcoord_scaling option.");
4336 aloopb = gmx_mtop_atomloop_block_init(sys);
4338 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4340 if (atom->q != 0 || atom->qB != 0)
4348 if (EEL_FULL(ir->coulombtype))
4351 "You are using full electrostatics treatment %s for a system without charges.\n"
4352 "This costs a lot of performance for just processing zeros, consider using %s "
4354 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4355 warning(wi, err_buf);
4360 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4363 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4364 "You might want to consider using %s electrostatics.\n",
4366 warning_note(wi, err_buf);
4370 /* Check if combination rules used in LJ-PME are the same as in the force field */
4371 if (EVDW_PME(ir->vdwtype))
4373 check_combination_rules(ir, sys, wi);
4376 /* Generalized reaction field */
4377 if (ir->coulombtype == eelGRF_NOTUSED)
4380 "Generalized reaction-field electrostatics is no longer supported. "
4381 "You can use normal reaction-field instead and compute the reaction-field "
4382 "constant by hand.");
4386 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4388 for (m = 0; (m < DIM); m++)
4390 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4399 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4400 for (const AtomProxy atomP : AtomRange(*sys))
4402 const t_atom& local = atomP.atom();
4403 int i = atomP.globalAtomNumber();
4404 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4407 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4409 for (m = 0; (m < DIM); m++)
4411 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4415 for (m = 0; (m < DIM); m++)
4417 if (fabs(acc[m]) > 1e-6)
4419 const char* dim[DIM] = { "X", "Y", "Z" };
4420 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4421 ir->nstcomm != 0 ? "" : "not");
4422 if (ir->nstcomm != 0 && m < ndof_com(ir))
4426 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4428 ir->opts.acc[i][m] -= acc[m];
4436 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4437 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4439 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4447 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4449 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4451 absolute_reference(ir, sys, FALSE, AbsRef);
4452 for (m = 0; m < DIM; m++)
4454 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4457 "You are using an absolute reference for pulling, but the rest of "
4458 "the system does not have an absolute reference. This will lead to "
4467 for (i = 0; i < 3; i++)
4469 for (m = 0; m <= i; m++)
4471 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4473 for (c = 0; c < ir->pull->ncoord; c++)
4475 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4478 "Can not have dynamic box while using pull geometry '%s' "
4480 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4491 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4493 char warn_buf[STRLEN];
4496 ptr = check_box(ir->pbcType, box);
4499 warning_error(wi, ptr);
4502 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4504 if (ir->shake_tol <= 0.0)
4506 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4507 warning_error(wi, warn_buf);
4511 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4513 /* If we have Lincs constraints: */
4514 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4517 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4518 warning_note(wi, warn_buf);
4521 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4524 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4526 warning_note(wi, warn_buf);
4528 if (ir->epc == epcMTTK)
4530 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4534 if (bHasAnyConstraints && ir->epc == epcMTTK)
4536 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4539 if (ir->LincsWarnAngle > 90.0)
4541 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4542 warning(wi, warn_buf);
4543 ir->LincsWarnAngle = 90.0;
4546 if (ir->pbcType != PbcType::No)
4548 if (ir->nstlist == 0)
4551 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4552 "atoms might cause the simulation to crash.");
4554 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4557 "ERROR: The cut-off length is longer than half the shortest box vector or "
4558 "longer than the smallest box diagonal element. Increase the box size or "
4559 "decrease rlist.\n");
4560 warning_error(wi, warn_buf);