2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
7 * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
9 * and including many others, as listed in the AUTHORS file in the
10 * top-level source directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
52 #include "gromacs/applied_forces/awh/read_params.h"
53 #include "gromacs/fileio/readinp.h"
54 #include "gromacs/fileio/warninp.h"
55 #include "gromacs/gmxlib/network.h"
56 #include "gromacs/gmxpreprocess/toputil.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/math/units.h"
59 #include "gromacs/math/utilities.h"
60 #include "gromacs/math/vec.h"
61 #include "gromacs/mdlib/calc_verletbuf.h"
62 #include "gromacs/mdlib/vcm.h"
63 #include "gromacs/mdrun/mdmodules.h"
64 #include "gromacs/mdtypes/awh_params.h"
65 #include "gromacs/mdtypes/inputrec.h"
66 #include "gromacs/mdtypes/md_enums.h"
67 #include "gromacs/mdtypes/multipletimestepping.h"
68 #include "gromacs/mdtypes/pull_params.h"
69 #include "gromacs/options/options.h"
70 #include "gromacs/options/treesupport.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/selection/indexutil.h"
73 #include "gromacs/topology/block.h"
74 #include "gromacs/topology/ifunc.h"
75 #include "gromacs/topology/index.h"
76 #include "gromacs/topology/mtop_util.h"
77 #include "gromacs/topology/symtab.h"
78 #include "gromacs/topology/topology.h"
79 #include "gromacs/utility/arrayref.h"
80 #include "gromacs/utility/cstringutil.h"
81 #include "gromacs/utility/exceptions.h"
82 #include "gromacs/utility/fatalerror.h"
83 #include "gromacs/utility/filestream.h"
84 #include "gromacs/utility/gmxassert.h"
85 #include "gromacs/utility/ikeyvaluetreeerror.h"
86 #include "gromacs/utility/keyvaluetree.h"
87 #include "gromacs/utility/keyvaluetreebuilder.h"
88 #include "gromacs/utility/keyvaluetreemdpwriter.h"
89 #include "gromacs/utility/keyvaluetreetransform.h"
90 #include "gromacs/utility/mdmodulesnotifiers.h"
91 #include "gromacs/utility/smalloc.h"
92 #include "gromacs/utility/strconvert.h"
93 #include "gromacs/utility/stringcompare.h"
94 #include "gromacs/utility/stringutil.h"
95 #include "gromacs/utility/textwriter.h"
99 using gmx::BasicVector;
101 /* Resource parameters
102 * Do not change any of these until you read the instruction
103 * in readinp.h. Some cpp's do not take spaces after the backslash
104 * (like the c-shell), which will give you a very weird compiler
108 struct gmx_inputrec_strings
110 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
111 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
112 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
113 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
114 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
115 char lambda_weights[STRLEN];
116 std::vector<std::string> pullGroupNames;
117 std::vector<std::string> rotateGroupNames;
118 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
121 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
122 static gmx_inputrec_strings* inputrecStrings = nullptr;
124 void init_inputrec_strings()
129 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
130 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
132 inputrecStrings = new gmx_inputrec_strings();
135 void done_inputrec_strings()
137 delete inputrecStrings;
138 inputrecStrings = nullptr;
144 egrptpALL, /* All particles have to be a member of a group. */
145 egrptpALL_GENREST, /* A rest group with name is generated for particles *
146 * that are not part of any group. */
147 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
148 * for the rest group. */
149 egrptpONE /* Merge all selected groups into one group, *
150 * make a rest group for the remaining particles. */
153 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
154 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
155 "h-angles", "all-angles", nullptr };
157 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
158 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
160 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
165 for (i = 0; i < ntemps; i++)
167 /* simple linear scaling -- allows more control */
168 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
170 simtemp->temperatures[i] =
172 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
174 else if (simtemp->eSimTempScale
175 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
177 simtemp->temperatures[i] = simtemp->simtemp_low
178 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
179 static_cast<real>((1.0 * i) / (ntemps - 1)));
181 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
183 simtemp->temperatures[i] = simtemp->simtemp_low
184 + (simtemp->simtemp_high - simtemp->simtemp_low)
185 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
190 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
191 gmx_fatal(FARGS, "%s", errorstr);
197 static void _low_check(bool b, const char* s, warninp_t wi)
201 warning_error(wi, s);
205 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
209 if (*p > 0 && *p % nst != 0)
211 /* Round up to the next multiple of nst */
212 *p = ((*p) / nst + 1) * nst;
213 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
218 //! Convert legacy mdp entries to modern ones.
219 static void process_interaction_modifier(InteractionModifiers* eintmod)
221 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
223 *eintmod = InteractionModifiers::PotShift;
227 void check_ir(const char* mdparin,
228 const gmx::MDModulesNotifiers& mdModulesNotifiers,
232 /* Check internal consistency.
233 * NOTE: index groups are not set here yet, don't check things
234 * like temperature coupling group options here, but in triple_check
237 /* Strange macro: first one fills the err_buf, and then one can check
238 * the condition, which will print the message and increase the error
241 #define CHECK(b) _low_check(b, err_buf, wi)
242 char err_buf[256], warn_buf[STRLEN];
245 t_lambda* fep = ir->fepvals.get();
246 t_expanded* expand = ir->expandedvals.get();
248 set_warning_line(wi, mdparin, -1);
250 /* We cannot check MTS requirements with an invalid MTS setup
251 * and we will already have generated errors with an invalid MTS setup.
253 if (gmx::haveValidMtsSetup(*ir))
255 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
257 for (const auto& errorMessage : errorMessages)
259 warning_error(wi, errorMessage.c_str());
263 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
265 std::string message =
266 gmx::formatString("%s electrostatics is no longer supported",
267 enumValueToString(CoulombInteractionType::RFNecUnsupported));
268 warning_error(wi, message);
271 /* BASIC CUT-OFF STUFF */
272 if (ir->rcoulomb < 0)
274 warning_error(wi, "rcoulomb should be >= 0");
278 warning_error(wi, "rvdw should be >= 0");
280 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
282 warning_error(wi, "rlist should be >= 0");
285 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
286 "neighbour-list update scheme for efficient buffering for improved energy "
287 "conservation, please use the Verlet cut-off scheme instead.)");
288 CHECK(ir->nstlist < 0);
290 process_interaction_modifier(&ir->coulomb_modifier);
291 process_interaction_modifier(&ir->vdw_modifier);
293 if (ir->cutoff_scheme == CutoffScheme::Group)
296 "The group cutoff scheme has been removed since GROMACS 2020. "
297 "Please use the Verlet cutoff scheme.");
299 if (ir->cutoff_scheme == CutoffScheme::Verlet)
303 /* Normal Verlet type neighbor-list, currently only limited feature support */
304 if (inputrec2nboundeddim(ir) < 3)
306 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
309 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
310 if (ir->rcoulomb != ir->rvdw)
312 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
313 // for PME load balancing, we can support this exception.
314 bool bUsesPmeTwinRangeKernel =
315 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
316 && ir->rcoulomb > ir->rvdw);
317 if (!bUsesPmeTwinRangeKernel)
320 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
321 "rcoulomb>rvdw with PME electrostatics)");
325 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
327 if (ir->vdw_modifier == InteractionModifiers::None
328 || ir->vdw_modifier == InteractionModifiers::PotShift)
331 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
332 : InteractionModifiers::PotSwitch);
335 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
337 enumValueToString(ir->vdwtype),
338 enumValueToString(VanDerWaalsType::Cut),
339 enumValueToString(ir->vdw_modifier));
340 warning_note(wi, warn_buf);
342 ir->vdwtype = VanDerWaalsType::Cut;
347 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
348 enumValueToString(ir->vdwtype),
349 enumValueToString(ir->vdw_modifier));
350 warning_error(wi, warn_buf);
354 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
357 "With Verlet lists only cut-off and PME LJ interactions are supported");
359 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
360 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
363 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
364 "electrostatics are supported");
366 if (!(ir->coulomb_modifier == InteractionModifiers::None
367 || ir->coulomb_modifier == InteractionModifiers::PotShift))
369 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
370 warning_error(wi, warn_buf);
373 if (EEL_USER(ir->coulombtype))
376 "Coulomb type %s is not supported with the verlet scheme",
377 enumValueToString(ir->coulombtype));
378 warning_error(wi, warn_buf);
381 if (ir->nstlist <= 0)
383 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
386 if (ir->nstlist < 10)
389 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
390 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
394 rc_max = std::max(ir->rvdw, ir->rcoulomb);
398 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
399 ir->verletbuf_tol = 0;
402 else if (ir->verletbuf_tol <= 0)
404 if (ir->verletbuf_tol == 0)
406 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
409 if (ir->rlist < rc_max)
412 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
415 if (ir->rlist == rc_max && ir->nstlist > 1)
419 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
420 "buffer. The cluster pair list does have a buffering effect, but choosing "
421 "a larger rlist might be necessary for good energy conservation.");
426 if (ir->rlist > rc_max)
429 "You have set rlist larger than the interaction cut-off, but you also "
430 "have verlet-buffer-tolerance > 0. Will set rlist using "
431 "verlet-buffer-tolerance.");
434 if (ir->nstlist == 1)
436 /* No buffer required */
441 if (EI_DYNAMICS(ir->eI))
443 if (inputrec2nboundeddim(ir) < 3)
446 "The box volume is required for calculating rlist from the "
447 "energy drift with verlet-buffer-tolerance > 0. You are "
448 "using at least one unbounded dimension, so no volume can be "
449 "computed. Either use a finite box, or set rlist yourself "
450 "together with verlet-buffer-tolerance = -1.");
452 /* Set rlist temporarily so we can continue processing */
457 /* Set the buffer to 5% of the cut-off */
458 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
464 /* GENERAL INTEGRATOR STUFF */
467 if (ir->etc != TemperatureCoupling::No)
469 if (EI_RANDOM(ir->eI))
472 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
473 "implicitly. See the documentation for more information on which "
474 "parameters affect temperature for %s.",
475 enumValueToString(ir->etc),
476 enumValueToString(ir->eI),
477 enumValueToString(ir->eI));
482 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
484 enumValueToString(ir->etc),
485 enumValueToString(ir->eI));
487 warning_note(wi, warn_buf);
489 ir->etc = TemperatureCoupling::No;
491 if (ir->eI == IntegrationAlgorithm::VVAK)
494 "Integrator method %s is implemented primarily for validation purposes; for "
495 "molecular dynamics, you should probably be using %s or %s",
496 enumValueToString(IntegrationAlgorithm::VVAK),
497 enumValueToString(IntegrationAlgorithm::MD),
498 enumValueToString(IntegrationAlgorithm::VV));
499 warning_note(wi, warn_buf);
501 if (!EI_DYNAMICS(ir->eI))
503 if (ir->epc != PressureCoupling::No)
506 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
507 enumValueToString(ir->epc),
508 enumValueToString(ir->eI));
509 warning_note(wi, warn_buf);
511 ir->epc = PressureCoupling::No;
513 if (EI_DYNAMICS(ir->eI))
515 if (ir->nstcalcenergy < 0)
517 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
518 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
520 /* nstcalcenergy larger than nstener does not make sense.
521 * We ideally want nstcalcenergy=nstener.
525 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
529 ir->nstcalcenergy = ir->nstenergy;
533 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
534 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
535 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
538 const char* nsten = "nstenergy";
539 const char* nstdh = "nstdhdl";
540 const char* min_name = nsten;
541 int min_nst = ir->nstenergy;
543 /* find the smallest of ( nstenergy, nstdhdl ) */
544 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
545 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
547 min_nst = ir->fepvals->nstdhdl;
550 /* If the user sets nstenergy small, we should respect that */
551 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
552 warning_note(wi, warn_buf);
553 ir->nstcalcenergy = min_nst;
556 if (ir->epc != PressureCoupling::No)
558 if (ir->nstpcouple < 0)
560 ir->nstpcouple = ir_optimal_nstpcouple(ir);
562 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
565 "With multiple time stepping, nstpcouple should be a mutiple of "
570 if (ir->nstcalcenergy > 0)
572 if (ir->efep != FreeEnergyPerturbationType::No)
574 /* nstdhdl should be a multiple of nstcalcenergy */
575 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
579 /* nstexpanded should be a multiple of nstcalcenergy */
580 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
582 /* for storing exact averages nstenergy should be
583 * a multiple of nstcalcenergy
585 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
588 // Inquire all MDModules, if their parameters match with the energy
589 // calculation frequency
590 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
591 mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
593 // Emit all errors from the energy calculation frequency checks
594 for (const std::string& energyFrequencyErrorMessage :
595 energyCalculationFrequencyErrors.errorMessages())
597 warning_error(wi, energyFrequencyErrorMessage);
601 if (ir->nsteps == 0 && !ir->bContinuation)
604 "For a correct single-point energy evaluation with nsteps = 0, use "
605 "continuation = yes to avoid constraining the input coordinates.");
609 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
612 "You are doing a continuation with SD or BD, make sure that ld_seed is "
613 "different from the previous run (using ld_seed=-1 will ensure this)");
619 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
620 CHECK(ir->pbcType != PbcType::Xyz);
621 sprintf(err_buf, "with TPI nstlist should be larger than zero");
622 CHECK(ir->nstlist <= 0);
623 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
624 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
628 if ((opts->nshake > 0) && (opts->bMorse))
630 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
631 warning(wi, warn_buf);
634 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
637 "You are doing a continuation with SD or BD, make sure that ld_seed is "
638 "different from the previous run (using ld_seed=-1 will ensure this)");
640 /* verify simulated tempering options */
644 bool bAllTempZero = TRUE;
645 for (i = 0; i < fep->n_lambda; i++)
648 "Entry %d for %s must be between 0 and 1, instead is %g",
650 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
651 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
652 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
653 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
655 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
657 bAllTempZero = FALSE;
660 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
661 CHECK(bAllTempZero == TRUE);
663 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
664 CHECK(ir->eI != IntegrationAlgorithm::VV);
666 /* check compatability of the temperature coupling with simulated tempering */
668 if (ir->etc == TemperatureCoupling::NoseHoover)
671 "Nose-Hoover based temperature control such as [%s] my not be "
672 "entirelyconsistent with simulated tempering",
673 enumValueToString(ir->etc));
674 warning_note(wi, warn_buf);
677 /* check that the temperatures make sense */
680 "Higher simulated tempering temperature (%g) must be >= than the simulated "
681 "tempering lower temperature (%g)",
682 ir->simtempvals->simtemp_high,
683 ir->simtempvals->simtemp_low);
684 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
687 "Higher simulated tempering temperature (%g) must be >= zero",
688 ir->simtempvals->simtemp_high);
689 CHECK(ir->simtempvals->simtemp_high <= 0);
692 "Lower simulated tempering temperature (%g) must be >= zero",
693 ir->simtempvals->simtemp_low);
694 CHECK(ir->simtempvals->simtemp_low <= 0);
697 /* verify free energy options */
699 if (ir->efep != FreeEnergyPerturbationType::No)
701 fep = ir->fepvals.get();
702 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
703 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
706 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
708 static_cast<int>(fep->sc_r_power));
709 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
712 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
715 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
718 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
720 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
722 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
723 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
725 sprintf(err_buf, "Free-energy not implemented for Ewald");
726 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
728 /* check validty of lambda inputs */
729 if (fep->n_lambda == 0)
731 /* Clear output in case of no states:*/
732 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
733 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
738 "initial thermodynamic state %d does not exist, only goes to %d",
741 CHECK((fep->init_fep_state >= fep->n_lambda));
745 "Lambda state must be set, either with init-lambda-state or with init-lambda");
746 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
749 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
750 "init-lambda-state or with init-lambda, but not both",
752 fep->init_fep_state);
753 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
756 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
760 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
762 if (fep->separate_dvdl[i])
767 if (n_lambda_terms > 1)
770 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
771 "use init-lambda to set lambda state (except for slow growth). Use "
772 "init-lambda-state instead.");
773 warning(wi, warn_buf);
776 if (n_lambda_terms < 2 && fep->n_lambda > 0)
779 "init-lambda is deprecated for setting lambda state (except for slow "
780 "growth). Use init-lambda-state instead.");
784 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
786 for (i = 0; i < fep->n_lambda; i++)
788 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
790 "Entry %d for %s must be between 0 and 1, instead is %g",
792 enumValueToString(enumValue),
793 fep->all_lambda[j][i]);
794 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
798 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
800 for (i = 0; i < fep->n_lambda; i++)
803 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
804 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
805 "crashes, and is not supported.",
807 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
808 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
809 CHECK((fep->sc_alpha > 0)
810 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
811 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
812 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
813 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
818 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
820 real sigma, lambda, r_sc;
823 /* Maximum estimate for A and B charges equal with lambda power 1 */
825 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
826 1.0 / fep->sc_r_power);
828 "With PME there is a minor soft core effect present at the cut-off, "
829 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
830 "energy conservation, but usually other effects dominate. With a common sigma "
831 "value of %g nm the fraction of the particle-particle potential at the cut-off "
832 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
838 warning_note(wi, warn_buf);
841 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
842 be treated differently, but that's the next step */
844 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
846 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
847 for (j = 0; j < fep->n_lambda; j++)
849 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
850 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
854 if (fep->softcoreFunction == SoftcoreType::Gapsys)
856 if (fep->sc_alpha < 0.0)
859 "sc_alpha is equal %g but must be >= 0 when used with sc_function=gapsys.",
861 warning_note(wi, warn_buf);
864 if ((fep->sc_sigma < 0.0) || (fep->sc_sigma >= 1.0))
867 "sc_sigma is equal %g but must be in [0,1) when used with "
868 "sc_function=gapsys.",
870 warning_note(wi, warn_buf);
875 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
877 fep = ir->fepvals.get();
879 /* checking equilibration of weights inputs for validity */
882 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
884 expand->equil_n_at_lam,
885 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
886 CHECK((expand->equil_n_at_lam > 0)
887 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
890 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
892 expand->equil_samples,
893 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
894 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
897 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
899 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
900 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
903 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
904 expand->equil_samples,
905 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
906 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
909 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
911 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
912 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
915 "weight-equil-number-all-lambda (%d) must be a positive integer if "
916 "lmc-weights-equil=%s",
917 expand->equil_n_at_lam,
918 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
919 CHECK((expand->equil_n_at_lam <= 0)
920 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
923 "weight-equil-number-samples (%d) must be a positive integer if "
924 "lmc-weights-equil=%s",
925 expand->equil_samples,
926 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
927 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
930 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
932 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
933 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
936 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
937 expand->equil_wl_delta,
938 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
939 CHECK((expand->equil_wl_delta <= 0)
940 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
943 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
945 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
946 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
949 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
950 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
951 enumValueToString(LambdaWeightCalculation::WL),
952 enumValueToString(LambdaWeightCalculation::WWL));
953 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!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 != "
965 expand->lmc_forced_nstart);
966 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
967 && (expand->elmcmove != LambdaMoveCalculation::No));
968 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
969 CHECK((expand->lmc_forced_nstart < 0));
971 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
972 fep->init_fep_state);
973 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
975 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
976 CHECK((expand->init_wl_delta < 0));
977 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
978 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
979 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
980 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
982 /* if there is no temperature control, we need to specify an MC temperature */
983 if (!integratorHasReferenceTemperature(ir)
984 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
987 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
988 "to a positive number");
989 warning_error(wi, err_buf);
991 if (expand->nstTij > 0)
993 sprintf(err_buf, "nstlog must be non-zero");
994 CHECK(ir->nstlog == 0);
995 // Avoid modulus by zero in the case that already triggered an error exit.
999 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
1002 CHECK((expand->nstTij % ir->nstlog) != 0);
1008 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
1009 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
1012 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
1014 if (ir->pbcType == PbcType::No)
1016 if (ir->epc != PressureCoupling::No)
1018 warning(wi, "Turning off pressure coupling for vacuum system");
1019 ir->epc = PressureCoupling::No;
1025 "Can not have pressure coupling with pbc=%s",
1026 c_pbcTypeNames[ir->pbcType].c_str());
1027 CHECK(ir->epc != PressureCoupling::No);
1029 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1030 CHECK(EEL_FULL(ir->coulombtype));
1033 "Can not have dispersion correction with pbc=%s",
1034 c_pbcTypeNames[ir->pbcType].c_str());
1035 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1038 if (ir->rlist == 0.0)
1041 "can only have neighborlist cut-off zero (=infinite)\n"
1042 "with coulombtype = %s or coulombtype = %s\n"
1043 "without periodic boundary conditions (pbc = %s) and\n"
1044 "rcoulomb and rvdw set to zero",
1045 enumValueToString(CoulombInteractionType::Cut),
1046 enumValueToString(CoulombInteractionType::User),
1047 c_pbcTypeNames[PbcType::No].c_str());
1048 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1049 && (ir->coulombtype != CoulombInteractionType::User))
1050 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1052 if (ir->nstlist > 0)
1055 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1056 "nstype=simple and only one MPI rank");
1061 if (ir->nstcomm == 0)
1063 // TODO Change this behaviour. There should be exactly one way
1064 // to turn off an algorithm.
1065 ir->comm_mode = ComRemovalAlgorithm::No;
1067 if (ir->comm_mode != ComRemovalAlgorithm::No)
1069 if (ir->nstcomm < 0)
1071 // TODO Such input was once valid. Now that we've been
1072 // helpful for a few years, we should reject such input,
1073 // lest we have to support every historical decision
1076 "If you want to remove the rotation around the center of mass, you should set "
1077 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1078 "its absolute value");
1079 ir->nstcomm = abs(ir->nstcomm);
1082 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy
1083 && ir->comm_mode != ComRemovalAlgorithm::LinearAccelerationCorrection)
1086 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider "
1087 "setting nstcomm equal to nstcalcenergy for less overhead");
1090 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1093 "Can not remove the rotation around the center of mass with periodic "
1095 CHECK(ir->bPeriodicMols);
1096 if (ir->pbcType != PbcType::No)
1099 "Removing the rotation around the center of mass in a periodic system, "
1100 "this can lead to artifacts. Only use this on a single (cluster of) "
1101 "molecules. This cluster should not cross periodic boundaries.");
1106 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1107 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1110 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1111 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1113 enumValueToString(IntegrationAlgorithm::SD1));
1114 warning_note(wi, warn_buf);
1117 /* TEMPERATURE COUPLING */
1118 if (ir->etc == TemperatureCoupling::Yes)
1120 ir->etc = TemperatureCoupling::Berendsen;
1122 "Old option for temperature coupling given: "
1123 "changing \"yes\" to \"Berendsen\"\n");
1126 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1128 if (ir->opts.nhchainlength < 1)
1131 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1133 ir->opts.nhchainlength);
1134 ir->opts.nhchainlength = 1;
1135 warning(wi, warn_buf);
1138 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1142 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1143 ir->opts.nhchainlength = 1;
1148 ir->opts.nhchainlength = 0;
1151 if (ir->eI == IntegrationAlgorithm::VVAK)
1154 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1156 enumValueToString(IntegrationAlgorithm::VVAK));
1157 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1160 if (ETC_ANDERSEN(ir->etc))
1163 "%s temperature control not supported for integrator %s.",
1164 enumValueToString(ir->etc),
1165 enumValueToString(ir->eI));
1166 CHECK(!(EI_VV(ir->eI)));
1168 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1171 "Center of mass removal not necessary for %s. All velocities of coupled "
1172 "groups are rerandomized periodically, so flying ice cube errors will not "
1174 enumValueToString(ir->etc));
1175 warning_note(wi, warn_buf);
1179 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1180 "randomized every time step",
1182 enumValueToString(ir->etc));
1183 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1186 if (ir->etc == TemperatureCoupling::Berendsen)
1189 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1190 "might want to consider using the %s thermostat.",
1191 enumValueToString(ir->etc),
1192 enumValueToString(TemperatureCoupling::VRescale));
1193 warning_note(wi, warn_buf);
1196 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1197 && ir->epc == PressureCoupling::Berendsen)
1200 "Using Berendsen pressure coupling invalidates the "
1201 "true ensemble for the thermostat");
1202 warning(wi, warn_buf);
1205 /* PRESSURE COUPLING */
1206 if (ir->epc == PressureCoupling::Isotropic)
1208 ir->epc = PressureCoupling::Berendsen;
1210 "Old option for pressure coupling given: "
1211 "changing \"Isotropic\" to \"Berendsen\"\n");
1214 if (ir->epc != PressureCoupling::No)
1216 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1218 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1219 CHECK(ir->tau_p <= 0);
1221 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1224 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1225 "times larger than nstpcouple*dt (%g)",
1226 enumValueToString(ir->epc),
1228 pcouple_min_integration_steps(ir->epc),
1230 warning(wi, warn_buf);
1234 "compressibility must be > 0 when using pressure"
1236 enumValueToString(ir->epc));
1237 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1238 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1239 && ir->compress[ZZ][YY] <= 0));
1241 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1244 "You are generating velocities so I am assuming you "
1245 "are equilibrating a system. You are using "
1246 "%s pressure coupling, but this can be "
1247 "unstable for equilibration. If your system crashes, try "
1248 "equilibrating first with Berendsen pressure coupling. If "
1249 "you are not equilibrating the system, you can probably "
1250 "ignore this warning.",
1251 enumValueToString(ir->epc));
1252 warning(wi, warn_buf);
1258 if (ir->epc == PressureCoupling::Mttk)
1260 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1264 /* ELECTROSTATICS */
1265 /* More checks are in triple check (grompp.c) */
1267 if (ir->coulombtype == CoulombInteractionType::Switch)
1270 "coulombtype = %s is only for testing purposes and can lead to serious "
1271 "artifacts, advice: use coulombtype = %s",
1272 enumValueToString(ir->coulombtype),
1273 enumValueToString(CoulombInteractionType::RFZero));
1274 warning(wi, warn_buf);
1277 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1280 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1281 "format and exchanging epsilon-r and epsilon-rf",
1283 warning(wi, warn_buf);
1284 ir->epsilon_rf = ir->epsilon_r;
1285 ir->epsilon_r = 1.0;
1288 if (ir->epsilon_r == 0)
1291 "It is pointless to use long-range electrostatics with infinite relative "
1293 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1295 CHECK(EEL_FULL(ir->coulombtype));
1298 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1300 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1301 CHECK(ir->epsilon_r < 0);
1304 if (EEL_RF(ir->coulombtype))
1306 /* reaction field (at the cut-off) */
1308 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1311 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1312 enumValueToString(ir->coulombtype));
1313 warning(wi, warn_buf);
1314 ir->epsilon_rf = 0.0;
1317 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1318 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1319 if (ir->epsilon_rf == ir->epsilon_r)
1322 "Using epsilon-rf = epsilon-r with %s does not make sense",
1323 enumValueToString(ir->coulombtype));
1324 warning(wi, warn_buf);
1327 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1328 * means the interaction is zero outside rcoulomb, but it helps to
1329 * provide accurate energy conservation.
1331 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1333 if (ir_coulomb_switched(ir))
1336 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1337 "potential modifier options!",
1338 enumValueToString(ir->coulombtype));
1339 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1343 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1346 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1347 "secondary coulomb-modifier.");
1348 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1350 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1353 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1354 "secondary vdw-modifier.");
1355 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1358 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1359 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1362 "The switch/shift interaction settings are just for compatibility; you will get "
1364 "performance from applying potential modifiers to your interactions!\n");
1365 warning_note(wi, warn_buf);
1368 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1369 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1371 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1373 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1375 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1376 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1377 "will be good regardless, since ewald_rtol = %g.",
1379 ir->rcoulomb_switch,
1382 warning(wi, warn_buf);
1386 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1388 if (ir->rvdw_switch == 0)
1391 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1392 "potential. This suggests it was not set in the mdp, which can lead to large "
1393 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1394 "switching range.");
1395 warning(wi, warn_buf);
1399 if (EEL_FULL(ir->coulombtype))
1401 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1402 || ir->coulombtype == CoulombInteractionType::PmeUser
1403 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1406 "With coulombtype = %s, rcoulomb must be <= rlist",
1407 enumValueToString(ir->coulombtype));
1408 CHECK(ir->rcoulomb > ir->rlist);
1412 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1414 // TODO: Move these checks into the ewald module with the options class
1416 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1418 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1421 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1422 enumValueToString(ir->coulombtype),
1425 warning_error(wi, warn_buf);
1429 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1431 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1434 "With pbc=%s you should use ewald-geometry=%s",
1435 c_pbcTypeNames[ir->pbcType].c_str(),
1436 enumValueToString(EwaldGeometry::ThreeDC));
1437 warning(wi, warn_buf);
1439 /* This check avoids extra pbc coding for exclusion corrections */
1440 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1441 CHECK(ir->wall_ewald_zfac < 2);
1443 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1444 && EEL_FULL(ir->coulombtype))
1447 "With %s and ewald_geometry = %s you should use pbc = %s",
1448 enumValueToString(ir->coulombtype),
1449 enumValueToString(EwaldGeometry::ThreeDC),
1450 c_pbcTypeNames[PbcType::XY].c_str());
1451 warning(wi, warn_buf);
1453 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1455 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1456 CHECK(ir->bPeriodicMols);
1457 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1458 warning_note(wi, warn_buf);
1460 "With epsilon_surface > 0 you can only use domain decomposition "
1461 "when there are only small molecules with all bonds constrained (mdrun will check "
1463 warning_note(wi, warn_buf);
1466 if (ir_vdw_switched(ir))
1468 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1469 CHECK(ir->rvdw_switch >= ir->rvdw);
1471 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1474 "You are applying a switch function to vdw forces or potentials from %g to %g "
1475 "nm, which is more than half the interaction range, whereas switch functions "
1476 "are intended to act only close to the cut-off.",
1479 warning_note(wi, warn_buf);
1483 if (ir->vdwtype == VanDerWaalsType::Pme)
1485 if (!(ir->vdw_modifier == InteractionModifiers::None
1486 || ir->vdw_modifier == InteractionModifiers::PotShift))
1489 "With vdwtype = %s, the only supported modifiers are %s and %s",
1490 enumValueToString(ir->vdwtype),
1491 enumValueToString(InteractionModifiers::PotShift),
1492 enumValueToString(InteractionModifiers::None));
1493 warning_error(wi, err_buf);
1497 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1500 "You have selected user tables with dispersion correction, the dispersion "
1501 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1502 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1503 "really want dispersion correction to -C6/r^6.");
1506 if (ir->eI == IntegrationAlgorithm::LBFGS
1507 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1510 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1513 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1515 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1518 /* IMPLICIT SOLVENT */
1519 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1521 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1522 warning_error(wi, warn_buf);
1527 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1532 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1535 // cosine acceleration is only supported in leap-frog
1536 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1538 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1542 /* interpret a number of doubles from a string and put them in an array,
1543 after allocating space for them.
1544 str = the input string
1545 n = the (pre-allocated) number of doubles read
1546 r = the output array of doubles. */
1547 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1549 auto values = gmx::splitString(str);
1552 std::vector<real> r;
1553 for (int i = 0; i < *n; i++)
1557 r.emplace_back(gmx::fromString<real>(values[i]));
1559 catch (gmx::GromacsException&)
1562 "Invalid value " + values[i]
1563 + " in string in mdp file. Expected a real number.");
1570 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1573 int i, j, max_n_lambda, nweights;
1574 t_lambda* fep = ir->fepvals.get();
1575 t_expanded* expand = ir->expandedvals.get();
1576 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1577 bool bOneLambda = TRUE;
1578 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1580 /* FEP input processing */
1581 /* first, identify the number of lambda values for each type.
1582 All that are nonzero must have the same number */
1584 for (auto i : keysOf(nfep))
1586 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1589 /* now, determine the number of components. All must be either zero, or equal. */
1592 for (auto i : keysOf(nfep))
1594 if (nfep[i] > max_n_lambda)
1596 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1597 must have the same number if its not zero.*/
1602 for (auto i : keysOf(nfep))
1606 ir->fepvals->separate_dvdl[i] = FALSE;
1608 else if (nfep[i] == max_n_lambda)
1610 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1611 the derivative with respect to the temperature currently */
1613 ir->fepvals->separate_dvdl[i] = TRUE;
1619 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1622 enumValueToString(i),
1626 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1627 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1629 /* the number of lambdas is the number we've read in, which is either zero
1630 or the same for all */
1631 fep->n_lambda = max_n_lambda;
1633 /* if init_lambda is defined, we need to set lambda */
1634 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1636 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1638 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1639 for (auto i : keysOf(nfep))
1641 fep->all_lambda[i].resize(fep->n_lambda);
1642 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1645 for (j = 0; j < fep->n_lambda; j++)
1647 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1652 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1653 internal bookkeeping -- for now, init_lambda */
1655 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1657 for (i = 0; i < fep->n_lambda; i++)
1659 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1663 /* check to see if only a single component lambda is defined, and soft core is defined.
1664 In this case, turn on coulomb soft core */
1666 if (max_n_lambda == 0)
1672 for (auto i : keysOf(nfep))
1674 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1680 if ((bOneLambda) && (fep->sc_alpha > 0))
1682 fep->bScCoul = TRUE;
1685 /* Fill in the others with the efptFEP if they are not explicitly
1686 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1687 they are all zero. */
1689 for (auto i : keysOf(nfep))
1691 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1693 for (j = 0; j < fep->n_lambda; j++)
1695 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1701 /* now read in the weights */
1702 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1705 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1707 else if (nweights != fep->n_lambda)
1710 "Number of weights (%d) is not equal to number of lambda values (%d)",
1714 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1716 expand->nstexpanded = fep->nstdhdl;
1717 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1722 static void do_simtemp_params(t_inputrec* ir)
1724 ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
1725 getSimTemps(ir->fepvals->n_lambda,
1726 ir->simtempvals.get(),
1727 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1730 template<typename T>
1731 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1734 for (const auto& input : inputs)
1738 outputs[i] = gmx::fromStdString<T>(input);
1740 catch (gmx::GromacsException&)
1742 auto message = gmx::formatString(
1743 "Invalid value for mdp option %s. %s should only consist of integers separated "
1747 warning_error(wi, message);
1753 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1756 for (const auto& input : inputs)
1760 outputs[i] = gmx::fromString<real>(input);
1762 catch (gmx::GromacsException&)
1764 auto message = gmx::formatString(
1765 "Invalid value for mdp option %s. %s should only consist of real numbers "
1766 "separated by spaces.",
1769 warning_error(wi, message);
1775 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1777 opts->wall_atomtype[0] = nullptr;
1778 opts->wall_atomtype[1] = nullptr;
1780 ir->wall_atomtype[0] = -1;
1781 ir->wall_atomtype[1] = -1;
1782 ir->wall_density[0] = 0;
1783 ir->wall_density[1] = 0;
1787 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1788 if (wallAtomTypes.size() != size_t(ir->nwall))
1791 "Expected %d elements for wall_atomtype, found %zu",
1793 wallAtomTypes.size());
1795 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1796 for (int i = 0; i < ir->nwall; i++)
1798 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1801 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1803 auto wallDensity = gmx::splitString(wall_density);
1804 if (wallDensity.size() != size_t(ir->nwall))
1807 "Expected %d elements for wall-density, found %zu",
1809 wallDensity.size());
1811 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1812 for (int i = 0; i < ir->nwall; i++)
1814 if (ir->wall_density[i] <= 0)
1816 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1823 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1827 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1828 for (int i = 0; i < nwall; i++)
1830 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1831 grps->emplace_back(groups->groupNames.size() - 1);
1836 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1838 /* read expanded ensemble parameters */
1839 printStringNewline(inp, "expanded ensemble variables");
1840 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1841 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1842 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1843 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1844 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1845 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1846 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1847 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1848 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1849 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1850 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1851 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1852 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1853 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1854 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1855 expand->bSymmetrizedTMatrix =
1856 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1857 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1858 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1859 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1860 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1861 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1862 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1863 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1866 /*! \brief Return whether an end state with the given coupling-lambda
1867 * value describes fully-interacting VDW.
1869 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1870 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1872 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1874 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1880 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1883 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1885 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1887 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1890 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1891 std::string message = gmx::formatExceptionMessageToString(*ex);
1892 warning_error(wi_, message.c_str());
1897 std::string getOptionName(const gmx::KeyValueTreePath& context)
1899 if (mapping_ != nullptr)
1901 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1902 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1905 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1910 const gmx::IKeyValueTreeBackMapping* mapping_;
1915 void get_ir(const char* mdparin,
1916 const char* mdparout,
1917 gmx::MDModules* mdModules,
1920 WriteMdpHeader writeMdpHeader,
1924 double dumdub[2][6];
1926 char warn_buf[STRLEN];
1927 t_lambda* fep = ir->fepvals.get();
1928 t_expanded* expand = ir->expandedvals.get();
1930 const char* no_names[] = { "no", nullptr };
1932 init_inputrec_strings();
1933 gmx::TextInputFile stream(mdparin);
1934 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1936 snew(dumstr[0], STRLEN);
1937 snew(dumstr[1], STRLEN);
1939 /* ignore the following deprecated commands */
1940 replace_inp_entry(inp, "title", nullptr);
1941 replace_inp_entry(inp, "cpp", nullptr);
1942 replace_inp_entry(inp, "domain-decomposition", nullptr);
1943 replace_inp_entry(inp, "andersen-seed", nullptr);
1944 replace_inp_entry(inp, "dihre", nullptr);
1945 replace_inp_entry(inp, "dihre-fc", nullptr);
1946 replace_inp_entry(inp, "dihre-tau", nullptr);
1947 replace_inp_entry(inp, "nstdihreout", nullptr);
1948 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1949 replace_inp_entry(inp, "optimize-fft", nullptr);
1950 replace_inp_entry(inp, "adress_type", nullptr);
1951 replace_inp_entry(inp, "adress_const_wf", nullptr);
1952 replace_inp_entry(inp, "adress_ex_width", nullptr);
1953 replace_inp_entry(inp, "adress_hy_width", nullptr);
1954 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1955 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1956 replace_inp_entry(inp, "adress_site", nullptr);
1957 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1958 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1959 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1960 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1961 replace_inp_entry(inp, "rlistlong", nullptr);
1962 replace_inp_entry(inp, "nstcalclr", nullptr);
1963 replace_inp_entry(inp, "pull-print-com2", nullptr);
1964 replace_inp_entry(inp, "gb-algorithm", nullptr);
1965 replace_inp_entry(inp, "nstgbradii", nullptr);
1966 replace_inp_entry(inp, "rgbradii", nullptr);
1967 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1968 replace_inp_entry(inp, "gb-saltconc", nullptr);
1969 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1970 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1971 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1972 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1973 replace_inp_entry(inp, "sa-algorithm", nullptr);
1974 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1975 replace_inp_entry(inp, "ns-type", nullptr);
1977 /* replace the following commands with the clearer new versions*/
1978 replace_inp_entry(inp, "unconstrained-start", "continuation");
1979 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1980 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1981 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1982 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1983 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1984 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1986 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1987 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1988 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1989 setStringEntry(&inp, "include", opts->include, nullptr);
1990 printStringNoNewline(
1991 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1992 setStringEntry(&inp, "define", opts->define, nullptr);
1994 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1995 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
1996 printStringNoNewline(&inp, "Start time and timestep in ps");
1997 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1998 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1999 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
2000 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
2001 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
2002 printStringNoNewline(
2003 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
2004 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
2005 printStringNoNewline(&inp, "Multiple time-stepping");
2006 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
2009 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
2010 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
2011 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
2012 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
2014 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2015 if (!EI_DYNAMICS(ir->eI))
2020 printStringNoNewline(&inp, "mode for center of mass motion removal");
2021 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
2022 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2023 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2024 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2025 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2027 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2028 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2029 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2030 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2033 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2034 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2035 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2036 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2037 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2038 ir->niter = get_eint(&inp, "niter", 20, wi);
2039 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2040 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2041 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2042 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2043 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2045 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2046 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2048 /* Output options */
2049 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2050 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2051 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2052 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2053 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2054 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2055 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2056 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2057 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2058 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2059 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2060 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2061 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2062 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2063 printStringNoNewline(&inp, "default, all atoms will be written.");
2064 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2065 printStringNoNewline(&inp, "Selection of energy groups");
2066 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2068 /* Neighbor searching */
2069 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2070 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2071 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2072 printStringNoNewline(&inp, "nblist update frequency");
2073 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2074 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2075 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2076 std::vector<const char*> pbcTypesNamesChar;
2077 for (const auto& pbcTypeName : c_pbcTypeNames)
2079 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2081 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2082 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2083 printStringNoNewline(&inp,
2084 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2085 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2086 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2087 printStringNoNewline(&inp, "nblist cut-off");
2088 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2089 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2091 /* Electrostatics */
2092 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2093 printStringNoNewline(&inp, "Method for doing electrostatics");
2094 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2095 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2096 printStringNoNewline(&inp, "cut-off lengths");
2097 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2098 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2099 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2100 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2101 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2102 printStringNoNewline(&inp, "Method for doing Van der Waals");
2103 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2104 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2105 printStringNoNewline(&inp, "cut-off lengths");
2106 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2107 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2108 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2109 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2110 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2111 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2112 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2113 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2114 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2115 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2116 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2117 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2118 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2119 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2120 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2121 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2122 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2123 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2124 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2125 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2126 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2128 /* Implicit solvation is no longer supported, but we need grompp
2129 to be able to refuse old .mdp files that would have built a tpr
2130 to run it. Thus, only "no" is accepted. */
2131 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2133 /* Coupling stuff */
2134 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2135 printStringNoNewline(&inp, "Temperature coupling");
2136 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2137 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2138 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2139 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2140 printStringNoNewline(&inp, "Groups to couple separately");
2141 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2142 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2143 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2144 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2145 printStringNoNewline(&inp, "pressure coupling");
2146 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2147 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2148 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2149 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2150 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2151 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2152 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2153 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2154 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2157 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2158 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2159 printStringNoNewline(&inp, "Groups treated with MiMiC");
2160 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2162 /* Simulated annealing */
2163 printStringNewline(&inp, "SIMULATED ANNEALING");
2164 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2165 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2166 printStringNoNewline(&inp,
2167 "Number of time points to use for specifying annealing in each group");
2168 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2169 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2170 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2171 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2172 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2175 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2176 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2177 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2178 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2181 printStringNewline(&inp, "OPTIONS FOR BONDS");
2182 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2183 printStringNoNewline(&inp, "Type of constraint algorithm");
2184 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2185 printStringNoNewline(&inp, "Do not constrain the start configuration");
2186 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2187 printStringNoNewline(&inp,
2188 "Use successive overrelaxation to reduce the number of shake iterations");
2189 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2190 printStringNoNewline(&inp, "Relative tolerance of shake");
2191 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2192 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2193 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2194 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2195 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2196 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2197 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2198 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2199 printStringNoNewline(&inp, "rotates over more degrees than");
2200 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2201 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2202 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2204 /* Energy group exclusions */
2205 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2206 printStringNoNewline(
2207 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2208 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2211 printStringNewline(&inp, "WALLS");
2212 printStringNoNewline(
2213 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2214 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2215 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2216 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2217 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2218 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2219 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2222 printStringNewline(&inp, "COM PULLING");
2223 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2226 ir->pull = std::make_unique<pull_params_t>();
2227 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2231 for (int c = 0; c < ir->pull->ncoord; c++)
2233 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2236 "Constraint COM pulling is not supported in combination with "
2237 "multiple time stepping");
2245 NOTE: needs COM pulling or free energy input */
2246 printStringNewline(&inp, "AWH biasing");
2247 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2250 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
2253 /* Enforced rotation */
2254 printStringNewline(&inp, "ENFORCED ROTATION");
2255 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2256 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2260 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2263 /* Interactive MD */
2265 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2266 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2267 if (inputrecStrings->imd_grp[0] != '\0')
2274 printStringNewline(&inp, "NMR refinement stuff");
2275 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2276 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2277 printStringNoNewline(
2278 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2279 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2280 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2281 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2282 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2283 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2284 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2285 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2286 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2287 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2288 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2289 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2290 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2291 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2292 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2293 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2295 /* free energy variables */
2296 printStringNewline(&inp, "Free energy variables");
2297 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2298 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2299 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2300 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2301 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2303 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2305 it was not entered */
2306 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2307 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2308 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2309 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2310 setStringEntry(&inp, "fep-lambdas", "");
2311 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2312 setStringEntry(&inp, "mass-lambdas", "");
2313 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2314 setStringEntry(&inp, "coul-lambdas", "");
2315 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2316 setStringEntry(&inp, "vdw-lambdas", "");
2317 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2318 setStringEntry(&inp, "bonded-lambdas", "");
2319 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2320 setStringEntry(&inp, "restraint-lambdas", "");
2321 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2322 setStringEntry(&inp, "temperature-lambdas", "");
2323 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2324 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2325 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2326 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2327 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2328 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2329 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2330 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2331 fep->softcoreFunction = getEnum<SoftcoreType>(&inp, "sc-function", wi);
2332 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2333 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2334 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2335 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2336 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2337 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2339 /* Non-equilibrium MD stuff */
2340 printStringNewline(&inp, "Non-equilibrium MD stuff");
2341 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2342 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2343 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2344 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2346 /* simulated tempering variables */
2347 printStringNewline(&inp, "simulated tempering variables");
2348 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2349 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2350 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2351 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2353 /* expanded ensemble variables */
2354 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2356 read_expandedparams(&inp, expand, wi);
2359 /* Electric fields */
2361 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2362 gmx::KeyValueTreeTransformer transform;
2363 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2364 mdModules->initMdpTransform(transform.rules());
2365 for (const auto& path : transform.mappedPaths())
2367 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2368 mark_einp_set(inp, path[0].c_str());
2370 MdpErrorHandler errorHandler(wi);
2371 auto result = transform.transform(convertedValues, &errorHandler);
2372 ir->params = new gmx::KeyValueTreeObject(result.object());
2373 mdModules->adjustInputrecBasedOnModules(ir);
2374 errorHandler.setBackMapping(result.backMapping());
2375 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2378 /* Ion/water position swapping ("computational electrophysiology") */
2379 printStringNewline(&inp,
2380 "Ion/water position swapping for computational electrophysiology setups");
2381 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2382 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2383 if (ir->eSwapCoords != SwapType::No)
2390 printStringNoNewline(&inp, "Swap attempt frequency");
2391 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2392 printStringNoNewline(&inp, "Number of ion types to be controlled");
2393 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2396 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2398 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2399 snew(ir->swap->grp, ir->swap->ngrp);
2400 for (i = 0; i < ir->swap->ngrp; i++)
2402 snew(ir->swap->grp[i].molname, STRLEN);
2404 printStringNoNewline(&inp,
2405 "Two index groups that contain the compartment-partitioning atoms");
2406 setStringEntry(&inp,
2408 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2410 setStringEntry(&inp,
2412 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2414 printStringNoNewline(&inp,
2415 "Use center of mass of split groups (yes/no), otherwise center of "
2416 "geometry is used");
2417 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2418 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2420 printStringNoNewline(&inp, "Name of solvent molecules");
2421 setStringEntry(&inp,
2423 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2426 printStringNoNewline(&inp,
2427 "Split cylinder: radius, upper and lower extension (nm) (this will "
2428 "define the channels)");
2429 printStringNoNewline(&inp,
2430 "Note that the split cylinder settings do not have an influence on "
2431 "the swapping protocol,");
2432 printStringNoNewline(
2434 "however, if correctly defined, the permeation events are recorded per channel");
2435 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2436 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2437 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2438 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2439 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2440 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2442 printStringNoNewline(
2444 "Average the number of ions per compartment over these many swap attempt steps");
2445 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2447 printStringNoNewline(
2448 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2449 printStringNoNewline(
2450 &inp, "and the requested number of ions of this type in compartments A and B");
2451 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2452 for (i = 0; i < nIonTypes; i++)
2454 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2456 sprintf(buf, "iontype%d-name", i);
2457 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2458 sprintf(buf, "iontype%d-in-A", i);
2459 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2460 sprintf(buf, "iontype%d-in-B", i);
2461 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2464 printStringNoNewline(
2466 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2467 printStringNoNewline(
2469 "at maximum distance (= bulk concentration) to the split group layers. However,");
2470 printStringNoNewline(&inp,
2471 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2472 "layer from the middle at 0.0");
2473 printStringNoNewline(&inp,
2474 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2475 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2476 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2477 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2478 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2480 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2483 printStringNoNewline(
2484 &inp, "Start to swap ions if threshold difference to requested count is reached");
2485 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2488 /* AdResS is no longer supported, but we need grompp to be able to
2489 refuse to process old .mdp files that used it. */
2490 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2492 /* User defined thingies */
2493 printStringNewline(&inp, "User defined thingies");
2494 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2495 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2496 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2497 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2498 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2499 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2500 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2501 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2502 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2503 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2508 gmx::TextOutputFile stream(mdparout);
2509 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2511 // Transform module data into a flat key-value tree for output.
2512 gmx::KeyValueTreeBuilder builder;
2513 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2514 mdModules->buildMdpOutput(&builderObject);
2516 gmx::TextWriter writer(&stream);
2517 writeKeyValueTreeAsMdp(&writer, builder.build());
2522 /* Process options if necessary */
2523 for (m = 0; m < 2; m++)
2525 for (i = 0; i < 2 * DIM; i++)
2529 if (ir->epc != PressureCoupling::No)
2533 case PressureCouplingType::Isotropic:
2534 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2538 "Pressure coupling incorrect number of values (I need exactly 1)");
2540 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2542 case PressureCouplingType::SemiIsotropic:
2543 case PressureCouplingType::SurfaceTension:
2544 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2548 "Pressure coupling incorrect number of values (I need exactly 2)");
2550 dumdub[m][YY] = dumdub[m][XX];
2552 case PressureCouplingType::Anisotropic:
2553 if (sscanf(dumstr[m],
2554 "%lf%lf%lf%lf%lf%lf",
2565 "Pressure coupling incorrect number of values (I need exactly 6)");
2570 "Pressure coupling type %s not implemented yet",
2571 enumValueToString(ir->epct));
2575 clear_mat(ir->ref_p);
2576 clear_mat(ir->compress);
2577 for (i = 0; i < DIM; i++)
2579 ir->ref_p[i][i] = dumdub[1][i];
2580 ir->compress[i][i] = dumdub[0][i];
2582 if (ir->epct == PressureCouplingType::Anisotropic)
2584 ir->ref_p[XX][YY] = dumdub[1][3];
2585 ir->ref_p[XX][ZZ] = dumdub[1][4];
2586 ir->ref_p[YY][ZZ] = dumdub[1][5];
2587 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2590 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2591 "apply a threefold shear stress?\n");
2593 ir->compress[XX][YY] = dumdub[0][3];
2594 ir->compress[XX][ZZ] = dumdub[0][4];
2595 ir->compress[YY][ZZ] = dumdub[0][5];
2596 for (i = 0; i < DIM; i++)
2598 for (m = 0; m < i; m++)
2600 ir->ref_p[i][m] = ir->ref_p[m][i];
2601 ir->compress[i][m] = ir->compress[m][i];
2606 if (ir->comm_mode == ComRemovalAlgorithm::No)
2611 opts->couple_moltype = nullptr;
2612 if (strlen(inputrecStrings->couple_moltype) > 0)
2614 if (ir->efep != FreeEnergyPerturbationType::No)
2616 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2617 if (opts->couple_lam0 == opts->couple_lam1)
2619 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2621 if (ir->eI == IntegrationAlgorithm::MD
2622 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2626 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2633 "Free energy is turned off, so we will not decouple the molecule listed "
2637 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2638 if (ir->efep != FreeEnergyPerturbationType::No)
2640 if (fep->delta_lambda != 0)
2642 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2646 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2648 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2650 "Old option for dhdl-print-energy given: "
2651 "changing \"yes\" to \"total\"\n");
2654 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2656 /* always print out the energy to dhdl if we are doing
2657 expanded ensemble, since we need the total energy for
2658 analysis if the temperature is changing. In some
2659 conditions one may only want the potential energy, so
2660 we will allow that if the appropriate mdp setting has
2661 been enabled. Otherwise, total it is:
2663 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2666 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2668 ir->bExpanded = FALSE;
2669 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2671 ir->bExpanded = TRUE;
2673 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2674 if (ir->bSimTemp) /* done after fep params */
2676 do_simtemp_params(ir);
2679 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2680 * setup and not on the old way of specifying the free-energy setup,
2681 * we should check for using soft-core when not needed, since that
2682 * can complicate the sampling significantly.
2683 * Note that we only check for the automated coupling setup.
2684 * If the (advanced) user does FEP through manual topology changes,
2685 * this check will not be triggered.
2687 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2688 && ir->fepvals->sc_alpha != 0
2689 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2692 "You are using soft-core interactions while the Van der Waals interactions are "
2693 "not decoupled (note that the sc-coul option is only active when using lambda "
2694 "states). Although this will not lead to errors, you will need much more "
2695 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2700 ir->fepvals->n_lambda = 0;
2703 /* WALL PARAMETERS */
2705 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2707 /* ORIENTATION RESTRAINT PARAMETERS */
2709 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2711 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2714 /* DEFORMATION PARAMETERS */
2716 clear_mat(ir->deform);
2717 for (i = 0; i < 6; i++)
2722 double gmx_unused canary;
2723 int ndeform = sscanf(inputrecStrings->deform,
2724 "%lf %lf %lf %lf %lf %lf %lf",
2733 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2737 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2738 inputrecStrings->deform)
2741 for (i = 0; i < 3; i++)
2743 ir->deform[i][i] = dumdub[0][i];
2745 ir->deform[YY][XX] = dumdub[0][3];
2746 ir->deform[ZZ][XX] = dumdub[0][4];
2747 ir->deform[ZZ][YY] = dumdub[0][5];
2748 if (ir->epc != PressureCoupling::No)
2750 for (i = 0; i < 3; i++)
2752 for (j = 0; j <= i; j++)
2754 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2756 warning_error(wi, "A box element has deform set and compressibility > 0");
2760 for (i = 0; i < 3; i++)
2762 for (j = 0; j < i; j++)
2764 if (ir->deform[i][j] != 0)
2766 for (m = j; m < DIM; m++)
2768 if (ir->compress[m][j] != 0)
2771 "An off-diagonal box element has deform set while "
2772 "compressibility > 0 for the same component of another box "
2773 "vector, this might lead to spurious periodicity effects.");
2774 warning(wi, warn_buf);
2782 /* Ion/water position swapping checks */
2783 if (ir->eSwapCoords != SwapType::No)
2785 if (ir->swap->nstswap < 1)
2787 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2789 if (ir->swap->nAverage < 1)
2791 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2793 if (ir->swap->threshold < 1.0)
2795 warning_error(wi, "Ion count threshold must be at least 1.\n");
2799 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2802 std::vector<std::string> errorMessages;
2803 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2805 for (const auto& errorMessage : errorMessages)
2807 warning_error(wi, errorMessage.c_str());
2813 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2820 /* We would like gn to be const as well, but C doesn't allow this */
2821 /* TODO this is utility functionality (search for the index of a
2822 string in a collection), so should be refactored and located more
2824 int search_string(const char* s, int ng, char* gn[])
2828 for (i = 0; (i < ng); i++)
2830 if (gmx_strcasecmp(s, gn[i]) == 0)
2837 "Group %s referenced in the .mdp file was not found in the index file.\n"
2838 "Group names must match either [moleculetype] names or custom index group\n"
2839 "names, in which case you must supply an index file to the '-n' option\n"
2844 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2846 /* Now go over the atoms in the group */
2847 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2849 int aj = block.a[j];
2851 /* Range checking */
2852 if ((aj < 0) || (aj >= natoms))
2854 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2859 static void do_numbering(int natoms,
2860 SimulationGroups* groups,
2861 gmx::ArrayRef<std::string> groupsFromMdpFile,
2864 SimulationAtomGroupType gtype,
2870 unsigned short* cbuf;
2871 AtomGroupIndices* grps = &(groups->groups[gtype]);
2874 char warn_buf[STRLEN];
2876 title = shortName(gtype);
2879 /* Mark all id's as not set */
2880 for (int i = 0; (i < natoms); i++)
2885 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2887 /* Lookup the group name in the block structure */
2888 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2889 if ((grptp != egrptpONE) || (i == 0))
2891 grps->emplace_back(gid);
2893 GMX_ASSERT(block, "Can't have a nullptr block");
2894 atomGroupRangeValidation(natoms, gid, *block);
2895 /* Now go over the atoms in the group */
2896 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2898 const int aj = block->a[j];
2899 /* Lookup up the old group number */
2900 const int ognr = cbuf[aj];
2903 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2907 /* Store the group number in buffer */
2908 if (grptp == egrptpONE)
2921 /* Now check whether we have done all atoms */
2924 if (grptp == egrptpALL)
2926 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2928 else if (grptp == egrptpPART)
2930 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2931 warning_note(wi, warn_buf);
2933 /* Assign all atoms currently unassigned to a rest group */
2934 for (int j = 0; (j < natoms); j++)
2936 if (cbuf[j] == NOGID)
2938 cbuf[j] = grps->size();
2941 if (grptp != egrptpPART)
2945 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2947 /* Add group name "rest" */
2948 grps->emplace_back(restnm);
2950 /* Assign the rest name to all atoms not currently assigned to a group */
2951 for (int j = 0; (j < natoms); j++)
2953 if (cbuf[j] == NOGID)
2955 // group size was not updated before this here, so need to use -1.
2956 cbuf[j] = grps->size() - 1;
2962 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2964 /* All atoms are part of one (or no) group, no index required */
2965 groups->groupNumbers[gtype].clear();
2969 for (int j = 0; (j < natoms); j++)
2971 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2978 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2981 pull_params_t* pull;
2982 int natoms, imin, jmin;
2983 int * nrdf2, *na_vcm, na_tot;
2984 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2989 * First calc 3xnr-atoms for each group
2990 * then subtract half a degree of freedom for each constraint
2992 * Only atoms and nuclei contribute to the degrees of freedom...
2997 const SimulationGroups& groups = mtop->groups;
2998 natoms = mtop->natoms;
3000 /* Allocate one more for a possible rest group */
3001 /* We need to sum degrees of freedom into doubles,
3002 * since floats give too low nrdf's above 3 million atoms.
3004 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
3005 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3006 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3007 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3008 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3010 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3014 for (gmx::index i = 0;
3015 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3019 clear_ivec(dof_vcm[i]);
3021 nrdf_vcm_sub[i] = 0;
3023 snew(nrdf2, natoms);
3024 for (const AtomProxy atomP : AtomRange(*mtop))
3026 const t_atom& local = atomP.atom();
3027 int i = atomP.globalAtomNumber();
3029 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3031 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3032 for (int d = 0; d < DIM; d++)
3034 if (opts->nFreeze[g][d] == 0)
3036 /* Add one DOF for particle i (counted as 2*1) */
3038 /* VCM group i has dim d as a DOF */
3039 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3043 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3045 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3051 for (const gmx_molblock_t& molb : mtop->molblock)
3053 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3054 const t_atom* atom = molt.atoms.atom;
3055 for (int mol = 0; mol < molb.nmol; mol++)
3057 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3059 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3060 for (int i = 0; i < molt.ilist[ftype].size();)
3062 /* Subtract degrees of freedom for the constraints,
3063 * if the particles still have degrees of freedom left.
3064 * If one of the particles is a vsite or a shell, then all
3065 * constraint motion will go there, but since they do not
3066 * contribute to the constraints the degrees of freedom do not
3069 int ai = as + ia[i + 1];
3070 int aj = as + ia[i + 2];
3071 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3072 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3073 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3074 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3092 imin = std::min(imin, nrdf2[ai]);
3093 jmin = std::min(jmin, nrdf2[aj]);
3096 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3098 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3100 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3102 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3105 i += interaction_function[ftype].nratoms + 1;
3108 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3109 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3111 /* Subtract 1 dof from every atom in the SETTLE */
3112 for (int j = 0; j < 3; j++)
3114 int ai = as + ia[i + 1 + j];
3115 imin = std::min(2, nrdf2[ai]);
3117 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3119 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3124 as += molt.atoms.nr;
3130 /* Correct nrdf for the COM constraints.
3131 * We correct using the TC and VCM group of the first atom
3132 * in the reference and pull group. If atoms in one pull group
3133 * belong to different TC or VCM groups it is anyhow difficult
3134 * to determine the optimal nrdf assignment.
3136 pull = ir->pull.get();
3138 for (int i = 0; i < pull->ncoord; i++)
3140 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3147 for (int j = 0; j < 2; j++)
3149 const t_pull_group* pgrp;
3151 pgrp = &pull->group[pull->coord[i].group[j]];
3153 if (!pgrp->ind.empty())
3155 /* Subtract 1/2 dof from each group */
3156 int ai = pgrp->ind[0];
3157 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3159 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3161 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3164 "Center of mass pulling constraints caused the number of degrees "
3165 "of freedom for temperature coupling group %s to be negative",
3166 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3167 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3172 /* We need to subtract the whole DOF from group j=1 */
3179 if (ir->nstcomm != 0)
3181 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3182 "Expect at least one group when removing COM motion");
3184 /* We remove COM motion up to dim ndof_com() */
3185 const int ndim_rm_vcm = ndof_com(ir);
3187 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3188 * the number of degrees of freedom in each vcm group when COM
3189 * translation is removed and 6 when rotation is removed as well.
3190 * Note that we do not and should not include the rest group here.
3192 for (gmx::index j = 0;
3193 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3196 switch (ir->comm_mode)
3198 case ComRemovalAlgorithm::Linear:
3199 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3200 nrdf_vcm_sub[j] = 0;
3201 for (int d = 0; d < ndim_rm_vcm; d++)
3209 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3210 default: gmx_incons("Checking comm_mode");
3214 for (gmx::index i = 0;
3215 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3218 /* Count the number of atoms of TC group i for every VCM group */
3219 for (gmx::index j = 0;
3220 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3226 for (int ai = 0; ai < natoms; ai++)
3228 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3230 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3234 /* Correct for VCM removal according to the fraction of each VCM
3235 * group present in this TC group.
3237 nrdf_uc = nrdf_tc[i];
3239 for (gmx::index j = 0;
3240 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3243 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3245 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3246 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3251 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3253 opts->nrdf[i] = nrdf_tc[i];
3254 if (opts->nrdf[i] < 0)
3259 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3260 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3269 sfree(nrdf_vcm_sub);
3272 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3274 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3275 * But since this is much larger than STRLEN, such a line can not be parsed.
3276 * The real maximum is the number of names that fit in a string: STRLEN/2.
3281 auto names = gmx::splitString(val);
3282 if (names.size() % 2 != 0)
3284 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3286 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3288 for (size_t i = 0; i < names.size() / 2; i++)
3290 // TODO this needs to be replaced by a solution using std::find_if
3294 names[2 * i].c_str(),
3295 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3301 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3306 names[2 * i + 1].c_str(),
3307 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3313 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3315 if ((j < nr) && (k < nr))
3317 ir->opts.egp_flags[nr * j + k] |= flag;
3318 ir->opts.egp_flags[nr * k + j] |= flag;
3327 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3329 int ig = -1, i = 0, gind;
3333 /* Just a quick check here, more thorough checks are in mdrun */
3334 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3335 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3339 "The split groups can not both be '%s'.",
3340 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3343 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3344 for (ig = 0; ig < swap->ngrp; ig++)
3346 swapg = &swap->grp[ig];
3347 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3348 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3353 "%s group '%s' contains %d atoms.\n",
3354 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3355 swap->grp[ig].molname,
3357 snew(swapg->ind, swapg->nat);
3358 for (i = 0; i < swapg->nat; i++)
3360 swapg->ind[i] = grps->a[grps->index[gind] + i];
3365 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3371 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3376 ig = search_string(IMDgname, grps->nr, gnames);
3377 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3379 if (IMDgroup->nat > 0)
3382 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3386 snew(IMDgroup->ind, IMDgroup->nat);
3387 for (i = 0; i < IMDgroup->nat; i++)
3389 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3394 /* Checks whether atoms are both part of a COM removal group and frozen.
3395 * If a fully frozen atom is part of a COM removal group, it is removed
3396 * from the COM removal group. A note is issued if such atoms are present.
3397 * A warning is issued for atom with one or two dimensions frozen that
3398 * are part of a COM removal group (mdrun would need to compute COM mass
3399 * per dimension to handle this correctly).
3400 * Also issues a warning when non-frozen atoms are not part of a COM
3401 * removal group while COM removal is active.
3403 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3405 const t_grpopts& opts,
3408 const int vcmRestGroup =
3409 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3411 int numFullyFrozenVcmAtoms = 0;
3412 int numPartiallyFrozenVcmAtoms = 0;
3413 int numNonVcmAtoms = 0;
3414 for (int a = 0; a < numAtoms; a++)
3416 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3417 int numFrozenDims = 0;
3418 for (int d = 0; d < DIM; d++)
3420 numFrozenDims += opts.nFreeze[freezeGroup][d];
3423 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3424 if (vcmGroup < vcmRestGroup)
3426 if (numFrozenDims == DIM)
3428 /* Do not remove COM motion for this fully frozen atom */
3429 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3431 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3434 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3435 numFullyFrozenVcmAtoms++;
3437 else if (numFrozenDims > 0)
3439 numPartiallyFrozenVcmAtoms++;
3442 else if (numFrozenDims < DIM)
3448 if (numFullyFrozenVcmAtoms > 0)
3450 std::string warningText = gmx::formatString(
3451 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3452 "removing these atoms from the COMM removal group(s)",
3453 numFullyFrozenVcmAtoms);
3454 warning_note(wi, warningText.c_str());
3456 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3458 std::string warningText = gmx::formatString(
3459 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3460 "removal group(s), due to limitations in the code these still contribute to the "
3461 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3463 numPartiallyFrozenVcmAtoms,
3465 warning(wi, warningText.c_str());
3467 if (numNonVcmAtoms > 0)
3469 std::string warningText = gmx::formatString(
3470 "%d atoms are not part of any center of mass motion removal group.\n"
3471 "This may lead to artifacts.\n"
3472 "In most cases one should use one group for the whole system.",
3474 warning(wi, warningText.c_str());
3478 void do_index(const char* mdparin,
3482 const gmx::MDModulesNotifiers& mdModulesNotifiers,
3486 t_blocka* defaultIndexGroups;
3494 int i, j, k, restnm;
3495 bool bExcl, bTable, bAnneal;
3496 char warn_buf[STRLEN];
3500 fprintf(stderr, "processing index file...\n");
3504 snew(defaultIndexGroups, 1);
3505 snew(defaultIndexGroups->index, 1);
3507 atoms_all = gmx_mtop_global_atoms(*mtop);
3508 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3509 done_atom(&atoms_all);
3513 defaultIndexGroups = init_index(ndx, &gnames);
3516 SimulationGroups* groups = &mtop->groups;
3517 natoms = mtop->natoms;
3518 symtab = &mtop->symtab;
3520 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3522 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3524 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3525 restnm = groups->groupNames.size() - 1;
3526 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3527 srenew(gnames, defaultIndexGroups->nr + 1);
3528 gnames[restnm] = *(groups->groupNames.back());
3530 set_warning_line(wi, mdparin, -1);
3532 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3533 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3534 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3535 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3536 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3539 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3541 temperatureCouplingGroupNames.size(),
3542 temperatureCouplingReferenceValues.size(),
3543 temperatureCouplingTauValues.size());
3546 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3547 do_numbering(natoms,
3549 temperatureCouplingGroupNames,
3552 SimulationAtomGroupType::TemperatureCoupling,
3554 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3557 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3559 snew(ir->opts.nrdf, nr);
3560 snew(ir->opts.tau_t, nr);
3561 snew(ir->opts.ref_t, nr);
3562 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3564 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3567 if (useReferenceTemperature)
3569 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3571 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3575 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3576 for (i = 0; (i < nr); i++)
3578 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3581 "With integrator %s tau-t should be larger than 0",
3582 enumValueToString(ir->eI));
3583 warning_error(wi, warn_buf);
3586 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3590 "tau-t = -1 is the value to signal that a group should not have "
3591 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3594 if (ir->opts.tau_t[i] >= 0)
3596 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3599 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3601 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3606 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3609 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3610 "md-vv; use either vrescale temperature with berendsen pressure or "
3611 "Nose-Hoover temperature with MTTK pressure");
3613 if (ir->epc == PressureCoupling::Mttk)
3615 if (ir->etc != TemperatureCoupling::NoseHoover)
3618 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3623 if (ir->nstpcouple != ir->nsttcouple)
3625 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3626 ir->nstpcouple = ir->nsttcouple = mincouple;
3628 "for current Trotter decomposition methods with vv, nsttcouple and "
3629 "nstpcouple must be equal. Both have been reset to "
3630 "min(nsttcouple,nstpcouple) = %d",
3632 warning_note(wi, warn_buf);
3637 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3638 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3640 if (ETC_ANDERSEN(ir->etc))
3642 if (ir->nsttcouple != 1)
3646 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3647 "need for larger nsttcouple > 1, since no global parameters are computed. "
3648 "nsttcouple has been reset to 1");
3649 warning_note(wi, warn_buf);
3652 nstcmin = tcouple_min_integration_steps(ir->etc);
3655 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3658 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3659 "least %d times larger than nsttcouple*dt (%g)",
3660 enumValueToString(ir->etc),
3663 ir->nsttcouple * ir->delta_t);
3664 warning(wi, warn_buf);
3667 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3668 for (i = 0; (i < nr); i++)
3670 if (ir->opts.ref_t[i] < 0)
3672 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3675 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3676 if we are in this conditional) if mc_temp is negative */
3677 if (ir->expandedvals->mc_temp < 0)
3679 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3683 /* Simulated annealing for each group. There are nr groups */
3684 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3685 if (simulatedAnnealingGroupNames.size() == 1
3686 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3688 simulatedAnnealingGroupNames.resize(0);
3690 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3693 "Wrong number of annealing values: %zu (for %d groups)\n",
3694 simulatedAnnealingGroupNames.size(),
3699 snew(ir->opts.annealing, nr);
3700 snew(ir->opts.anneal_npoints, nr);
3701 snew(ir->opts.anneal_time, nr);
3702 snew(ir->opts.anneal_temp, nr);
3703 for (i = 0; i < nr; i++)
3705 ir->opts.annealing[i] = SimulatedAnnealing::No;
3706 ir->opts.anneal_npoints[i] = 0;
3707 ir->opts.anneal_time[i] = nullptr;
3708 ir->opts.anneal_temp[i] = nullptr;
3710 if (!simulatedAnnealingGroupNames.empty())
3713 for (i = 0; i < nr; i++)
3715 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3717 ir->opts.annealing[i] = SimulatedAnnealing::No;
3719 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3721 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3724 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3726 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3732 /* Read the other fields too */
3733 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3734 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3737 "Found %zu annealing-npoints values for %zu groups\n",
3738 simulatedAnnealingPoints.size(),
3739 simulatedAnnealingGroupNames.size());
3741 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3742 size_t numSimulatedAnnealingFields = 0;
3743 for (i = 0; i < nr; i++)
3745 if (ir->opts.anneal_npoints[i] == 1)
3749 "Please specify at least a start and an end point for annealing\n");
3751 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3752 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3753 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3756 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3758 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3761 "Found %zu annealing-time values, wanted %zu\n",
3762 simulatedAnnealingTimes.size(),
3763 numSimulatedAnnealingFields);
3765 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3766 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3769 "Found %zu annealing-temp values, wanted %zu\n",
3770 simulatedAnnealingTemperatures.size(),
3771 numSimulatedAnnealingFields);
3774 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3775 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3776 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3778 simulatedAnnealingTemperatures,
3780 allSimulatedAnnealingTemperatures.data());
3781 for (i = 0, k = 0; i < nr; i++)
3783 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3785 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3786 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3789 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3791 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3797 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3800 "Annealing timepoints out of order: t=%f comes after "
3802 ir->opts.anneal_time[i][j],
3803 ir->opts.anneal_time[i][j - 1]);
3806 if (ir->opts.anneal_temp[i][j] < 0)
3809 "Found negative temperature in annealing: %f\n",
3810 ir->opts.anneal_temp[i][j]);
3815 /* Print out some summary information, to make sure we got it right */
3816 for (i = 0; i < nr; i++)
3818 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3820 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3822 "Simulated annealing for group %s: %s, %d timepoints\n",
3823 *(groups->groupNames[j]),
3824 enumValueToString(ir->opts.annealing[i]),
3825 ir->opts.anneal_npoints[i]);
3826 fprintf(stderr, "Time (ps) Temperature (K)\n");
3827 /* All terms except the last one */
3828 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3832 ir->opts.anneal_time[i][j],
3833 ir->opts.anneal_temp[i][j]);
3836 /* Finally the last one */
3837 j = ir->opts.anneal_npoints[i] - 1;
3838 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3842 ir->opts.anneal_time[i][j],
3843 ir->opts.anneal_temp[i][j]);
3849 ir->opts.anneal_time[i][j],
3850 ir->opts.anneal_temp[i][j]);
3851 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3854 "There is a temperature jump when your annealing "
3866 for (int i = 1; i < ir->pull->ngroup; i++)
3868 const int gid = search_string(
3869 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3870 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3871 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3874 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3876 checkPullCoords(ir->pull->group, ir->pull->coord);
3881 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3884 if (ir->eSwapCoords != SwapType::No)
3886 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3889 /* Make indices for IMD session */
3892 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3895 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3896 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3897 mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
3899 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3900 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3901 if (freezeDims.size() != DIM * freezeGroupNames.size())
3904 "Invalid Freezing input: %zu groups and %zu freeze values",
3905 freezeGroupNames.size(),
3908 do_numbering(natoms,
3913 SimulationAtomGroupType::Freeze,
3918 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3919 ir->opts.ngfrz = nr;
3920 snew(ir->opts.nFreeze, nr);
3921 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3923 for (j = 0; (j < DIM); j++, k++)
3925 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3926 if (!ir->opts.nFreeze[i][j])
3928 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3931 "Please use Y(ES) or N(O) for freezedim only "
3933 freezeDims[k].c_str());
3934 warning(wi, warn_buf);
3939 for (; (i < nr); i++)
3941 for (j = 0; (j < DIM); j++)
3943 ir->opts.nFreeze[i][j] = 0;
3947 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3948 do_numbering(natoms,
3953 SimulationAtomGroupType::EnergyOutput,
3958 add_wall_energrps(groups, ir->nwall, symtab);
3959 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3960 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3961 do_numbering(natoms,
3966 SimulationAtomGroupType::MassCenterVelocityRemoval,
3968 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3972 if (ir->comm_mode != ComRemovalAlgorithm::No)
3974 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3977 /* Now we have filled the freeze struct, so we can calculate NRDF */
3978 calc_nrdf(mtop, ir, gnames);
3980 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3981 do_numbering(natoms,
3986 SimulationAtomGroupType::User1,
3991 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3992 do_numbering(natoms,
3997 SimulationAtomGroupType::User2,
4002 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
4003 do_numbering(natoms,
4005 compressedXGroupNames,
4008 SimulationAtomGroupType::CompressedPositionOutput,
4013 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
4014 do_numbering(natoms,
4016 orirefFitGroupNames,
4019 SimulationAtomGroupType::OrientationRestraintsFit,
4025 /* MiMiC QMMM input processing */
4026 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4027 if (qmGroupNames.size() > 1)
4029 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4031 /* group rest, if any, is always MM! */
4032 do_numbering(natoms,
4037 SimulationAtomGroupType::QuantumMechanics,
4042 ir->opts.ngQM = qmGroupNames.size();
4044 /* end of MiMiC QMMM input */
4048 for (auto group : gmx::keysOf(groups->groups))
4050 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4051 for (const auto& entry : groups->groups[group])
4053 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4055 fprintf(stderr, "\n");
4059 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4060 snew(ir->opts.egp_flags, nr * nr);
4062 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4063 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4065 warning_error(wi, "Energy group exclusions are currently not supported");
4067 if (bExcl && EEL_FULL(ir->coulombtype))
4069 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4072 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4073 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4074 && !(ir->coulombtype == CoulombInteractionType::User)
4075 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4076 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4079 "Can only have energy group pair tables in combination with user tables for VdW "
4083 /* final check before going out of scope if simulated tempering variables
4084 * need to be set to default values.
4086 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4088 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4091 "the value for nstexpanded was not specified for "
4092 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4093 "by default, but it is recommended to set it to an explicit value!",
4094 ir->expandedvals->nstexpanded));
4096 for (i = 0; (i < defaultIndexGroups->nr); i++)
4101 done_blocka(defaultIndexGroups);
4102 sfree(defaultIndexGroups);
4106 static void check_disre(const gmx_mtop_t& mtop)
4108 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4110 const gmx_ffparams_t& ffparams = mtop.ffparams;
4113 for (int i = 0; i < ffparams.numTypes(); i++)
4115 int ftype = ffparams.functype[i];
4116 if (ftype == F_DISRES)
4118 int label = ffparams.iparams[i].disres.label;
4119 if (label == old_label)
4121 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4130 "Found %d double distance restraint indices,\n"
4131 "probably the parameters for multiple pairs in one restraint "
4132 "are not identical\n",
4138 //! Returns whether dimensions have an absolute reference due to walls, pbc or freezing
4139 static BasicVector<bool> haveAbsoluteReference(const t_inputrec& ir)
4141 BasicVector<bool> absRef = { false, false, false };
4143 /* Check the degrees of freedom of the COM (not taking COMM removal into account) */
4144 for (int d = 0; d < DIM; d++)
4146 absRef[d] = (d >= ndof_com(&ir));
4148 /* Check for freeze groups */
4149 for (int g = 0; g < ir.opts.ngfrz; g++)
4151 for (int d = 0; d < DIM; d++)
4153 if (ir.opts.nFreeze[g][d] != 0)
4163 //! Returns whether position restraints are used for dimensions
4164 static BasicVector<bool> havePositionRestraints(const gmx_mtop_t& sys)
4166 BasicVector<bool> havePosres = { false, false, false };
4168 for (const auto ilists : IListRange(sys))
4170 const auto& posResList = ilists.list()[F_POSRES];
4171 const auto& fbPosResList = ilists.list()[F_FBPOSRES];
4172 if (ilists.nmol() > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
4174 for (int i = 0; i < posResList.size(); i += 2)
4176 const t_iparams& pr = sys.ffparams.iparams[posResList.iatoms[i]];
4177 for (int d = 0; d < DIM; d++)
4179 if (pr.posres.fcA[d] != 0)
4181 havePosres[d] = true;
4185 for (int i = 0; i < fbPosResList.size(); i += 2)
4187 /* Check for flat-bottom posres */
4188 const t_iparams& pr = sys.ffparams.iparams[fbPosResList.iatoms[i]];
4189 if (pr.fbposres.k != 0)
4191 switch (pr.fbposres.geom)
4193 case efbposresSPHERE: havePosres = { true, true, true }; break;
4194 case efbposresCYLINDERX: havePosres[YY] = havePosres[ZZ] = true; break;
4195 case efbposresCYLINDERY: havePosres[XX] = havePosres[ZZ] = true; break;
4196 case efbposresCYLINDER:
4197 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4198 case efbposresCYLINDERZ: havePosres[XX] = havePosres[YY] = true; break;
4199 case efbposresX: /* d=XX */
4200 case efbposresY: /* d=YY */
4201 case efbposresZ: /* d=ZZ */
4202 havePosres[pr.fbposres.geom - efbposresX] = true;
4206 "Invalid geometry for flat-bottom position restraint.\n"
4207 "Expected nr between 1 and %d. Found %d\n",
4219 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4221 bool* bC6ParametersWorkWithGeometricRules,
4222 bool* bC6ParametersWorkWithLBRules,
4223 bool* bLBRulesPossible)
4225 int ntypes, tpi, tpj;
4228 double c6i, c6j, c12i, c12j;
4229 double c6, c6_geometric, c6_LB;
4230 double sigmai, sigmaj, epsi, epsj;
4231 bool bCanDoLBRules, bCanDoGeometricRules;
4234 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4235 * force-field floating point parameters.
4238 ptr = getenv("GMX_LJCOMB_TOL");
4242 double gmx_unused canary;
4244 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4247 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4252 *bC6ParametersWorkWithLBRules = TRUE;
4253 *bC6ParametersWorkWithGeometricRules = TRUE;
4254 bCanDoLBRules = TRUE;
4255 ntypes = mtop.ffparams.atnr;
4256 snew(typecount, ntypes);
4257 gmx_mtop_count_atomtypes(mtop, state, typecount);
4258 *bLBRulesPossible = TRUE;
4259 for (tpi = 0; tpi < ntypes; ++tpi)
4261 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4262 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4263 for (tpj = tpi; tpj < ntypes; ++tpj)
4265 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4266 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4267 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4268 c6_geometric = std::sqrt(c6i * c6j);
4269 if (!gmx_numzero(c6_geometric))
4271 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4273 sigmai = gmx::sixthroot(c12i / c6i);
4274 sigmaj = gmx::sixthroot(c12j / c6j);
4275 epsi = c6i * c6i / (4.0 * c12i);
4276 epsj = c6j * c6j / (4.0 * c12j);
4277 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4281 *bLBRulesPossible = FALSE;
4282 c6_LB = c6_geometric;
4284 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4289 *bC6ParametersWorkWithLBRules = FALSE;
4292 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4294 if (!bCanDoGeometricRules)
4296 *bC6ParametersWorkWithGeometricRules = FALSE;
4303 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4305 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4307 check_combination_rule_differences(
4308 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4309 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4311 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4314 "You are using arithmetic-geometric combination rules "
4315 "in LJ-PME, but your non-bonded C6 parameters do not "
4316 "follow these rules.");
4321 if (!bC6ParametersWorkWithGeometricRules)
4323 if (ir->eDispCorr != DispersionCorrectionType::No)
4326 "You are using geometric combination rules in "
4327 "LJ-PME, but your non-bonded C6 parameters do "
4328 "not follow these rules. "
4329 "This will introduce very small errors in the forces and energies in "
4330 "your simulations. Dispersion correction will correct total energy "
4331 "and/or pressure for isotropic systems, but not forces or surface "
4337 "You are using geometric combination rules in "
4338 "LJ-PME, but your non-bonded C6 parameters do "
4339 "not follow these rules. "
4340 "This will introduce very small errors in the forces and energies in "
4341 "your simulations. If your system is homogeneous, consider using "
4342 "dispersion correction "
4343 "for the total energy and pressure.");
4349 static bool allTrue(const BasicVector<bool>& boolVector)
4351 return boolVector[0] && boolVector[1] && boolVector[2];
4354 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4356 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4357 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4359 char err_buf[STRLEN];
4362 gmx_mtop_atomloop_block_t aloopb;
4363 char warn_buf[STRLEN];
4365 set_warning_line(wi, mdparin, -1);
4367 if (ir->comm_mode != ComRemovalAlgorithm::No && allTrue(havePositionRestraints(*sys)))
4370 "Removing center of mass motion in the presence of position restraints might "
4371 "cause artifacts. When you are using position restraints to equilibrate a "
4372 "macro-molecule, the artifacts are usually negligible.");
4375 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4376 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4377 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4379 /* Check if a too small Verlet buffer might potentially
4380 * cause more drift than the thermostat can couple off.
4382 /* Temperature error fraction for warning and suggestion */
4383 const real T_error_warn = 0.002;
4384 const real T_error_suggest = 0.001;
4385 /* For safety: 2 DOF per atom (typical with constraints) */
4386 const real nrdf_at = 2;
4387 real T, tau, max_T_error;
4392 for (i = 0; i < ir->opts.ngtc; i++)
4394 T = std::max(T, ir->opts.ref_t[i]);
4395 tau = std::max(tau, ir->opts.tau_t[i]);
4399 /* This is a worst case estimate of the temperature error,
4400 * assuming perfect buffer estimation and no cancelation
4401 * of errors. The factor 0.5 is because energy distributes
4402 * equally over Ekin and Epot.
4404 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4405 if (max_T_error > T_error_warn)
4408 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4409 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4410 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4411 "%.0e or decrease tau_t.",
4416 100 * T_error_suggest,
4417 ir->verletbuf_tol * T_error_suggest / max_T_error);
4418 warning(wi, warn_buf);
4423 if (ETC_ANDERSEN(ir->etc))
4427 for (i = 0; i < ir->opts.ngtc; i++)
4430 "all tau_t must currently be equal using Andersen temperature control, "
4431 "violated for group %d",
4433 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4435 "all tau_t must be positive using Andersen temperature control, "
4439 CHECK(ir->opts.tau_t[i] < 0);
4442 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4444 for (i = 0; i < ir->opts.ngtc; i++)
4446 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4448 "tau_t/delta_t for group %d for temperature control method %s must be a "
4449 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4450 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4453 enumValueToString(ir->etc),
4457 CHECK(nsteps % ir->nstcomm != 0);
4462 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4463 && ir->comm_mode == ComRemovalAlgorithm::No
4464 && !(allTrue(haveAbsoluteReference(*ir)) || allTrue(havePositionRestraints(*sys)) || ir->nsteps <= 10)
4465 && !ETC_ANDERSEN(ir->etc))
4468 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4469 "rounding errors can lead to build up of kinetic energy of the center of mass");
4472 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4475 for (int g = 0; g < ir->opts.ngtc; g++)
4477 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4479 if (ir->tau_p < 1.9 * tau_t_max)
4481 std::string message = gmx::formatString(
4482 "With %s T-coupling and %s p-coupling, "
4483 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4484 enumValueToString(ir->etc),
4485 enumValueToString(ir->epc),
4490 warning(wi, message.c_str());
4494 /* Check for pressure coupling with absolute position restraints */
4495 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4497 const BasicVector<bool> havePosres = havePositionRestraints(*sys);
4499 for (m = 0; m < DIM; m++)
4501 if (havePosres[m] && norm2(ir->compress[m]) > 0)
4504 "You are using pressure coupling with absolute position restraints, "
4505 "this will give artifacts. Use the refcoord_scaling option.");
4513 aloopb = gmx_mtop_atomloop_block_init(*sys);
4515 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4517 if (atom->q != 0 || atom->qB != 0)
4525 if (EEL_FULL(ir->coulombtype))
4528 "You are using full electrostatics treatment %s for a system without charges.\n"
4529 "This costs a lot of performance for just processing zeros, consider using %s "
4531 enumValueToString(ir->coulombtype),
4532 enumValueToString(CoulombInteractionType::Cut));
4533 warning(wi, err_buf);
4538 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4541 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4542 "You might want to consider using %s electrostatics.\n",
4543 enumValueToString(CoulombInteractionType::Pme));
4544 warning_note(wi, err_buf);
4548 /* Check if combination rules used in LJ-PME are the same as in the force field */
4549 if (EVDW_PME(ir->vdwtype))
4551 check_combination_rules(ir, *sys, wi);
4554 /* Generalized reaction field */
4555 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4558 "Generalized reaction-field electrostatics is no longer supported. "
4559 "You can use normal reaction-field instead and compute the reaction-field "
4560 "constant by hand.");
4563 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4564 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4566 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4574 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4576 if (ir->pull->coord[i].eGeom != PullGroupGeometry::Transformation
4577 && (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0))
4579 const auto absRef = haveAbsoluteReference(*ir);
4580 const auto havePosres = havePositionRestraints(*sys);
4581 for (m = 0; m < DIM; m++)
4583 if (ir->pull->coord[i].dim[m] && !(absRef[m] || havePosres[m]))
4586 "You are using an absolute reference for pulling, but the rest of "
4587 "the system does not have an absolute reference. This will lead to "
4596 for (i = 0; i < 3; i++)
4598 for (m = 0; m <= i; m++)
4600 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4602 for (c = 0; c < ir->pull->ncoord; c++)
4604 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4605 && ir->pull->coord[c].vec[m] != 0)
4608 "Can not have dynamic box while using pull geometry '%s' "
4610 enumValueToString(ir->pull->coord[c].eGeom),
4622 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4624 char warn_buf[STRLEN];
4627 ptr = check_box(ir->pbcType, box);
4630 warning_error(wi, ptr);
4633 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4635 if (ir->shake_tol <= 0.0)
4637 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4638 warning_error(wi, warn_buf);
4642 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4644 /* If we have Lincs constraints: */
4645 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4646 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4649 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4650 warning_note(wi, warn_buf);
4653 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4654 && (ir->nProjOrder < 8))
4657 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4658 enumValueToString(ir->eI));
4659 warning_note(wi, warn_buf);
4661 if (ir->epc == PressureCoupling::Mttk)
4663 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4667 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4669 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4672 if (ir->LincsWarnAngle > 90.0)
4674 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4675 warning(wi, warn_buf);
4676 ir->LincsWarnAngle = 90.0;
4679 if (ir->pbcType != PbcType::No)
4681 if (ir->nstlist == 0)
4684 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4685 "atoms might cause the simulation to crash.");
4687 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4690 "ERROR: The cut-off length is longer than half the shortest box vector or "
4691 "longer than the smallest box diagonal element. Increase the box size or "
4692 "decrease rlist.\n");
4693 warning_error(wi, warn_buf);