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/mdrun/mdmodules.h"
63 #include "gromacs/mdtypes/awh_params.h"
64 #include "gromacs/mdtypes/inputrec.h"
65 #include "gromacs/mdtypes/md_enums.h"
66 #include "gromacs/mdtypes/multipletimestepping.h"
67 #include "gromacs/mdtypes/pull_params.h"
68 #include "gromacs/options/options.h"
69 #include "gromacs/options/treesupport.h"
70 #include "gromacs/pbcutil/pbc.h"
71 #include "gromacs/selection/indexutil.h"
72 #include "gromacs/topology/block.h"
73 #include "gromacs/topology/ifunc.h"
74 #include "gromacs/topology/index.h"
75 #include "gromacs/topology/mtop_util.h"
76 #include "gromacs/topology/symtab.h"
77 #include "gromacs/topology/topology.h"
78 #include "gromacs/utility/arrayref.h"
79 #include "gromacs/utility/cstringutil.h"
80 #include "gromacs/utility/exceptions.h"
81 #include "gromacs/utility/fatalerror.h"
82 #include "gromacs/utility/filestream.h"
83 #include "gromacs/utility/gmxassert.h"
84 #include "gromacs/utility/ikeyvaluetreeerror.h"
85 #include "gromacs/utility/keyvaluetree.h"
86 #include "gromacs/utility/keyvaluetreebuilder.h"
87 #include "gromacs/utility/keyvaluetreemdpwriter.h"
88 #include "gromacs/utility/keyvaluetreetransform.h"
89 #include "gromacs/utility/mdmodulenotification.h"
90 #include "gromacs/utility/smalloc.h"
91 #include "gromacs/utility/strconvert.h"
92 #include "gromacs/utility/stringcompare.h"
93 #include "gromacs/utility/stringutil.h"
94 #include "gromacs/utility/textwriter.h"
99 /* Resource parameters
100 * Do not change any of these until you read the instruction
101 * in readinp.h. Some cpp's do not take spaces after the backslash
102 * (like the c-shell), which will give you a very weird compiler
106 struct gmx_inputrec_strings
108 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
109 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
110 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
111 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
112 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
113 char lambda_weights[STRLEN];
114 std::vector<std::string> pullGroupNames;
115 std::vector<std::string> rotateGroupNames;
116 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
119 static gmx_inputrec_strings* inputrecStrings = nullptr;
121 void init_inputrec_strings()
126 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
127 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
129 inputrecStrings = new gmx_inputrec_strings();
132 void done_inputrec_strings()
134 delete inputrecStrings;
135 inputrecStrings = nullptr;
141 egrptpALL, /* All particles have to be a member of a group. */
142 egrptpALL_GENREST, /* A rest group with name is generated for particles *
143 * that are not part of any group. */
144 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
145 * for the rest group. */
146 egrptpONE /* Merge all selected groups into one group, *
147 * make a rest group for the remaining particles. */
150 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
151 "h-angles", "all-angles", nullptr };
153 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
155 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
160 for (i = 0; i < ntemps; i++)
162 /* simple linear scaling -- allows more control */
163 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
165 simtemp->temperatures[i] =
167 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
169 else if (simtemp->eSimTempScale
170 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
172 simtemp->temperatures[i] = simtemp->simtemp_low
173 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
174 static_cast<real>((1.0 * i) / (ntemps - 1)));
176 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
178 simtemp->temperatures[i] = simtemp->simtemp_low
179 + (simtemp->simtemp_high - simtemp->simtemp_low)
180 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
185 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
186 gmx_fatal(FARGS, "%s", errorstr);
192 static void _low_check(bool b, const char* s, warninp_t wi)
196 warning_error(wi, s);
200 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
204 if (*p > 0 && *p % nst != 0)
206 /* Round up to the next multiple of nst */
207 *p = ((*p) / nst + 1) * nst;
208 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
213 //! Convert legacy mdp entries to modern ones.
214 static void process_interaction_modifier(InteractionModifiers* eintmod)
216 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
218 *eintmod = InteractionModifiers::PotShift;
222 void check_ir(const char* mdparin,
223 const gmx::MDModulesNotifiers& mdModulesNotifiers,
227 /* Check internal consistency.
228 * NOTE: index groups are not set here yet, don't check things
229 * like temperature coupling group options here, but in triple_check
232 /* Strange macro: first one fills the err_buf, and then one can check
233 * the condition, which will print the message and increase the error
236 #define CHECK(b) _low_check(b, err_buf, wi)
237 char err_buf[256], warn_buf[STRLEN];
240 t_lambda* fep = ir->fepvals.get();
241 t_expanded* expand = ir->expandedvals.get();
243 set_warning_line(wi, mdparin, -1);
245 /* We cannot check MTS requirements with an invalid MTS setup
246 * and we will already have generated errors with an invalid MTS setup.
248 if (gmx::haveValidMtsSetup(*ir))
250 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
252 for (const auto& errorMessage : errorMessages)
254 warning_error(wi, errorMessage.c_str());
258 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
260 std::string message =
261 gmx::formatString("%s electrostatics is no longer supported",
262 enumValueToString(CoulombInteractionType::RFNecUnsupported));
263 warning_error(wi, message);
266 /* BASIC CUT-OFF STUFF */
267 if (ir->rcoulomb < 0)
269 warning_error(wi, "rcoulomb should be >= 0");
273 warning_error(wi, "rvdw should be >= 0");
275 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
277 warning_error(wi, "rlist should be >= 0");
280 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
281 "neighbour-list update scheme for efficient buffering for improved energy "
282 "conservation, please use the Verlet cut-off scheme instead.)");
283 CHECK(ir->nstlist < 0);
285 process_interaction_modifier(&ir->coulomb_modifier);
286 process_interaction_modifier(&ir->vdw_modifier);
288 if (ir->cutoff_scheme == CutoffScheme::Group)
291 "The group cutoff scheme has been removed since GROMACS 2020. "
292 "Please use the Verlet cutoff scheme.");
294 if (ir->cutoff_scheme == CutoffScheme::Verlet)
298 /* Normal Verlet type neighbor-list, currently only limited feature support */
299 if (inputrec2nboundeddim(ir) < 3)
301 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
304 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
305 if (ir->rcoulomb != ir->rvdw)
307 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
308 // for PME load balancing, we can support this exception.
309 bool bUsesPmeTwinRangeKernel =
310 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
311 && ir->rcoulomb > ir->rvdw);
312 if (!bUsesPmeTwinRangeKernel)
315 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
316 "rcoulomb>rvdw with PME electrostatics)");
320 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
322 if (ir->vdw_modifier == InteractionModifiers::None
323 || ir->vdw_modifier == InteractionModifiers::PotShift)
326 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
327 : InteractionModifiers::PotSwitch);
330 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
332 enumValueToString(ir->vdwtype),
333 enumValueToString(VanDerWaalsType::Cut),
334 enumValueToString(ir->vdw_modifier));
335 warning_note(wi, warn_buf);
337 ir->vdwtype = VanDerWaalsType::Cut;
342 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
343 enumValueToString(ir->vdwtype),
344 enumValueToString(ir->vdw_modifier));
345 warning_error(wi, warn_buf);
349 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
352 "With Verlet lists only cut-off and PME LJ interactions are supported");
354 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
355 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
358 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
359 "electrostatics are supported");
361 if (!(ir->coulomb_modifier == InteractionModifiers::None
362 || ir->coulomb_modifier == InteractionModifiers::PotShift))
364 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
365 warning_error(wi, warn_buf);
368 if (EEL_USER(ir->coulombtype))
371 "Coulomb type %s is not supported with the verlet scheme",
372 enumValueToString(ir->coulombtype));
373 warning_error(wi, warn_buf);
376 if (ir->nstlist <= 0)
378 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
381 if (ir->nstlist < 10)
384 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
385 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
389 rc_max = std::max(ir->rvdw, ir->rcoulomb);
393 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
394 ir->verletbuf_tol = 0;
397 else if (ir->verletbuf_tol <= 0)
399 if (ir->verletbuf_tol == 0)
401 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
404 if (ir->rlist < rc_max)
407 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
410 if (ir->rlist == rc_max && ir->nstlist > 1)
414 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
415 "buffer. The cluster pair list does have a buffering effect, but choosing "
416 "a larger rlist might be necessary for good energy conservation.");
421 if (ir->rlist > rc_max)
424 "You have set rlist larger than the interaction cut-off, but you also "
425 "have verlet-buffer-tolerance > 0. Will set rlist using "
426 "verlet-buffer-tolerance.");
429 if (ir->nstlist == 1)
431 /* No buffer required */
436 if (EI_DYNAMICS(ir->eI))
438 if (inputrec2nboundeddim(ir) < 3)
441 "The box volume is required for calculating rlist from the "
442 "energy drift with verlet-buffer-tolerance > 0. You are "
443 "using at least one unbounded dimension, so no volume can be "
444 "computed. Either use a finite box, or set rlist yourself "
445 "together with verlet-buffer-tolerance = -1.");
447 /* Set rlist temporarily so we can continue processing */
452 /* Set the buffer to 5% of the cut-off */
453 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
459 /* GENERAL INTEGRATOR STUFF */
462 if (ir->etc != TemperatureCoupling::No)
464 if (EI_RANDOM(ir->eI))
467 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
468 "implicitly. See the documentation for more information on which "
469 "parameters affect temperature for %s.",
470 enumValueToString(ir->etc),
471 enumValueToString(ir->eI),
472 enumValueToString(ir->eI));
477 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
479 enumValueToString(ir->etc),
480 enumValueToString(ir->eI));
482 warning_note(wi, warn_buf);
484 ir->etc = TemperatureCoupling::No;
486 if (ir->eI == IntegrationAlgorithm::VVAK)
489 "Integrator method %s is implemented primarily for validation purposes; for "
490 "molecular dynamics, you should probably be using %s or %s",
491 enumValueToString(IntegrationAlgorithm::VVAK),
492 enumValueToString(IntegrationAlgorithm::MD),
493 enumValueToString(IntegrationAlgorithm::VV));
494 warning_note(wi, warn_buf);
496 if (!EI_DYNAMICS(ir->eI))
498 if (ir->epc != PressureCoupling::No)
501 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
502 enumValueToString(ir->epc),
503 enumValueToString(ir->eI));
504 warning_note(wi, warn_buf);
506 ir->epc = PressureCoupling::No;
508 if (EI_DYNAMICS(ir->eI))
510 if (ir->nstcalcenergy < 0)
512 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
513 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
515 /* nstcalcenergy larger than nstener does not make sense.
516 * We ideally want nstcalcenergy=nstener.
520 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
524 ir->nstcalcenergy = ir->nstenergy;
528 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
529 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
530 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
533 const char* nsten = "nstenergy";
534 const char* nstdh = "nstdhdl";
535 const char* min_name = nsten;
536 int min_nst = ir->nstenergy;
538 /* find the smallest of ( nstenergy, nstdhdl ) */
539 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
540 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
542 min_nst = ir->fepvals->nstdhdl;
545 /* If the user sets nstenergy small, we should respect that */
546 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
547 warning_note(wi, warn_buf);
548 ir->nstcalcenergy = min_nst;
551 if (ir->epc != PressureCoupling::No)
553 if (ir->nstpcouple < 0)
555 ir->nstpcouple = ir_optimal_nstpcouple(ir);
557 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
560 "With multiple time stepping, nstpcouple should be a mutiple of "
565 if (ir->nstcalcenergy > 0)
567 if (ir->efep != FreeEnergyPerturbationType::No)
569 /* nstdhdl should be a multiple of nstcalcenergy */
570 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
574 /* nstexpanded should be a multiple of nstcalcenergy */
575 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
577 /* for storing exact averages nstenergy should be
578 * a multiple of nstcalcenergy
580 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
583 // Inquire all MDModules, if their parameters match with the energy
584 // calculation frequency
585 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
586 mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
588 // Emit all errors from the energy calculation frequency checks
589 for (const std::string& energyFrequencyErrorMessage :
590 energyCalculationFrequencyErrors.errorMessages())
592 warning_error(wi, energyFrequencyErrorMessage);
596 if (ir->nsteps == 0 && !ir->bContinuation)
599 "For a correct single-point energy evaluation with nsteps = 0, use "
600 "continuation = yes to avoid constraining the input coordinates.");
604 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
607 "You are doing a continuation with SD or BD, make sure that ld_seed is "
608 "different from the previous run (using ld_seed=-1 will ensure this)");
614 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
615 CHECK(ir->pbcType != PbcType::Xyz);
616 sprintf(err_buf, "with TPI nstlist should be larger than zero");
617 CHECK(ir->nstlist <= 0);
618 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
619 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
623 if ((opts->nshake > 0) && (opts->bMorse))
625 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
626 warning(wi, warn_buf);
629 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
632 "You are doing a continuation with SD or BD, make sure that ld_seed is "
633 "different from the previous run (using ld_seed=-1 will ensure this)");
635 /* verify simulated tempering options */
639 bool bAllTempZero = TRUE;
640 for (i = 0; i < fep->n_lambda; i++)
643 "Entry %d for %s must be between 0 and 1, instead is %g",
645 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
646 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
647 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
648 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
650 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
652 bAllTempZero = FALSE;
655 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
656 CHECK(bAllTempZero == TRUE);
658 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
659 CHECK(ir->eI != IntegrationAlgorithm::VV);
661 /* check compatability of the temperature coupling with simulated tempering */
663 if (ir->etc == TemperatureCoupling::NoseHoover)
666 "Nose-Hoover based temperature control such as [%s] my not be "
667 "entirelyconsistent with simulated tempering",
668 enumValueToString(ir->etc));
669 warning_note(wi, warn_buf);
672 /* check that the temperatures make sense */
675 "Higher simulated tempering temperature (%g) must be >= than the simulated "
676 "tempering lower temperature (%g)",
677 ir->simtempvals->simtemp_high,
678 ir->simtempvals->simtemp_low);
679 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
682 "Higher simulated tempering temperature (%g) must be >= zero",
683 ir->simtempvals->simtemp_high);
684 CHECK(ir->simtempvals->simtemp_high <= 0);
687 "Lower simulated tempering temperature (%g) must be >= zero",
688 ir->simtempvals->simtemp_low);
689 CHECK(ir->simtempvals->simtemp_low <= 0);
692 /* verify free energy options */
694 if (ir->efep != FreeEnergyPerturbationType::No)
696 fep = ir->fepvals.get();
697 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
698 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
701 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
703 static_cast<int>(fep->sc_r_power));
704 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
707 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
710 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
713 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
715 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
717 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
718 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
720 sprintf(err_buf, "Free-energy not implemented for Ewald");
721 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
723 /* check validty of lambda inputs */
724 if (fep->n_lambda == 0)
726 /* Clear output in case of no states:*/
727 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
728 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
733 "initial thermodynamic state %d does not exist, only goes to %d",
736 CHECK((fep->init_fep_state >= fep->n_lambda));
740 "Lambda state must be set, either with init-lambda-state or with init-lambda");
741 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
744 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
745 "init-lambda-state or with init-lambda, but not both",
747 fep->init_fep_state);
748 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
751 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
755 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
757 if (fep->separate_dvdl[i])
762 if (n_lambda_terms > 1)
765 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
766 "use init-lambda to set lambda state (except for slow growth). Use "
767 "init-lambda-state instead.");
768 warning(wi, warn_buf);
771 if (n_lambda_terms < 2 && fep->n_lambda > 0)
774 "init-lambda is deprecated for setting lambda state (except for slow "
775 "growth). Use init-lambda-state instead.");
779 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
781 for (i = 0; i < fep->n_lambda; i++)
783 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
785 "Entry %d for %s must be between 0 and 1, instead is %g",
787 enumValueToString(enumValue),
788 fep->all_lambda[j][i]);
789 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
793 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
795 for (i = 0; i < fep->n_lambda; i++)
798 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
799 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
800 "crashes, and is not supported.",
802 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
803 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
804 CHECK((fep->sc_alpha > 0)
805 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
806 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
807 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
808 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
813 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
815 real sigma, lambda, r_sc;
818 /* Maximum estimate for A and B charges equal with lambda power 1 */
820 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
821 1.0 / fep->sc_r_power);
823 "With PME there is a minor soft core effect present at the cut-off, "
824 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
825 "energy conservation, but usually other effects dominate. With a common sigma "
826 "value of %g nm the fraction of the particle-particle potential at the cut-off "
827 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
833 warning_note(wi, warn_buf);
836 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
837 be treated differently, but that's the next step */
839 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
841 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
842 for (j = 0; j < fep->n_lambda; j++)
844 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
845 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
850 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
852 fep = ir->fepvals.get();
854 /* checking equilibration of weights inputs for validity */
857 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
859 expand->equil_n_at_lam,
860 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
861 CHECK((expand->equil_n_at_lam > 0)
862 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
865 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
867 expand->equil_samples,
868 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
869 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
872 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
874 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
875 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
878 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
879 expand->equil_samples,
880 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
881 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
884 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
886 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
887 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
890 "weight-equil-number-all-lambda (%d) must be a positive integer if "
891 "lmc-weights-equil=%s",
892 expand->equil_n_at_lam,
893 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
894 CHECK((expand->equil_n_at_lam <= 0)
895 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
898 "weight-equil-number-samples (%d) must be a positive integer if "
899 "lmc-weights-equil=%s",
900 expand->equil_samples,
901 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
902 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
905 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
907 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
908 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
911 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
912 expand->equil_wl_delta,
913 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
914 CHECK((expand->equil_wl_delta <= 0)
915 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
918 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
920 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
921 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
924 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
925 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
926 enumValueToString(LambdaWeightCalculation::WL),
927 enumValueToString(LambdaWeightCalculation::WWL));
928 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
930 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
931 CHECK((expand->lmc_repeats <= 0));
932 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
933 CHECK((expand->minvarmin <= 0));
934 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
935 CHECK((expand->c_range < 0));
937 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
940 expand->lmc_forced_nstart);
941 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
942 && (expand->elmcmove != LambdaMoveCalculation::No));
943 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
944 CHECK((expand->lmc_forced_nstart < 0));
946 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
947 fep->init_fep_state);
948 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
950 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
951 CHECK((expand->init_wl_delta < 0));
952 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
953 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
954 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
955 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
957 /* if there is no temperature control, we need to specify an MC temperature */
958 if (!integratorHasReferenceTemperature(ir)
959 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
962 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
963 "to a positive number");
964 warning_error(wi, err_buf);
966 if (expand->nstTij > 0)
968 sprintf(err_buf, "nstlog must be non-zero");
969 CHECK(ir->nstlog == 0);
970 // Avoid modulus by zero in the case that already triggered an error exit.
974 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
977 CHECK((expand->nstTij % ir->nstlog) != 0);
983 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
984 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
987 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
989 if (ir->pbcType == PbcType::No)
991 if (ir->epc != PressureCoupling::No)
993 warning(wi, "Turning off pressure coupling for vacuum system");
994 ir->epc = PressureCoupling::No;
1000 "Can not have pressure coupling with pbc=%s",
1001 c_pbcTypeNames[ir->pbcType].c_str());
1002 CHECK(ir->epc != PressureCoupling::No);
1004 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1005 CHECK(EEL_FULL(ir->coulombtype));
1008 "Can not have dispersion correction with pbc=%s",
1009 c_pbcTypeNames[ir->pbcType].c_str());
1010 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1013 if (ir->rlist == 0.0)
1016 "can only have neighborlist cut-off zero (=infinite)\n"
1017 "with coulombtype = %s or coulombtype = %s\n"
1018 "without periodic boundary conditions (pbc = %s) and\n"
1019 "rcoulomb and rvdw set to zero",
1020 enumValueToString(CoulombInteractionType::Cut),
1021 enumValueToString(CoulombInteractionType::User),
1022 c_pbcTypeNames[PbcType::No].c_str());
1023 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1024 && (ir->coulombtype != CoulombInteractionType::User))
1025 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1027 if (ir->nstlist > 0)
1030 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1031 "nstype=simple and only one MPI rank");
1036 if (ir->nstcomm == 0)
1038 // TODO Change this behaviour. There should be exactly one way
1039 // to turn off an algorithm.
1040 ir->comm_mode = ComRemovalAlgorithm::No;
1042 if (ir->comm_mode != ComRemovalAlgorithm::No)
1044 if (ir->nstcomm < 0)
1046 // TODO Such input was once valid. Now that we've been
1047 // helpful for a few years, we should reject such input,
1048 // lest we have to support every historical decision
1051 "If you want to remove the rotation around the center of mass, you should set "
1052 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1053 "its absolute value");
1054 ir->nstcomm = abs(ir->nstcomm);
1057 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1060 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1061 "nstcomm to nstcalcenergy");
1062 ir->nstcomm = ir->nstcalcenergy;
1065 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1068 "Can not remove the rotation around the center of mass with periodic "
1070 CHECK(ir->bPeriodicMols);
1071 if (ir->pbcType != PbcType::No)
1074 "Removing the rotation around the center of mass in a periodic system, "
1075 "this can lead to artifacts. Only use this on a single (cluster of) "
1076 "molecules. This cluster should not cross periodic boundaries.");
1081 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1082 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1085 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1086 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1088 enumValueToString(IntegrationAlgorithm::SD1));
1089 warning_note(wi, warn_buf);
1092 /* TEMPERATURE COUPLING */
1093 if (ir->etc == TemperatureCoupling::Yes)
1095 ir->etc = TemperatureCoupling::Berendsen;
1097 "Old option for temperature coupling given: "
1098 "changing \"yes\" to \"Berendsen\"\n");
1101 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1103 if (ir->opts.nhchainlength < 1)
1106 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1108 ir->opts.nhchainlength);
1109 ir->opts.nhchainlength = 1;
1110 warning(wi, warn_buf);
1113 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1117 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1118 ir->opts.nhchainlength = 1;
1123 ir->opts.nhchainlength = 0;
1126 if (ir->eI == IntegrationAlgorithm::VVAK)
1129 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1131 enumValueToString(IntegrationAlgorithm::VVAK));
1132 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1135 if (ETC_ANDERSEN(ir->etc))
1138 "%s temperature control not supported for integrator %s.",
1139 enumValueToString(ir->etc),
1140 enumValueToString(ir->eI));
1141 CHECK(!(EI_VV(ir->eI)));
1143 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1146 "Center of mass removal not necessary for %s. All velocities of coupled "
1147 "groups are rerandomized periodically, so flying ice cube errors will not "
1149 enumValueToString(ir->etc));
1150 warning_note(wi, warn_buf);
1154 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1155 "randomized every time step",
1157 enumValueToString(ir->etc));
1158 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1161 if (ir->etc == TemperatureCoupling::Berendsen)
1164 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1165 "might want to consider using the %s thermostat.",
1166 enumValueToString(ir->etc),
1167 enumValueToString(TemperatureCoupling::VRescale));
1168 warning_note(wi, warn_buf);
1171 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1172 && ir->epc == PressureCoupling::Berendsen)
1175 "Using Berendsen pressure coupling invalidates the "
1176 "true ensemble for the thermostat");
1177 warning(wi, warn_buf);
1180 /* PRESSURE COUPLING */
1181 if (ir->epc == PressureCoupling::Isotropic)
1183 ir->epc = PressureCoupling::Berendsen;
1185 "Old option for pressure coupling given: "
1186 "changing \"Isotropic\" to \"Berendsen\"\n");
1189 if (ir->epc != PressureCoupling::No)
1191 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1193 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1194 CHECK(ir->tau_p <= 0);
1196 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1199 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1200 "times larger than nstpcouple*dt (%g)",
1201 enumValueToString(ir->epc),
1203 pcouple_min_integration_steps(ir->epc),
1205 warning(wi, warn_buf);
1209 "compressibility must be > 0 when using pressure"
1211 enumValueToString(ir->epc));
1212 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1213 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1214 && ir->compress[ZZ][YY] <= 0));
1216 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1219 "You are generating velocities so I am assuming you "
1220 "are equilibrating a system. You are using "
1221 "%s pressure coupling, but this can be "
1222 "unstable for equilibration. If your system crashes, try "
1223 "equilibrating first with Berendsen pressure coupling. If "
1224 "you are not equilibrating the system, you can probably "
1225 "ignore this warning.",
1226 enumValueToString(ir->epc));
1227 warning(wi, warn_buf);
1233 if (ir->epc == PressureCoupling::Mttk)
1235 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1239 /* ELECTROSTATICS */
1240 /* More checks are in triple check (grompp.c) */
1242 if (ir->coulombtype == CoulombInteractionType::Switch)
1245 "coulombtype = %s is only for testing purposes and can lead to serious "
1246 "artifacts, advice: use coulombtype = %s",
1247 enumValueToString(ir->coulombtype),
1248 enumValueToString(CoulombInteractionType::RFZero));
1249 warning(wi, warn_buf);
1252 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1255 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1256 "format and exchanging epsilon-r and epsilon-rf",
1258 warning(wi, warn_buf);
1259 ir->epsilon_rf = ir->epsilon_r;
1260 ir->epsilon_r = 1.0;
1263 if (ir->epsilon_r == 0)
1266 "It is pointless to use long-range electrostatics with infinite relative "
1268 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1270 CHECK(EEL_FULL(ir->coulombtype));
1273 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1275 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1276 CHECK(ir->epsilon_r < 0);
1279 if (EEL_RF(ir->coulombtype))
1281 /* reaction field (at the cut-off) */
1283 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1286 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1287 enumValueToString(ir->coulombtype));
1288 warning(wi, warn_buf);
1289 ir->epsilon_rf = 0.0;
1292 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1293 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1294 if (ir->epsilon_rf == ir->epsilon_r)
1297 "Using epsilon-rf = epsilon-r with %s does not make sense",
1298 enumValueToString(ir->coulombtype));
1299 warning(wi, warn_buf);
1302 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1303 * means the interaction is zero outside rcoulomb, but it helps to
1304 * provide accurate energy conservation.
1306 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1308 if (ir_coulomb_switched(ir))
1311 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1312 "potential modifier options!",
1313 enumValueToString(ir->coulombtype));
1314 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1318 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1321 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1322 "secondary coulomb-modifier.");
1323 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1325 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1328 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1329 "secondary vdw-modifier.");
1330 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1333 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1334 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1337 "The switch/shift interaction settings are just for compatibility; you will get "
1339 "performance from applying potential modifiers to your interactions!\n");
1340 warning_note(wi, warn_buf);
1343 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1344 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1346 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1348 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1350 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1351 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1352 "will be good regardless, since ewald_rtol = %g.",
1354 ir->rcoulomb_switch,
1357 warning(wi, warn_buf);
1361 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1363 if (ir->rvdw_switch == 0)
1366 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1367 "potential. This suggests it was not set in the mdp, which can lead to large "
1368 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1369 "switching range.");
1370 warning(wi, warn_buf);
1374 if (EEL_FULL(ir->coulombtype))
1376 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1377 || ir->coulombtype == CoulombInteractionType::PmeUser
1378 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1381 "With coulombtype = %s, rcoulomb must be <= rlist",
1382 enumValueToString(ir->coulombtype));
1383 CHECK(ir->rcoulomb > ir->rlist);
1387 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1389 // TODO: Move these checks into the ewald module with the options class
1391 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1393 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1396 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1397 enumValueToString(ir->coulombtype),
1400 warning_error(wi, warn_buf);
1404 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1406 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1409 "With pbc=%s you should use ewald-geometry=%s",
1410 c_pbcTypeNames[ir->pbcType].c_str(),
1411 enumValueToString(EwaldGeometry::ThreeDC));
1412 warning(wi, warn_buf);
1414 /* This check avoids extra pbc coding for exclusion corrections */
1415 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1416 CHECK(ir->wall_ewald_zfac < 2);
1418 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1419 && EEL_FULL(ir->coulombtype))
1422 "With %s and ewald_geometry = %s you should use pbc = %s",
1423 enumValueToString(ir->coulombtype),
1424 enumValueToString(EwaldGeometry::ThreeDC),
1425 c_pbcTypeNames[PbcType::XY].c_str());
1426 warning(wi, warn_buf);
1428 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1430 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1431 CHECK(ir->bPeriodicMols);
1432 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1433 warning_note(wi, warn_buf);
1435 "With epsilon_surface > 0 you can only use domain decomposition "
1436 "when there are only small molecules with all bonds constrained (mdrun will check "
1438 warning_note(wi, warn_buf);
1441 if (ir_vdw_switched(ir))
1443 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1444 CHECK(ir->rvdw_switch >= ir->rvdw);
1446 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1449 "You are applying a switch function to vdw forces or potentials from %g to %g "
1450 "nm, which is more than half the interaction range, whereas switch functions "
1451 "are intended to act only close to the cut-off.",
1454 warning_note(wi, warn_buf);
1458 if (ir->vdwtype == VanDerWaalsType::Pme)
1460 if (!(ir->vdw_modifier == InteractionModifiers::None
1461 || ir->vdw_modifier == InteractionModifiers::PotShift))
1464 "With vdwtype = %s, the only supported modifiers are %s and %s",
1465 enumValueToString(ir->vdwtype),
1466 enumValueToString(InteractionModifiers::PotShift),
1467 enumValueToString(InteractionModifiers::None));
1468 warning_error(wi, err_buf);
1472 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1475 "You have selected user tables with dispersion correction, the dispersion "
1476 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1477 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1478 "really want dispersion correction to -C6/r^6.");
1481 if (ir->eI == IntegrationAlgorithm::LBFGS
1482 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1485 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1488 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1490 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1493 /* IMPLICIT SOLVENT */
1494 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1496 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1497 warning_error(wi, warn_buf);
1502 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1507 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1510 // cosine acceleration is only supported in leap-frog
1511 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1513 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1517 /* interpret a number of doubles from a string and put them in an array,
1518 after allocating space for them.
1519 str = the input string
1520 n = the (pre-allocated) number of doubles read
1521 r = the output array of doubles. */
1522 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1524 auto values = gmx::splitString(str);
1527 std::vector<real> r;
1528 for (int i = 0; i < *n; i++)
1532 r.emplace_back(gmx::fromString<real>(values[i]));
1534 catch (gmx::GromacsException&)
1537 "Invalid value " + values[i]
1538 + " in string in mdp file. Expected a real number.");
1545 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1548 int i, j, max_n_lambda, nweights;
1549 t_lambda* fep = ir->fepvals.get();
1550 t_expanded* expand = ir->expandedvals.get();
1551 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1552 bool bOneLambda = TRUE;
1553 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1555 /* FEP input processing */
1556 /* first, identify the number of lambda values for each type.
1557 All that are nonzero must have the same number */
1559 for (auto i : keysOf(nfep))
1561 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1564 /* now, determine the number of components. All must be either zero, or equal. */
1567 for (auto i : keysOf(nfep))
1569 if (nfep[i] > max_n_lambda)
1571 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1572 must have the same number if its not zero.*/
1577 for (auto i : keysOf(nfep))
1581 ir->fepvals->separate_dvdl[i] = FALSE;
1583 else if (nfep[i] == max_n_lambda)
1585 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1586 the derivative with respect to the temperature currently */
1588 ir->fepvals->separate_dvdl[i] = TRUE;
1594 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1597 enumValueToString(i),
1601 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1602 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1604 /* the number of lambdas is the number we've read in, which is either zero
1605 or the same for all */
1606 fep->n_lambda = max_n_lambda;
1608 /* if init_lambda is defined, we need to set lambda */
1609 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1611 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1613 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1614 for (auto i : keysOf(nfep))
1616 fep->all_lambda[i].resize(fep->n_lambda);
1617 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1620 for (j = 0; j < fep->n_lambda; j++)
1622 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1627 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1628 internal bookkeeping -- for now, init_lambda */
1630 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1632 for (i = 0; i < fep->n_lambda; i++)
1634 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1638 /* check to see if only a single component lambda is defined, and soft core is defined.
1639 In this case, turn on coulomb soft core */
1641 if (max_n_lambda == 0)
1647 for (auto i : keysOf(nfep))
1649 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1655 if ((bOneLambda) && (fep->sc_alpha > 0))
1657 fep->bScCoul = TRUE;
1660 /* Fill in the others with the efptFEP if they are not explicitly
1661 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1662 they are all zero. */
1664 for (auto i : keysOf(nfep))
1666 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1668 for (j = 0; j < fep->n_lambda; j++)
1670 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1676 /* now read in the weights */
1677 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1680 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1682 else if (nweights != fep->n_lambda)
1685 "Number of weights (%d) is not equal to number of lambda values (%d)",
1689 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1691 expand->nstexpanded = fep->nstdhdl;
1692 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1697 static void do_simtemp_params(t_inputrec* ir)
1699 ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
1700 getSimTemps(ir->fepvals->n_lambda,
1701 ir->simtempvals.get(),
1702 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1705 template<typename T>
1706 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1709 for (const auto& input : inputs)
1713 outputs[i] = gmx::fromStdString<T>(input);
1715 catch (gmx::GromacsException&)
1717 auto message = gmx::formatString(
1718 "Invalid value for mdp option %s. %s should only consist of integers separated "
1722 warning_error(wi, message);
1728 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1731 for (const auto& input : inputs)
1735 outputs[i] = gmx::fromString<real>(input);
1737 catch (gmx::GromacsException&)
1739 auto message = gmx::formatString(
1740 "Invalid value for mdp option %s. %s should only consist of real numbers "
1741 "separated by spaces.",
1744 warning_error(wi, message);
1750 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1752 opts->wall_atomtype[0] = nullptr;
1753 opts->wall_atomtype[1] = nullptr;
1755 ir->wall_atomtype[0] = -1;
1756 ir->wall_atomtype[1] = -1;
1757 ir->wall_density[0] = 0;
1758 ir->wall_density[1] = 0;
1762 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1763 if (wallAtomTypes.size() != size_t(ir->nwall))
1766 "Expected %d elements for wall_atomtype, found %zu",
1768 wallAtomTypes.size());
1770 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1771 for (int i = 0; i < ir->nwall; i++)
1773 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1776 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1778 auto wallDensity = gmx::splitString(wall_density);
1779 if (wallDensity.size() != size_t(ir->nwall))
1782 "Expected %d elements for wall-density, found %zu",
1784 wallDensity.size());
1786 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1787 for (int i = 0; i < ir->nwall; i++)
1789 if (ir->wall_density[i] <= 0)
1791 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1798 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1802 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1803 for (int i = 0; i < nwall; i++)
1805 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1806 grps->emplace_back(groups->groupNames.size() - 1);
1811 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1813 /* read expanded ensemble parameters */
1814 printStringNewline(inp, "expanded ensemble variables");
1815 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1816 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1817 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1818 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1819 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1820 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1821 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1822 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1823 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1824 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1825 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1826 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1827 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1828 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1829 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1830 expand->bSymmetrizedTMatrix =
1831 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1832 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1833 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1834 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1835 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1836 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1837 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1838 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1841 /*! \brief Return whether an end state with the given coupling-lambda
1842 * value describes fully-interacting VDW.
1844 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1845 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1847 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1849 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1855 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1858 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1860 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1862 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1865 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1866 std::string message = gmx::formatExceptionMessageToString(*ex);
1867 warning_error(wi_, message.c_str());
1872 std::string getOptionName(const gmx::KeyValueTreePath& context)
1874 if (mapping_ != nullptr)
1876 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1877 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1880 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1885 const gmx::IKeyValueTreeBackMapping* mapping_;
1890 void get_ir(const char* mdparin,
1891 const char* mdparout,
1892 gmx::MDModules* mdModules,
1895 WriteMdpHeader writeMdpHeader,
1899 double dumdub[2][6];
1901 char warn_buf[STRLEN];
1902 t_lambda* fep = ir->fepvals.get();
1903 t_expanded* expand = ir->expandedvals.get();
1905 const char* no_names[] = { "no", nullptr };
1907 init_inputrec_strings();
1908 gmx::TextInputFile stream(mdparin);
1909 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1911 snew(dumstr[0], STRLEN);
1912 snew(dumstr[1], STRLEN);
1914 /* ignore the following deprecated commands */
1915 replace_inp_entry(inp, "title", nullptr);
1916 replace_inp_entry(inp, "cpp", nullptr);
1917 replace_inp_entry(inp, "domain-decomposition", nullptr);
1918 replace_inp_entry(inp, "andersen-seed", nullptr);
1919 replace_inp_entry(inp, "dihre", nullptr);
1920 replace_inp_entry(inp, "dihre-fc", nullptr);
1921 replace_inp_entry(inp, "dihre-tau", nullptr);
1922 replace_inp_entry(inp, "nstdihreout", nullptr);
1923 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1924 replace_inp_entry(inp, "optimize-fft", nullptr);
1925 replace_inp_entry(inp, "adress_type", nullptr);
1926 replace_inp_entry(inp, "adress_const_wf", nullptr);
1927 replace_inp_entry(inp, "adress_ex_width", nullptr);
1928 replace_inp_entry(inp, "adress_hy_width", nullptr);
1929 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1930 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1931 replace_inp_entry(inp, "adress_site", nullptr);
1932 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1933 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1934 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1935 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1936 replace_inp_entry(inp, "rlistlong", nullptr);
1937 replace_inp_entry(inp, "nstcalclr", nullptr);
1938 replace_inp_entry(inp, "pull-print-com2", nullptr);
1939 replace_inp_entry(inp, "gb-algorithm", nullptr);
1940 replace_inp_entry(inp, "nstgbradii", nullptr);
1941 replace_inp_entry(inp, "rgbradii", nullptr);
1942 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1943 replace_inp_entry(inp, "gb-saltconc", nullptr);
1944 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1945 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1946 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1947 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1948 replace_inp_entry(inp, "sa-algorithm", nullptr);
1949 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1950 replace_inp_entry(inp, "ns-type", nullptr);
1952 /* replace the following commands with the clearer new versions*/
1953 replace_inp_entry(inp, "unconstrained-start", "continuation");
1954 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1955 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1956 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1957 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1958 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1959 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1961 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1962 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1963 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1964 setStringEntry(&inp, "include", opts->include, nullptr);
1965 printStringNoNewline(
1966 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1967 setStringEntry(&inp, "define", opts->define, nullptr);
1969 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1970 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
1971 printStringNoNewline(&inp, "Start time and timestep in ps");
1972 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1973 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1974 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1975 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1976 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1977 printStringNoNewline(
1978 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1979 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1980 printStringNoNewline(&inp, "Multiple time-stepping");
1981 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
1984 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
1985 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
1986 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
1987 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
1989 // We clear after reading without dynamics to not force the user to remove MTS mdp options
1990 if (!EI_DYNAMICS(ir->eI))
1995 printStringNoNewline(&inp, "mode for center of mass motion removal");
1996 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
1997 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1998 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1999 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2000 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2002 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2003 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2004 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2005 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2008 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2009 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2010 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2011 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2012 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2013 ir->niter = get_eint(&inp, "niter", 20, wi);
2014 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2015 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2016 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2017 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2018 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2020 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2021 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2023 /* Output options */
2024 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2025 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2026 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2027 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2028 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2029 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2030 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2031 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2032 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2033 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2034 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2035 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2036 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2037 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2038 printStringNoNewline(&inp, "default, all atoms will be written.");
2039 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2040 printStringNoNewline(&inp, "Selection of energy groups");
2041 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2043 /* Neighbor searching */
2044 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2045 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2046 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2047 printStringNoNewline(&inp, "nblist update frequency");
2048 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2049 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2050 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2051 std::vector<const char*> pbcTypesNamesChar;
2052 for (const auto& pbcTypeName : c_pbcTypeNames)
2054 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2056 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2057 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2058 printStringNoNewline(&inp,
2059 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2060 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2061 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2062 printStringNoNewline(&inp, "nblist cut-off");
2063 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2064 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2066 /* Electrostatics */
2067 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2068 printStringNoNewline(&inp, "Method for doing electrostatics");
2069 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2070 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2071 printStringNoNewline(&inp, "cut-off lengths");
2072 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2073 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2074 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2075 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2076 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2077 printStringNoNewline(&inp, "Method for doing Van der Waals");
2078 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2079 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2080 printStringNoNewline(&inp, "cut-off lengths");
2081 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2082 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2083 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2084 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2085 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2086 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2087 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2088 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2089 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2090 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2091 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2092 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2093 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2094 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2095 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2096 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2097 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2098 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2099 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2100 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2101 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2103 /* Implicit solvation is no longer supported, but we need grompp
2104 to be able to refuse old .mdp files that would have built a tpr
2105 to run it. Thus, only "no" is accepted. */
2106 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2108 /* Coupling stuff */
2109 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2110 printStringNoNewline(&inp, "Temperature coupling");
2111 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2112 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2113 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2114 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2115 printStringNoNewline(&inp, "Groups to couple separately");
2116 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2117 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2118 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2119 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2120 printStringNoNewline(&inp, "pressure coupling");
2121 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2122 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2123 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2124 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2125 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2126 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2127 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2128 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2129 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2132 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2133 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2134 printStringNoNewline(&inp, "Groups treated with MiMiC");
2135 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2137 /* Simulated annealing */
2138 printStringNewline(&inp, "SIMULATED ANNEALING");
2139 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2140 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2141 printStringNoNewline(&inp,
2142 "Number of time points to use for specifying annealing in each group");
2143 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2144 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2145 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2146 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2147 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2150 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2151 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2152 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2153 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2156 printStringNewline(&inp, "OPTIONS FOR BONDS");
2157 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2158 printStringNoNewline(&inp, "Type of constraint algorithm");
2159 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2160 printStringNoNewline(&inp, "Do not constrain the start configuration");
2161 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2162 printStringNoNewline(&inp,
2163 "Use successive overrelaxation to reduce the number of shake iterations");
2164 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2165 printStringNoNewline(&inp, "Relative tolerance of shake");
2166 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2167 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2168 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2169 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2170 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2171 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2172 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2173 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2174 printStringNoNewline(&inp, "rotates over more degrees than");
2175 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2176 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2177 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2179 /* Energy group exclusions */
2180 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2181 printStringNoNewline(
2182 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2183 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2186 printStringNewline(&inp, "WALLS");
2187 printStringNoNewline(
2188 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2189 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2190 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2191 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2192 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2193 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2194 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2197 printStringNewline(&inp, "COM PULLING");
2198 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2201 ir->pull = std::make_unique<pull_params_t>();
2202 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2206 for (int c = 0; c < ir->pull->ncoord; c++)
2208 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2211 "Constraint COM pulling is not supported in combination with "
2212 "multiple time stepping");
2220 NOTE: needs COM pulling or free energy input */
2221 printStringNewline(&inp, "AWH biasing");
2222 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2225 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
2228 /* Enforced rotation */
2229 printStringNewline(&inp, "ENFORCED ROTATION");
2230 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2231 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2235 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2238 /* Interactive MD */
2240 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2241 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2242 if (inputrecStrings->imd_grp[0] != '\0')
2249 printStringNewline(&inp, "NMR refinement stuff");
2250 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2251 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2252 printStringNoNewline(
2253 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2254 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2255 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2256 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2257 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2258 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2259 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2260 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2261 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2262 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2263 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2264 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2265 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2266 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2267 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2268 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2270 /* free energy variables */
2271 printStringNewline(&inp, "Free energy variables");
2272 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2273 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2274 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2275 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2276 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2278 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2280 it was not entered */
2281 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2282 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2283 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2284 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2285 setStringEntry(&inp, "fep-lambdas", "");
2286 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2287 setStringEntry(&inp, "mass-lambdas", "");
2288 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2289 setStringEntry(&inp, "coul-lambdas", "");
2290 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2291 setStringEntry(&inp, "vdw-lambdas", "");
2292 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2293 setStringEntry(&inp, "bonded-lambdas", "");
2294 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2295 setStringEntry(&inp, "restraint-lambdas", "");
2296 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2297 setStringEntry(&inp, "temperature-lambdas", "");
2298 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2299 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2300 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2301 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2302 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2303 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2304 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2305 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2306 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2307 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2308 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2309 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2310 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2311 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2313 /* Non-equilibrium MD stuff */
2314 printStringNewline(&inp, "Non-equilibrium MD stuff");
2315 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2316 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2317 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2318 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2320 /* simulated tempering variables */
2321 printStringNewline(&inp, "simulated tempering variables");
2322 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2323 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2324 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2325 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2327 /* expanded ensemble variables */
2328 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2330 read_expandedparams(&inp, expand, wi);
2333 /* Electric fields */
2335 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2336 gmx::KeyValueTreeTransformer transform;
2337 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2338 mdModules->initMdpTransform(transform.rules());
2339 for (const auto& path : transform.mappedPaths())
2341 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2342 mark_einp_set(inp, path[0].c_str());
2344 MdpErrorHandler errorHandler(wi);
2345 auto result = transform.transform(convertedValues, &errorHandler);
2346 ir->params = new gmx::KeyValueTreeObject(result.object());
2347 mdModules->adjustInputrecBasedOnModules(ir);
2348 errorHandler.setBackMapping(result.backMapping());
2349 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2352 /* Ion/water position swapping ("computational electrophysiology") */
2353 printStringNewline(&inp,
2354 "Ion/water position swapping for computational electrophysiology setups");
2355 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2356 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2357 if (ir->eSwapCoords != SwapType::No)
2364 printStringNoNewline(&inp, "Swap attempt frequency");
2365 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2366 printStringNoNewline(&inp, "Number of ion types to be controlled");
2367 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2370 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2372 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2373 snew(ir->swap->grp, ir->swap->ngrp);
2374 for (i = 0; i < ir->swap->ngrp; i++)
2376 snew(ir->swap->grp[i].molname, STRLEN);
2378 printStringNoNewline(&inp,
2379 "Two index groups that contain the compartment-partitioning atoms");
2380 setStringEntry(&inp,
2382 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2384 setStringEntry(&inp,
2386 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2388 printStringNoNewline(&inp,
2389 "Use center of mass of split groups (yes/no), otherwise center of "
2390 "geometry is used");
2391 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2392 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2394 printStringNoNewline(&inp, "Name of solvent molecules");
2395 setStringEntry(&inp,
2397 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2400 printStringNoNewline(&inp,
2401 "Split cylinder: radius, upper and lower extension (nm) (this will "
2402 "define the channels)");
2403 printStringNoNewline(&inp,
2404 "Note that the split cylinder settings do not have an influence on "
2405 "the swapping protocol,");
2406 printStringNoNewline(
2408 "however, if correctly defined, the permeation events are recorded per channel");
2409 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2410 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2411 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2412 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2413 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2414 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2416 printStringNoNewline(
2418 "Average the number of ions per compartment over these many swap attempt steps");
2419 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2421 printStringNoNewline(
2422 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2423 printStringNoNewline(
2424 &inp, "and the requested number of ions of this type in compartments A and B");
2425 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2426 for (i = 0; i < nIonTypes; i++)
2428 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2430 sprintf(buf, "iontype%d-name", i);
2431 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2432 sprintf(buf, "iontype%d-in-A", i);
2433 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2434 sprintf(buf, "iontype%d-in-B", i);
2435 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2438 printStringNoNewline(
2440 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2441 printStringNoNewline(
2443 "at maximum distance (= bulk concentration) to the split group layers. However,");
2444 printStringNoNewline(&inp,
2445 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2446 "layer from the middle at 0.0");
2447 printStringNoNewline(&inp,
2448 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2449 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2450 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2451 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2452 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2454 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2457 printStringNoNewline(
2458 &inp, "Start to swap ions if threshold difference to requested count is reached");
2459 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2462 /* AdResS is no longer supported, but we need grompp to be able to
2463 refuse to process old .mdp files that used it. */
2464 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2466 /* User defined thingies */
2467 printStringNewline(&inp, "User defined thingies");
2468 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2469 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2470 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2471 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2472 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2473 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2474 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2475 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2476 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2477 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2481 gmx::TextOutputFile stream(mdparout);
2482 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2484 // Transform module data into a flat key-value tree for output.
2485 gmx::KeyValueTreeBuilder builder;
2486 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2487 mdModules->buildMdpOutput(&builderObject);
2489 gmx::TextWriter writer(&stream);
2490 writeKeyValueTreeAsMdp(&writer, builder.build());
2495 /* Process options if necessary */
2496 for (m = 0; m < 2; m++)
2498 for (i = 0; i < 2 * DIM; i++)
2502 if (ir->epc != PressureCoupling::No)
2506 case PressureCouplingType::Isotropic:
2507 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2511 "Pressure coupling incorrect number of values (I need exactly 1)");
2513 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2515 case PressureCouplingType::SemiIsotropic:
2516 case PressureCouplingType::SurfaceTension:
2517 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2521 "Pressure coupling incorrect number of values (I need exactly 2)");
2523 dumdub[m][YY] = dumdub[m][XX];
2525 case PressureCouplingType::Anisotropic:
2526 if (sscanf(dumstr[m],
2527 "%lf%lf%lf%lf%lf%lf",
2538 "Pressure coupling incorrect number of values (I need exactly 6)");
2543 "Pressure coupling type %s not implemented yet",
2544 enumValueToString(ir->epct));
2548 clear_mat(ir->ref_p);
2549 clear_mat(ir->compress);
2550 for (i = 0; i < DIM; i++)
2552 ir->ref_p[i][i] = dumdub[1][i];
2553 ir->compress[i][i] = dumdub[0][i];
2555 if (ir->epct == PressureCouplingType::Anisotropic)
2557 ir->ref_p[XX][YY] = dumdub[1][3];
2558 ir->ref_p[XX][ZZ] = dumdub[1][4];
2559 ir->ref_p[YY][ZZ] = dumdub[1][5];
2560 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2563 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2564 "apply a threefold shear stress?\n");
2566 ir->compress[XX][YY] = dumdub[0][3];
2567 ir->compress[XX][ZZ] = dumdub[0][4];
2568 ir->compress[YY][ZZ] = dumdub[0][5];
2569 for (i = 0; i < DIM; i++)
2571 for (m = 0; m < i; m++)
2573 ir->ref_p[i][m] = ir->ref_p[m][i];
2574 ir->compress[i][m] = ir->compress[m][i];
2579 if (ir->comm_mode == ComRemovalAlgorithm::No)
2584 opts->couple_moltype = nullptr;
2585 if (strlen(inputrecStrings->couple_moltype) > 0)
2587 if (ir->efep != FreeEnergyPerturbationType::No)
2589 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2590 if (opts->couple_lam0 == opts->couple_lam1)
2592 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2594 if (ir->eI == IntegrationAlgorithm::MD
2595 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2599 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2606 "Free energy is turned off, so we will not decouple the molecule listed "
2610 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2611 if (ir->efep != FreeEnergyPerturbationType::No)
2613 if (fep->delta_lambda != 0)
2615 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2619 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2621 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2623 "Old option for dhdl-print-energy given: "
2624 "changing \"yes\" to \"total\"\n");
2627 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2629 /* always print out the energy to dhdl if we are doing
2630 expanded ensemble, since we need the total energy for
2631 analysis if the temperature is changing. In some
2632 conditions one may only want the potential energy, so
2633 we will allow that if the appropriate mdp setting has
2634 been enabled. Otherwise, total it is:
2636 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2639 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2641 ir->bExpanded = FALSE;
2642 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2644 ir->bExpanded = TRUE;
2646 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2647 if (ir->bSimTemp) /* done after fep params */
2649 do_simtemp_params(ir);
2652 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2653 * setup and not on the old way of specifying the free-energy setup,
2654 * we should check for using soft-core when not needed, since that
2655 * can complicate the sampling significantly.
2656 * Note that we only check for the automated coupling setup.
2657 * If the (advanced) user does FEP through manual topology changes,
2658 * this check will not be triggered.
2660 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2661 && ir->fepvals->sc_alpha != 0
2662 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2665 "You are using soft-core interactions while the Van der Waals interactions are "
2666 "not decoupled (note that the sc-coul option is only active when using lambda "
2667 "states). Although this will not lead to errors, you will need much more "
2668 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2673 ir->fepvals->n_lambda = 0;
2676 /* WALL PARAMETERS */
2678 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2680 /* ORIENTATION RESTRAINT PARAMETERS */
2682 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2684 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2687 /* DEFORMATION PARAMETERS */
2689 clear_mat(ir->deform);
2690 for (i = 0; i < 6; i++)
2695 double gmx_unused canary;
2696 int ndeform = sscanf(inputrecStrings->deform,
2697 "%lf %lf %lf %lf %lf %lf %lf",
2706 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2710 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2711 inputrecStrings->deform)
2714 for (i = 0; i < 3; i++)
2716 ir->deform[i][i] = dumdub[0][i];
2718 ir->deform[YY][XX] = dumdub[0][3];
2719 ir->deform[ZZ][XX] = dumdub[0][4];
2720 ir->deform[ZZ][YY] = dumdub[0][5];
2721 if (ir->epc != PressureCoupling::No)
2723 for (i = 0; i < 3; i++)
2725 for (j = 0; j <= i; j++)
2727 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2729 warning_error(wi, "A box element has deform set and compressibility > 0");
2733 for (i = 0; i < 3; i++)
2735 for (j = 0; j < i; j++)
2737 if (ir->deform[i][j] != 0)
2739 for (m = j; m < DIM; m++)
2741 if (ir->compress[m][j] != 0)
2744 "An off-diagonal box element has deform set while "
2745 "compressibility > 0 for the same component of another box "
2746 "vector, this might lead to spurious periodicity effects.");
2747 warning(wi, warn_buf);
2755 /* Ion/water position swapping checks */
2756 if (ir->eSwapCoords != SwapType::No)
2758 if (ir->swap->nstswap < 1)
2760 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2762 if (ir->swap->nAverage < 1)
2764 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2766 if (ir->swap->threshold < 1.0)
2768 warning_error(wi, "Ion count threshold must be at least 1.\n");
2772 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2775 std::vector<std::string> errorMessages;
2776 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2778 for (const auto& errorMessage : errorMessages)
2780 warning_error(wi, errorMessage.c_str());
2786 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2793 /* We would like gn to be const as well, but C doesn't allow this */
2794 /* TODO this is utility functionality (search for the index of a
2795 string in a collection), so should be refactored and located more
2797 int search_string(const char* s, int ng, char* gn[])
2801 for (i = 0; (i < ng); i++)
2803 if (gmx_strcasecmp(s, gn[i]) == 0)
2810 "Group %s referenced in the .mdp file was not found in the index file.\n"
2811 "Group names must match either [moleculetype] names or custom index group\n"
2812 "names, in which case you must supply an index file to the '-n' option\n"
2817 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2819 /* Now go over the atoms in the group */
2820 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2822 int aj = block.a[j];
2824 /* Range checking */
2825 if ((aj < 0) || (aj >= natoms))
2827 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2832 static void do_numbering(int natoms,
2833 SimulationGroups* groups,
2834 gmx::ArrayRef<std::string> groupsFromMdpFile,
2837 SimulationAtomGroupType gtype,
2843 unsigned short* cbuf;
2844 AtomGroupIndices* grps = &(groups->groups[gtype]);
2847 char warn_buf[STRLEN];
2849 title = shortName(gtype);
2852 /* Mark all id's as not set */
2853 for (int i = 0; (i < natoms); i++)
2858 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2860 /* Lookup the group name in the block structure */
2861 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2862 if ((grptp != egrptpONE) || (i == 0))
2864 grps->emplace_back(gid);
2866 GMX_ASSERT(block, "Can't have a nullptr block");
2867 atomGroupRangeValidation(natoms, gid, *block);
2868 /* Now go over the atoms in the group */
2869 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2871 const int aj = block->a[j];
2872 /* Lookup up the old group number */
2873 const int ognr = cbuf[aj];
2876 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2880 /* Store the group number in buffer */
2881 if (grptp == egrptpONE)
2894 /* Now check whether we have done all atoms */
2897 if (grptp == egrptpALL)
2899 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2901 else if (grptp == egrptpPART)
2903 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2904 warning_note(wi, warn_buf);
2906 /* Assign all atoms currently unassigned to a rest group */
2907 for (int j = 0; (j < natoms); j++)
2909 if (cbuf[j] == NOGID)
2911 cbuf[j] = grps->size();
2914 if (grptp != egrptpPART)
2918 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2920 /* Add group name "rest" */
2921 grps->emplace_back(restnm);
2923 /* Assign the rest name to all atoms not currently assigned to a group */
2924 for (int j = 0; (j < natoms); j++)
2926 if (cbuf[j] == NOGID)
2928 // group size was not updated before this here, so need to use -1.
2929 cbuf[j] = grps->size() - 1;
2935 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2937 /* All atoms are part of one (or no) group, no index required */
2938 groups->groupNumbers[gtype].clear();
2942 for (int j = 0; (j < natoms); j++)
2944 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2951 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2954 pull_params_t* pull;
2955 int natoms, imin, jmin;
2956 int * nrdf2, *na_vcm, na_tot;
2957 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2962 * First calc 3xnr-atoms for each group
2963 * then subtract half a degree of freedom for each constraint
2965 * Only atoms and nuclei contribute to the degrees of freedom...
2970 const SimulationGroups& groups = mtop->groups;
2971 natoms = mtop->natoms;
2973 /* Allocate one more for a possible rest group */
2974 /* We need to sum degrees of freedom into doubles,
2975 * since floats give too low nrdf's above 3 million atoms.
2977 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2978 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2979 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2980 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2981 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2983 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2987 for (gmx::index i = 0;
2988 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
2992 clear_ivec(dof_vcm[i]);
2994 nrdf_vcm_sub[i] = 0;
2996 snew(nrdf2, natoms);
2997 for (const AtomProxy atomP : AtomRange(*mtop))
2999 const t_atom& local = atomP.atom();
3000 int i = atomP.globalAtomNumber();
3002 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3004 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3005 for (int d = 0; d < DIM; d++)
3007 if (opts->nFreeze[g][d] == 0)
3009 /* Add one DOF for particle i (counted as 2*1) */
3011 /* VCM group i has dim d as a DOF */
3012 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3016 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3018 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3024 for (const gmx_molblock_t& molb : mtop->molblock)
3026 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3027 const t_atom* atom = molt.atoms.atom;
3028 for (int mol = 0; mol < molb.nmol; mol++)
3030 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3032 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3033 for (int i = 0; i < molt.ilist[ftype].size();)
3035 /* Subtract degrees of freedom for the constraints,
3036 * if the particles still have degrees of freedom left.
3037 * If one of the particles is a vsite or a shell, then all
3038 * constraint motion will go there, but since they do not
3039 * contribute to the constraints the degrees of freedom do not
3042 int ai = as + ia[i + 1];
3043 int aj = as + ia[i + 2];
3044 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3045 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3046 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3047 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3065 imin = std::min(imin, nrdf2[ai]);
3066 jmin = std::min(jmin, nrdf2[aj]);
3069 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3071 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3073 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3075 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3078 i += interaction_function[ftype].nratoms + 1;
3081 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3082 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3084 /* Subtract 1 dof from every atom in the SETTLE */
3085 for (int j = 0; j < 3; j++)
3087 int ai = as + ia[i + 1 + j];
3088 imin = std::min(2, nrdf2[ai]);
3090 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3092 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3097 as += molt.atoms.nr;
3103 /* Correct nrdf for the COM constraints.
3104 * We correct using the TC and VCM group of the first atom
3105 * in the reference and pull group. If atoms in one pull group
3106 * belong to different TC or VCM groups it is anyhow difficult
3107 * to determine the optimal nrdf assignment.
3109 pull = ir->pull.get();
3111 for (int i = 0; i < pull->ncoord; i++)
3113 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3120 for (int j = 0; j < 2; j++)
3122 const t_pull_group* pgrp;
3124 pgrp = &pull->group[pull->coord[i].group[j]];
3126 if (!pgrp->ind.empty())
3128 /* Subtract 1/2 dof from each group */
3129 int ai = pgrp->ind[0];
3130 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3132 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3134 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3137 "Center of mass pulling constraints caused the number of degrees "
3138 "of freedom for temperature coupling group %s to be negative",
3139 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3140 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3145 /* We need to subtract the whole DOF from group j=1 */
3152 if (ir->nstcomm != 0)
3154 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3155 "Expect at least one group when removing COM motion");
3157 /* We remove COM motion up to dim ndof_com() */
3158 const int ndim_rm_vcm = ndof_com(ir);
3160 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3161 * the number of degrees of freedom in each vcm group when COM
3162 * translation is removed and 6 when rotation is removed as well.
3163 * Note that we do not and should not include the rest group here.
3165 for (gmx::index j = 0;
3166 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3169 switch (ir->comm_mode)
3171 case ComRemovalAlgorithm::Linear:
3172 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3173 nrdf_vcm_sub[j] = 0;
3174 for (int d = 0; d < ndim_rm_vcm; d++)
3182 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3183 default: gmx_incons("Checking comm_mode");
3187 for (gmx::index i = 0;
3188 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3191 /* Count the number of atoms of TC group i for every VCM group */
3192 for (gmx::index j = 0;
3193 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3199 for (int ai = 0; ai < natoms; ai++)
3201 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3203 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3207 /* Correct for VCM removal according to the fraction of each VCM
3208 * group present in this TC group.
3210 nrdf_uc = nrdf_tc[i];
3212 for (gmx::index j = 0;
3213 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3216 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3218 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3219 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3224 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3226 opts->nrdf[i] = nrdf_tc[i];
3227 if (opts->nrdf[i] < 0)
3232 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3233 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3242 sfree(nrdf_vcm_sub);
3245 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3247 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3248 * But since this is much larger than STRLEN, such a line can not be parsed.
3249 * The real maximum is the number of names that fit in a string: STRLEN/2.
3251 #define EGP_MAX (STRLEN / 2)
3255 auto names = gmx::splitString(val);
3256 if (names.size() % 2 != 0)
3258 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3260 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3262 for (size_t i = 0; i < names.size() / 2; i++)
3264 // TODO this needs to be replaced by a solution using std::find_if
3268 names[2 * i].c_str(),
3269 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3275 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3280 names[2 * i + 1].c_str(),
3281 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3287 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3289 if ((j < nr) && (k < nr))
3291 ir->opts.egp_flags[nr * j + k] |= flag;
3292 ir->opts.egp_flags[nr * k + j] |= flag;
3301 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3303 int ig = -1, i = 0, gind;
3307 /* Just a quick check here, more thorough checks are in mdrun */
3308 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3309 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3313 "The split groups can not both be '%s'.",
3314 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3317 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3318 for (ig = 0; ig < swap->ngrp; ig++)
3320 swapg = &swap->grp[ig];
3321 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3322 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3327 "%s group '%s' contains %d atoms.\n",
3328 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3329 swap->grp[ig].molname,
3331 snew(swapg->ind, swapg->nat);
3332 for (i = 0; i < swapg->nat; i++)
3334 swapg->ind[i] = grps->a[grps->index[gind] + i];
3339 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3345 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3350 ig = search_string(IMDgname, grps->nr, gnames);
3351 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3353 if (IMDgroup->nat > 0)
3356 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3360 snew(IMDgroup->ind, IMDgroup->nat);
3361 for (i = 0; i < IMDgroup->nat; i++)
3363 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3368 /* Checks whether atoms are both part of a COM removal group and frozen.
3369 * If a fully frozen atom is part of a COM removal group, it is removed
3370 * from the COM removal group. A note is issued if such atoms are present.
3371 * A warning is issued for atom with one or two dimensions frozen that
3372 * are part of a COM removal group (mdrun would need to compute COM mass
3373 * per dimension to handle this correctly).
3374 * Also issues a warning when non-frozen atoms are not part of a COM
3375 * removal group while COM removal is active.
3377 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3379 const t_grpopts& opts,
3382 const int vcmRestGroup =
3383 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3385 int numFullyFrozenVcmAtoms = 0;
3386 int numPartiallyFrozenVcmAtoms = 0;
3387 int numNonVcmAtoms = 0;
3388 for (int a = 0; a < numAtoms; a++)
3390 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3391 int numFrozenDims = 0;
3392 for (int d = 0; d < DIM; d++)
3394 numFrozenDims += opts.nFreeze[freezeGroup][d];
3397 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3398 if (vcmGroup < vcmRestGroup)
3400 if (numFrozenDims == DIM)
3402 /* Do not remove COM motion for this fully frozen atom */
3403 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3405 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3408 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3409 numFullyFrozenVcmAtoms++;
3411 else if (numFrozenDims > 0)
3413 numPartiallyFrozenVcmAtoms++;
3416 else if (numFrozenDims < DIM)
3422 if (numFullyFrozenVcmAtoms > 0)
3424 std::string warningText = gmx::formatString(
3425 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3426 "removing these atoms from the COMM removal group(s)",
3427 numFullyFrozenVcmAtoms);
3428 warning_note(wi, warningText.c_str());
3430 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3432 std::string warningText = gmx::formatString(
3433 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3434 "removal group(s), due to limitations in the code these still contribute to the "
3435 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3437 numPartiallyFrozenVcmAtoms,
3439 warning(wi, warningText.c_str());
3441 if (numNonVcmAtoms > 0)
3443 std::string warningText = gmx::formatString(
3444 "%d atoms are not part of any center of mass motion removal group.\n"
3445 "This may lead to artifacts.\n"
3446 "In most cases one should use one group for the whole system.",
3448 warning(wi, warningText.c_str());
3452 void do_index(const char* mdparin,
3456 const gmx::MDModulesNotifiers& mdModulesNotifiers,
3460 t_blocka* defaultIndexGroups;
3468 int i, j, k, restnm;
3469 bool bExcl, bTable, bAnneal;
3470 char warn_buf[STRLEN];
3474 fprintf(stderr, "processing index file...\n");
3478 snew(defaultIndexGroups, 1);
3479 snew(defaultIndexGroups->index, 1);
3481 atoms_all = gmx_mtop_global_atoms(*mtop);
3482 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3483 done_atom(&atoms_all);
3487 defaultIndexGroups = init_index(ndx, &gnames);
3490 SimulationGroups* groups = &mtop->groups;
3491 natoms = mtop->natoms;
3492 symtab = &mtop->symtab;
3494 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3496 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3498 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3499 restnm = groups->groupNames.size() - 1;
3500 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3501 srenew(gnames, defaultIndexGroups->nr + 1);
3502 gnames[restnm] = *(groups->groupNames.back());
3504 set_warning_line(wi, mdparin, -1);
3506 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3507 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3508 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3509 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3510 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3513 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3515 temperatureCouplingGroupNames.size(),
3516 temperatureCouplingReferenceValues.size(),
3517 temperatureCouplingTauValues.size());
3520 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3521 do_numbering(natoms,
3523 temperatureCouplingGroupNames,
3526 SimulationAtomGroupType::TemperatureCoupling,
3528 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3531 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3533 snew(ir->opts.nrdf, nr);
3534 snew(ir->opts.tau_t, nr);
3535 snew(ir->opts.ref_t, nr);
3536 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3538 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3541 if (useReferenceTemperature)
3543 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3545 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3549 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3550 for (i = 0; (i < nr); i++)
3552 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3555 "With integrator %s tau-t should be larger than 0",
3556 enumValueToString(ir->eI));
3557 warning_error(wi, warn_buf);
3560 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3564 "tau-t = -1 is the value to signal that a group should not have "
3565 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3568 if (ir->opts.tau_t[i] >= 0)
3570 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3573 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3575 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3580 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3583 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3584 "md-vv; use either vrescale temperature with berendsen pressure or "
3585 "Nose-Hoover temperature with MTTK pressure");
3587 if (ir->epc == PressureCoupling::Mttk)
3589 if (ir->etc != TemperatureCoupling::NoseHoover)
3592 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3597 if (ir->nstpcouple != ir->nsttcouple)
3599 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3600 ir->nstpcouple = ir->nsttcouple = mincouple;
3602 "for current Trotter decomposition methods with vv, nsttcouple and "
3603 "nstpcouple must be equal. Both have been reset to "
3604 "min(nsttcouple,nstpcouple) = %d",
3606 warning_note(wi, warn_buf);
3611 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3612 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3614 if (ETC_ANDERSEN(ir->etc))
3616 if (ir->nsttcouple != 1)
3620 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3621 "need for larger nsttcouple > 1, since no global parameters are computed. "
3622 "nsttcouple has been reset to 1");
3623 warning_note(wi, warn_buf);
3626 nstcmin = tcouple_min_integration_steps(ir->etc);
3629 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3632 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3633 "least %d times larger than nsttcouple*dt (%g)",
3634 enumValueToString(ir->etc),
3637 ir->nsttcouple * ir->delta_t);
3638 warning(wi, warn_buf);
3641 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3642 for (i = 0; (i < nr); i++)
3644 if (ir->opts.ref_t[i] < 0)
3646 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3649 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3650 if we are in this conditional) if mc_temp is negative */
3651 if (ir->expandedvals->mc_temp < 0)
3653 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3657 /* Simulated annealing for each group. There are nr groups */
3658 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3659 if (simulatedAnnealingGroupNames.size() == 1
3660 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3662 simulatedAnnealingGroupNames.resize(0);
3664 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3667 "Wrong number of annealing values: %zu (for %d groups)\n",
3668 simulatedAnnealingGroupNames.size(),
3673 snew(ir->opts.annealing, nr);
3674 snew(ir->opts.anneal_npoints, nr);
3675 snew(ir->opts.anneal_time, nr);
3676 snew(ir->opts.anneal_temp, nr);
3677 for (i = 0; i < nr; i++)
3679 ir->opts.annealing[i] = SimulatedAnnealing::No;
3680 ir->opts.anneal_npoints[i] = 0;
3681 ir->opts.anneal_time[i] = nullptr;
3682 ir->opts.anneal_temp[i] = nullptr;
3684 if (!simulatedAnnealingGroupNames.empty())
3687 for (i = 0; i < nr; i++)
3689 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3691 ir->opts.annealing[i] = SimulatedAnnealing::No;
3693 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3695 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3698 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3700 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3706 /* Read the other fields too */
3707 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3708 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3711 "Found %zu annealing-npoints values for %zu groups\n",
3712 simulatedAnnealingPoints.size(),
3713 simulatedAnnealingGroupNames.size());
3715 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3716 size_t numSimulatedAnnealingFields = 0;
3717 for (i = 0; i < nr; i++)
3719 if (ir->opts.anneal_npoints[i] == 1)
3723 "Please specify at least a start and an end point for annealing\n");
3725 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3726 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3727 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3730 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3732 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3735 "Found %zu annealing-time values, wanted %zu\n",
3736 simulatedAnnealingTimes.size(),
3737 numSimulatedAnnealingFields);
3739 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3740 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3743 "Found %zu annealing-temp values, wanted %zu\n",
3744 simulatedAnnealingTemperatures.size(),
3745 numSimulatedAnnealingFields);
3748 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3749 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3750 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3752 simulatedAnnealingTemperatures,
3754 allSimulatedAnnealingTemperatures.data());
3755 for (i = 0, k = 0; i < nr; i++)
3757 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3759 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3760 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3763 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3765 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3771 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3774 "Annealing timepoints out of order: t=%f comes after "
3776 ir->opts.anneal_time[i][j],
3777 ir->opts.anneal_time[i][j - 1]);
3780 if (ir->opts.anneal_temp[i][j] < 0)
3783 "Found negative temperature in annealing: %f\n",
3784 ir->opts.anneal_temp[i][j]);
3789 /* Print out some summary information, to make sure we got it right */
3790 for (i = 0; i < nr; i++)
3792 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3794 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3796 "Simulated annealing for group %s: %s, %d timepoints\n",
3797 *(groups->groupNames[j]),
3798 enumValueToString(ir->opts.annealing[i]),
3799 ir->opts.anneal_npoints[i]);
3800 fprintf(stderr, "Time (ps) Temperature (K)\n");
3801 /* All terms except the last one */
3802 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3806 ir->opts.anneal_time[i][j],
3807 ir->opts.anneal_temp[i][j]);
3810 /* Finally the last one */
3811 j = ir->opts.anneal_npoints[i] - 1;
3812 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3816 ir->opts.anneal_time[i][j],
3817 ir->opts.anneal_temp[i][j]);
3823 ir->opts.anneal_time[i][j],
3824 ir->opts.anneal_temp[i][j]);
3825 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3828 "There is a temperature jump when your annealing "
3840 for (int i = 1; i < ir->pull->ngroup; i++)
3842 const int gid = search_string(
3843 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3844 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3845 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3848 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3850 checkPullCoords(ir->pull->group, ir->pull->coord);
3855 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3858 if (ir->eSwapCoords != SwapType::No)
3860 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3863 /* Make indices for IMD session */
3866 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3869 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3870 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3871 mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
3873 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3874 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3875 if (freezeDims.size() != DIM * freezeGroupNames.size())
3878 "Invalid Freezing input: %zu groups and %zu freeze values",
3879 freezeGroupNames.size(),
3882 do_numbering(natoms,
3887 SimulationAtomGroupType::Freeze,
3892 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3893 ir->opts.ngfrz = nr;
3894 snew(ir->opts.nFreeze, nr);
3895 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3897 for (j = 0; (j < DIM); j++, k++)
3899 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3900 if (!ir->opts.nFreeze[i][j])
3902 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3905 "Please use Y(ES) or N(O) for freezedim only "
3907 freezeDims[k].c_str());
3908 warning(wi, warn_buf);
3913 for (; (i < nr); i++)
3915 for (j = 0; (j < DIM); j++)
3917 ir->opts.nFreeze[i][j] = 0;
3921 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3922 do_numbering(natoms,
3927 SimulationAtomGroupType::EnergyOutput,
3932 add_wall_energrps(groups, ir->nwall, symtab);
3933 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3934 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3935 do_numbering(natoms,
3940 SimulationAtomGroupType::MassCenterVelocityRemoval,
3942 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3946 if (ir->comm_mode != ComRemovalAlgorithm::No)
3948 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3951 /* Now we have filled the freeze struct, so we can calculate NRDF */
3952 calc_nrdf(mtop, ir, gnames);
3954 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3955 do_numbering(natoms,
3960 SimulationAtomGroupType::User1,
3965 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3966 do_numbering(natoms,
3971 SimulationAtomGroupType::User2,
3976 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3977 do_numbering(natoms,
3979 compressedXGroupNames,
3982 SimulationAtomGroupType::CompressedPositionOutput,
3987 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3988 do_numbering(natoms,
3990 orirefFitGroupNames,
3993 SimulationAtomGroupType::OrientationRestraintsFit,
3999 /* MiMiC QMMM input processing */
4000 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4001 if (qmGroupNames.size() > 1)
4003 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4005 /* group rest, if any, is always MM! */
4006 do_numbering(natoms,
4011 SimulationAtomGroupType::QuantumMechanics,
4016 ir->opts.ngQM = qmGroupNames.size();
4018 /* end of MiMiC QMMM input */
4022 for (auto group : gmx::keysOf(groups->groups))
4024 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4025 for (const auto& entry : groups->groups[group])
4027 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4029 fprintf(stderr, "\n");
4033 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4034 snew(ir->opts.egp_flags, nr * nr);
4036 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4037 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4039 warning_error(wi, "Energy group exclusions are currently not supported");
4041 if (bExcl && EEL_FULL(ir->coulombtype))
4043 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4046 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4047 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4048 && !(ir->coulombtype == CoulombInteractionType::User)
4049 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4050 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4053 "Can only have energy group pair tables in combination with user tables for VdW "
4057 /* final check before going out of scope if simulated tempering variables
4058 * need to be set to default values.
4060 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4062 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4065 "the value for nstexpanded was not specified for "
4066 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4067 "by default, but it is recommended to set it to an explicit value!",
4068 ir->expandedvals->nstexpanded));
4070 for (i = 0; (i < defaultIndexGroups->nr); i++)
4075 done_blocka(defaultIndexGroups);
4076 sfree(defaultIndexGroups);
4080 static void check_disre(const gmx_mtop_t& mtop)
4082 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4084 const gmx_ffparams_t& ffparams = mtop.ffparams;
4087 for (int i = 0; i < ffparams.numTypes(); i++)
4089 int ftype = ffparams.functype[i];
4090 if (ftype == F_DISRES)
4092 int label = ffparams.iparams[i].disres.label;
4093 if (label == old_label)
4095 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4104 "Found %d double distance restraint indices,\n"
4105 "probably the parameters for multiple pairs in one restraint "
4106 "are not identical\n",
4112 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t& sys, const bool posres_only, ivec AbsRef)
4115 const t_iparams* pr;
4122 for (d = 0; d < DIM; d++)
4124 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
4126 /* Check for freeze groups */
4127 for (g = 0; g < ir->opts.ngfrz; g++)
4129 for (d = 0; d < DIM; d++)
4131 if (ir->opts.nFreeze[g][d] != 0)
4139 /* Check for position restraints */
4140 for (const auto ilist : IListRange(sys))
4142 if (ilist.nmol() > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4144 for (int i = 0; i < ilist.list()[F_POSRES].size(); i += 2)
4146 pr = &sys.ffparams.iparams[ilist.list()[F_POSRES].iatoms[i]];
4147 for (d = 0; d < DIM; d++)
4149 if (pr->posres.fcA[d] != 0)
4155 for (i = 0; i < ilist.list()[F_FBPOSRES].size(); i += 2)
4157 /* Check for flat-bottom posres */
4158 pr = &sys.ffparams.iparams[ilist.list()[F_FBPOSRES].iatoms[i]];
4159 if (pr->fbposres.k != 0)
4161 switch (pr->fbposres.geom)
4163 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4164 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4165 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4166 case efbposresCYLINDER:
4167 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4168 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4169 case efbposresX: /* d=XX */
4170 case efbposresY: /* d=YY */
4171 case efbposresZ: /* d=ZZ */
4172 d = pr->fbposres.geom - efbposresX;
4177 " Invalid geometry for flat-bottom position restraint.\n"
4178 "Expected nr between 1 and %d. Found %d\n",
4187 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4190 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4192 bool* bC6ParametersWorkWithGeometricRules,
4193 bool* bC6ParametersWorkWithLBRules,
4194 bool* bLBRulesPossible)
4196 int ntypes, tpi, tpj;
4199 double c6i, c6j, c12i, c12j;
4200 double c6, c6_geometric, c6_LB;
4201 double sigmai, sigmaj, epsi, epsj;
4202 bool bCanDoLBRules, bCanDoGeometricRules;
4205 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4206 * force-field floating point parameters.
4209 ptr = getenv("GMX_LJCOMB_TOL");
4213 double gmx_unused canary;
4215 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4218 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4223 *bC6ParametersWorkWithLBRules = TRUE;
4224 *bC6ParametersWorkWithGeometricRules = TRUE;
4225 bCanDoLBRules = TRUE;
4226 ntypes = mtop.ffparams.atnr;
4227 snew(typecount, ntypes);
4228 gmx_mtop_count_atomtypes(mtop, state, typecount);
4229 *bLBRulesPossible = TRUE;
4230 for (tpi = 0; tpi < ntypes; ++tpi)
4232 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4233 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4234 for (tpj = tpi; tpj < ntypes; ++tpj)
4236 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4237 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4238 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4239 c6_geometric = std::sqrt(c6i * c6j);
4240 if (!gmx_numzero(c6_geometric))
4242 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4244 sigmai = gmx::sixthroot(c12i / c6i);
4245 sigmaj = gmx::sixthroot(c12j / c6j);
4246 epsi = c6i * c6i / (4.0 * c12i);
4247 epsj = c6j * c6j / (4.0 * c12j);
4248 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4252 *bLBRulesPossible = FALSE;
4253 c6_LB = c6_geometric;
4255 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4260 *bC6ParametersWorkWithLBRules = FALSE;
4263 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4265 if (!bCanDoGeometricRules)
4267 *bC6ParametersWorkWithGeometricRules = FALSE;
4274 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4276 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4278 check_combination_rule_differences(
4279 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4280 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4282 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4285 "You are using arithmetic-geometric combination rules "
4286 "in LJ-PME, but your non-bonded C6 parameters do not "
4287 "follow these rules.");
4292 if (!bC6ParametersWorkWithGeometricRules)
4294 if (ir->eDispCorr != DispersionCorrectionType::No)
4297 "You are using geometric combination rules in "
4298 "LJ-PME, but your non-bonded C6 parameters do "
4299 "not follow these rules. "
4300 "This will introduce very small errors in the forces and energies in "
4301 "your simulations. Dispersion correction will correct total energy "
4302 "and/or pressure for isotropic systems, but not forces or surface "
4308 "You are using geometric combination rules in "
4309 "LJ-PME, but your non-bonded C6 parameters do "
4310 "not follow these rules. "
4311 "This will introduce very small errors in the forces and energies in "
4312 "your simulations. If your system is homogeneous, consider using "
4313 "dispersion correction "
4314 "for the total energy and pressure.");
4320 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4322 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4323 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4325 char err_buf[STRLEN];
4328 gmx_mtop_atomloop_block_t aloopb;
4330 char warn_buf[STRLEN];
4332 set_warning_line(wi, mdparin, -1);
4334 if (absolute_reference(ir, *sys, false, AbsRef))
4337 "Removing center of mass motion in the presence of position restraints might "
4338 "cause artifacts. When you are using position restraints to equilibrate a "
4339 "macro-molecule, the artifacts are usually negligible.");
4342 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4343 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4344 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4346 /* Check if a too small Verlet buffer might potentially
4347 * cause more drift than the thermostat can couple off.
4349 /* Temperature error fraction for warning and suggestion */
4350 const real T_error_warn = 0.002;
4351 const real T_error_suggest = 0.001;
4352 /* For safety: 2 DOF per atom (typical with constraints) */
4353 const real nrdf_at = 2;
4354 real T, tau, max_T_error;
4359 for (i = 0; i < ir->opts.ngtc; i++)
4361 T = std::max(T, ir->opts.ref_t[i]);
4362 tau = std::max(tau, ir->opts.tau_t[i]);
4366 /* This is a worst case estimate of the temperature error,
4367 * assuming perfect buffer estimation and no cancelation
4368 * of errors. The factor 0.5 is because energy distributes
4369 * equally over Ekin and Epot.
4371 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4372 if (max_T_error > T_error_warn)
4375 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4376 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4377 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4378 "%.0e or decrease tau_t.",
4383 100 * T_error_suggest,
4384 ir->verletbuf_tol * T_error_suggest / max_T_error);
4385 warning(wi, warn_buf);
4390 if (ETC_ANDERSEN(ir->etc))
4394 for (i = 0; i < ir->opts.ngtc; i++)
4397 "all tau_t must currently be equal using Andersen temperature control, "
4398 "violated for group %d",
4400 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4402 "all tau_t must be positive using Andersen temperature control, "
4406 CHECK(ir->opts.tau_t[i] < 0);
4409 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4411 for (i = 0; i < ir->opts.ngtc; i++)
4413 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4415 "tau_t/delta_t for group %d for temperature control method %s must be a "
4416 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4417 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4420 enumValueToString(ir->etc),
4424 CHECK(nsteps % ir->nstcomm != 0);
4429 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4430 && ir->comm_mode == ComRemovalAlgorithm::No
4431 && !(absolute_reference(ir, *sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4434 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4435 "rounding errors can lead to build up of kinetic energy of the center of mass");
4438 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4441 for (int g = 0; g < ir->opts.ngtc; g++)
4443 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4445 if (ir->tau_p < 1.9 * tau_t_max)
4447 std::string message = gmx::formatString(
4448 "With %s T-coupling and %s p-coupling, "
4449 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4450 enumValueToString(ir->etc),
4451 enumValueToString(ir->epc),
4456 warning(wi, message.c_str());
4460 /* Check for pressure coupling with absolute position restraints */
4461 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4463 absolute_reference(ir, *sys, TRUE, AbsRef);
4465 for (m = 0; m < DIM; m++)
4467 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4470 "You are using pressure coupling with absolute position restraints, "
4471 "this will give artifacts. Use the refcoord_scaling option.");
4479 aloopb = gmx_mtop_atomloop_block_init(*sys);
4481 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4483 if (atom->q != 0 || atom->qB != 0)
4491 if (EEL_FULL(ir->coulombtype))
4494 "You are using full electrostatics treatment %s for a system without charges.\n"
4495 "This costs a lot of performance for just processing zeros, consider using %s "
4497 enumValueToString(ir->coulombtype),
4498 enumValueToString(CoulombInteractionType::Cut));
4499 warning(wi, err_buf);
4504 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4507 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4508 "You might want to consider using %s electrostatics.\n",
4509 enumValueToString(CoulombInteractionType::Pme));
4510 warning_note(wi, err_buf);
4514 /* Check if combination rules used in LJ-PME are the same as in the force field */
4515 if (EVDW_PME(ir->vdwtype))
4517 check_combination_rules(ir, *sys, wi);
4520 /* Generalized reaction field */
4521 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4524 "Generalized reaction-field electrostatics is no longer supported. "
4525 "You can use normal reaction-field instead and compute the reaction-field "
4526 "constant by hand.");
4529 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4530 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4532 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4540 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4542 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4544 absolute_reference(ir, *sys, FALSE, AbsRef);
4545 for (m = 0; m < DIM; m++)
4547 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4550 "You are using an absolute reference for pulling, but the rest of "
4551 "the system does not have an absolute reference. This will lead to "
4560 for (i = 0; i < 3; i++)
4562 for (m = 0; m <= i; m++)
4564 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4566 for (c = 0; c < ir->pull->ncoord; c++)
4568 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4569 && ir->pull->coord[c].vec[m] != 0)
4572 "Can not have dynamic box while using pull geometry '%s' "
4574 enumValueToString(ir->pull->coord[c].eGeom),
4586 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4588 char warn_buf[STRLEN];
4591 ptr = check_box(ir->pbcType, box);
4594 warning_error(wi, ptr);
4597 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4599 if (ir->shake_tol <= 0.0)
4601 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4602 warning_error(wi, warn_buf);
4606 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4608 /* If we have Lincs constraints: */
4609 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4610 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4613 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4614 warning_note(wi, warn_buf);
4617 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4618 && (ir->nProjOrder < 8))
4621 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4622 enumValueToString(ir->eI));
4623 warning_note(wi, warn_buf);
4625 if (ir->epc == PressureCoupling::Mttk)
4627 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4631 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4633 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4636 if (ir->LincsWarnAngle > 90.0)
4638 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4639 warning(wi, warn_buf);
4640 ir->LincsWarnAngle = 90.0;
4643 if (ir->pbcType != PbcType::No)
4645 if (ir->nstlist == 0)
4648 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4649 "atoms might cause the simulation to crash.");
4651 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4654 "ERROR: The cut-off length is longer than half the shortest box vector or "
4655 "longer than the smallest box diagonal element. Increase the box size or "
4656 "decrease rlist.\n");
4657 warning_error(wi, warn_buf);