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40 #include "gromacs/utility/enumerationhelpers.h"
53 #include "gromacs/applied_forces/awh/read_params.h"
54 #include "gromacs/fileio/readinp.h"
55 #include "gromacs/fileio/warninp.h"
56 #include "gromacs/gmxlib/network.h"
57 #include "gromacs/gmxpreprocess/toputil.h"
58 #include "gromacs/math/functions.h"
59 #include "gromacs/math/units.h"
60 #include "gromacs/math/vec.h"
61 #include "gromacs/mdlib/calc_verletbuf.h"
62 #include "gromacs/mdrun/mdmodules.h"
63 #include "gromacs/mdtypes/inputrec.h"
64 #include "gromacs/mdtypes/md_enums.h"
65 #include "gromacs/mdtypes/multipletimestepping.h"
66 #include "gromacs/mdtypes/pull_params.h"
67 #include "gromacs/options/options.h"
68 #include "gromacs/options/treesupport.h"
69 #include "gromacs/pbcutil/pbc.h"
70 #include "gromacs/selection/indexutil.h"
71 #include "gromacs/topology/block.h"
72 #include "gromacs/topology/ifunc.h"
73 #include "gromacs/topology/index.h"
74 #include "gromacs/topology/mtop_util.h"
75 #include "gromacs/topology/symtab.h"
76 #include "gromacs/topology/topology.h"
77 #include "gromacs/utility/arrayref.h"
78 #include "gromacs/utility/cstringutil.h"
79 #include "gromacs/utility/exceptions.h"
80 #include "gromacs/utility/fatalerror.h"
81 #include "gromacs/utility/filestream.h"
82 #include "gromacs/utility/gmxassert.h"
83 #include "gromacs/utility/ikeyvaluetreeerror.h"
84 #include "gromacs/utility/keyvaluetree.h"
85 #include "gromacs/utility/keyvaluetreebuilder.h"
86 #include "gromacs/utility/keyvaluetreemdpwriter.h"
87 #include "gromacs/utility/keyvaluetreetransform.h"
88 #include "gromacs/utility/mdmodulenotification.h"
89 #include "gromacs/utility/smalloc.h"
90 #include "gromacs/utility/strconvert.h"
91 #include "gromacs/utility/stringcompare.h"
92 #include "gromacs/utility/stringutil.h"
93 #include "gromacs/utility/textwriter.h"
98 /* Resource parameters
99 * Do not change any of these until you read the instruction
100 * in readinp.h. Some cpp's do not take spaces after the backslash
101 * (like the c-shell), which will give you a very weird compiler
105 struct gmx_inputrec_strings
107 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
108 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
109 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
110 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
111 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
112 char lambda_weights[STRLEN];
113 std::vector<std::string> pullGroupNames;
114 std::vector<std::string> rotateGroupNames;
115 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
118 static gmx_inputrec_strings* inputrecStrings = nullptr;
120 void init_inputrec_strings()
125 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
126 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
128 inputrecStrings = new gmx_inputrec_strings();
131 void done_inputrec_strings()
133 delete inputrecStrings;
134 inputrecStrings = nullptr;
140 egrptpALL, /* All particles have to be a member of a group. */
141 egrptpALL_GENREST, /* A rest group with name is generated for particles *
142 * that are not part of any group. */
143 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
144 * for the rest group. */
145 egrptpONE /* Merge all selected groups into one group, *
146 * make a rest group for the remaining particles. */
149 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
150 "h-angles", "all-angles", nullptr };
152 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
154 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
159 for (i = 0; i < ntemps; i++)
161 /* simple linear scaling -- allows more control */
162 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
164 simtemp->temperatures[i] =
166 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
168 else if (simtemp->eSimTempScale
169 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
171 simtemp->temperatures[i] = simtemp->simtemp_low
172 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
173 static_cast<real>((1.0 * i) / (ntemps - 1)));
175 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
177 simtemp->temperatures[i] = simtemp->simtemp_low
178 + (simtemp->simtemp_high - simtemp->simtemp_low)
179 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
184 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
185 gmx_fatal(FARGS, "%s", errorstr);
191 static void _low_check(bool b, const char* s, warninp_t wi)
195 warning_error(wi, s);
199 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
203 if (*p > 0 && *p % nst != 0)
205 /* Round up to the next multiple of nst */
206 *p = ((*p) / nst + 1) * nst;
207 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
212 //! Convert legacy mdp entries to modern ones.
213 static void process_interaction_modifier(InteractionModifiers* eintmod)
215 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
217 *eintmod = InteractionModifiers::PotShift;
221 void check_ir(const char* mdparin,
222 const gmx::MdModulesNotifier& mdModulesNotifier,
226 /* Check internal consistency.
227 * NOTE: index groups are not set here yet, don't check things
228 * like temperature coupling group options here, but in triple_check
231 /* Strange macro: first one fills the err_buf, and then one can check
232 * the condition, which will print the message and increase the error
235 #define CHECK(b) _low_check(b, err_buf, wi)
236 char err_buf[256], warn_buf[STRLEN];
239 t_lambda* fep = ir->fepvals.get();
240 t_expanded* expand = ir->expandedvals.get();
242 set_warning_line(wi, mdparin, -1);
244 /* We cannot check MTS requirements with an invalid MTS setup
245 * and we will already have generated errors with an invalid MTS setup.
247 if (gmx::haveValidMtsSetup(*ir))
249 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
251 for (const auto& errorMessage : errorMessages)
253 warning_error(wi, errorMessage.c_str());
257 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
259 std::string message =
260 gmx::formatString("%s electrostatics is no longer supported",
261 enumValueToString(CoulombInteractionType::RFNecUnsupported));
262 warning_error(wi, message);
265 /* BASIC CUT-OFF STUFF */
266 if (ir->rcoulomb < 0)
268 warning_error(wi, "rcoulomb should be >= 0");
272 warning_error(wi, "rvdw should be >= 0");
274 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
276 warning_error(wi, "rlist should be >= 0");
279 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
280 "neighbour-list update scheme for efficient buffering for improved energy "
281 "conservation, please use the Verlet cut-off scheme instead.)");
282 CHECK(ir->nstlist < 0);
284 process_interaction_modifier(&ir->coulomb_modifier);
285 process_interaction_modifier(&ir->vdw_modifier);
287 if (ir->cutoff_scheme == CutoffScheme::Group)
290 "The group cutoff scheme has been removed since GROMACS 2020. "
291 "Please use the Verlet cutoff scheme.");
293 if (ir->cutoff_scheme == CutoffScheme::Verlet)
297 /* Normal Verlet type neighbor-list, currently only limited feature support */
298 if (inputrec2nboundeddim(ir) < 3)
300 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
303 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
304 if (ir->rcoulomb != ir->rvdw)
306 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
307 // for PME load balancing, we can support this exception.
308 bool bUsesPmeTwinRangeKernel =
309 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
310 && ir->rcoulomb > ir->rvdw);
311 if (!bUsesPmeTwinRangeKernel)
314 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
315 "rcoulomb>rvdw with PME electrostatics)");
319 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
321 if (ir->vdw_modifier == InteractionModifiers::None
322 || ir->vdw_modifier == InteractionModifiers::PotShift)
325 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
326 : InteractionModifiers::PotSwitch);
329 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
331 enumValueToString(ir->vdwtype),
332 enumValueToString(VanDerWaalsType::Cut),
333 enumValueToString(ir->vdw_modifier));
334 warning_note(wi, warn_buf);
336 ir->vdwtype = VanDerWaalsType::Cut;
341 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
342 enumValueToString(ir->vdwtype),
343 enumValueToString(ir->vdw_modifier));
344 warning_error(wi, warn_buf);
348 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
351 "With Verlet lists only cut-off and PME LJ interactions are supported");
353 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
354 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
357 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
358 "electrostatics are supported");
360 if (!(ir->coulomb_modifier == InteractionModifiers::None
361 || ir->coulomb_modifier == InteractionModifiers::PotShift))
363 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
364 warning_error(wi, warn_buf);
367 if (EEL_USER(ir->coulombtype))
370 "Coulomb type %s is not supported with the verlet scheme",
371 enumValueToString(ir->coulombtype));
372 warning_error(wi, warn_buf);
375 if (ir->nstlist <= 0)
377 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
380 if (ir->nstlist < 10)
383 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
384 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
388 rc_max = std::max(ir->rvdw, ir->rcoulomb);
392 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
393 ir->verletbuf_tol = 0;
396 else if (ir->verletbuf_tol <= 0)
398 if (ir->verletbuf_tol == 0)
400 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
403 if (ir->rlist < rc_max)
406 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
409 if (ir->rlist == rc_max && ir->nstlist > 1)
413 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
414 "buffer. The cluster pair list does have a buffering effect, but choosing "
415 "a larger rlist might be necessary for good energy conservation.");
420 if (ir->rlist > rc_max)
423 "You have set rlist larger than the interaction cut-off, but you also "
424 "have verlet-buffer-tolerance > 0. Will set rlist using "
425 "verlet-buffer-tolerance.");
428 if (ir->nstlist == 1)
430 /* No buffer required */
435 if (EI_DYNAMICS(ir->eI))
437 if (inputrec2nboundeddim(ir) < 3)
440 "The box volume is required for calculating rlist from the "
441 "energy drift with verlet-buffer-tolerance > 0. You are "
442 "using at least one unbounded dimension, so no volume can be "
443 "computed. Either use a finite box, or set rlist yourself "
444 "together with verlet-buffer-tolerance = -1.");
446 /* Set rlist temporarily so we can continue processing */
451 /* Set the buffer to 5% of the cut-off */
452 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
458 /* GENERAL INTEGRATOR STUFF */
461 if (ir->etc != TemperatureCoupling::No)
463 if (EI_RANDOM(ir->eI))
466 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
467 "implicitly. See the documentation for more information on which "
468 "parameters affect temperature for %s.",
469 enumValueToString(ir->etc),
470 enumValueToString(ir->eI),
471 enumValueToString(ir->eI));
476 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
478 enumValueToString(ir->etc),
479 enumValueToString(ir->eI));
481 warning_note(wi, warn_buf);
483 ir->etc = TemperatureCoupling::No;
485 if (ir->eI == IntegrationAlgorithm::VVAK)
488 "Integrator method %s is implemented primarily for validation purposes; for "
489 "molecular dynamics, you should probably be using %s or %s",
490 enumValueToString(IntegrationAlgorithm::VVAK),
491 enumValueToString(IntegrationAlgorithm::MD),
492 enumValueToString(IntegrationAlgorithm::VV));
493 warning_note(wi, warn_buf);
495 if (!EI_DYNAMICS(ir->eI))
497 if (ir->epc != PressureCoupling::No)
500 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
501 enumValueToString(ir->epc),
502 enumValueToString(ir->eI));
503 warning_note(wi, warn_buf);
505 ir->epc = PressureCoupling::No;
507 if (EI_DYNAMICS(ir->eI))
509 if (ir->nstcalcenergy < 0)
511 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
512 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
514 /* nstcalcenergy larger than nstener does not make sense.
515 * We ideally want nstcalcenergy=nstener.
519 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
523 ir->nstcalcenergy = ir->nstenergy;
527 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
528 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
529 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
532 const char* nsten = "nstenergy";
533 const char* nstdh = "nstdhdl";
534 const char* min_name = nsten;
535 int min_nst = ir->nstenergy;
537 /* find the smallest of ( nstenergy, nstdhdl ) */
538 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
539 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
541 min_nst = ir->fepvals->nstdhdl;
544 /* If the user sets nstenergy small, we should respect that */
545 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
546 warning_note(wi, warn_buf);
547 ir->nstcalcenergy = min_nst;
550 if (ir->epc != PressureCoupling::No)
552 if (ir->nstpcouple < 0)
554 ir->nstpcouple = ir_optimal_nstpcouple(ir);
556 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
559 "With multiple time stepping, nstpcouple should be a mutiple of "
564 if (ir->nstcalcenergy > 0)
566 if (ir->efep != FreeEnergyPerturbationType::No)
568 /* nstdhdl should be a multiple of nstcalcenergy */
569 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
573 /* nstexpanded should be a multiple of nstcalcenergy */
574 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
576 /* for storing exact averages nstenergy should be
577 * a multiple of nstcalcenergy
579 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
582 // Inquire all MdModules, if their parameters match with the energy
583 // calculation frequency
584 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
585 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
587 // Emit all errors from the energy calculation frequency checks
588 for (const std::string& energyFrequencyErrorMessage :
589 energyCalculationFrequencyErrors.errorMessages())
591 warning_error(wi, energyFrequencyErrorMessage);
595 if (ir->nsteps == 0 && !ir->bContinuation)
598 "For a correct single-point energy evaluation with nsteps = 0, use "
599 "continuation = yes to avoid constraining the input coordinates.");
603 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
606 "You are doing a continuation with SD or BD, make sure that ld_seed is "
607 "different from the previous run (using ld_seed=-1 will ensure this)");
613 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
614 CHECK(ir->pbcType != PbcType::Xyz);
615 sprintf(err_buf, "with TPI nstlist should be larger than zero");
616 CHECK(ir->nstlist <= 0);
617 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
618 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
622 if ((opts->nshake > 0) && (opts->bMorse))
624 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
625 warning(wi, warn_buf);
628 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
631 "You are doing a continuation with SD or BD, make sure that ld_seed is "
632 "different from the previous run (using ld_seed=-1 will ensure this)");
634 /* verify simulated tempering options */
638 bool bAllTempZero = TRUE;
639 for (i = 0; i < fep->n_lambda; i++)
642 "Entry %d for %s must be between 0 and 1, instead is %g",
644 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
645 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
646 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
647 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
649 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
651 bAllTempZero = FALSE;
654 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
655 CHECK(bAllTempZero == TRUE);
657 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
658 CHECK(ir->eI != IntegrationAlgorithm::VV);
660 /* check compatability of the temperature coupling with simulated tempering */
662 if (ir->etc == TemperatureCoupling::NoseHoover)
665 "Nose-Hoover based temperature control such as [%s] my not be "
666 "entirelyconsistent with simulated tempering",
667 enumValueToString(ir->etc));
668 warning_note(wi, warn_buf);
671 /* check that the temperatures make sense */
674 "Higher simulated tempering temperature (%g) must be >= than the simulated "
675 "tempering lower temperature (%g)",
676 ir->simtempvals->simtemp_high,
677 ir->simtempvals->simtemp_low);
678 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
681 "Higher simulated tempering temperature (%g) must be >= zero",
682 ir->simtempvals->simtemp_high);
683 CHECK(ir->simtempvals->simtemp_high <= 0);
686 "Lower simulated tempering temperature (%g) must be >= zero",
687 ir->simtempvals->simtemp_low);
688 CHECK(ir->simtempvals->simtemp_low <= 0);
691 /* verify free energy options */
693 if (ir->efep != FreeEnergyPerturbationType::No)
695 fep = ir->fepvals.get();
696 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
697 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
700 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
702 static_cast<int>(fep->sc_r_power));
703 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
706 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
709 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
712 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
714 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
716 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
717 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
719 sprintf(err_buf, "Free-energy not implemented for Ewald");
720 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
722 /* check validty of lambda inputs */
723 if (fep->n_lambda == 0)
725 /* Clear output in case of no states:*/
726 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
727 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
732 "initial thermodynamic state %d does not exist, only goes to %d",
735 CHECK((fep->init_fep_state >= fep->n_lambda));
739 "Lambda state must be set, either with init-lambda-state or with init-lambda");
740 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
743 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
744 "init-lambda-state or with init-lambda, but not both",
746 fep->init_fep_state);
747 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
750 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
754 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
756 if (fep->separate_dvdl[i])
761 if (n_lambda_terms > 1)
764 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
765 "use init-lambda to set lambda state (except for slow growth). Use "
766 "init-lambda-state instead.");
767 warning(wi, warn_buf);
770 if (n_lambda_terms < 2 && fep->n_lambda > 0)
773 "init-lambda is deprecated for setting lambda state (except for slow "
774 "growth). Use init-lambda-state instead.");
778 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
780 for (i = 0; i < fep->n_lambda; i++)
782 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
784 "Entry %d for %s must be between 0 and 1, instead is %g",
786 enumValueToString(enumValue),
787 fep->all_lambda[j][i]);
788 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
792 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
794 for (i = 0; i < fep->n_lambda; i++)
797 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
798 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
799 "crashes, and is not supported.",
801 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
802 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
803 CHECK((fep->sc_alpha > 0)
804 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
805 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
806 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
807 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
812 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
814 real sigma, lambda, r_sc;
817 /* Maximum estimate for A and B charges equal with lambda power 1 */
819 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
820 1.0 / fep->sc_r_power);
822 "With PME there is a minor soft core effect present at the cut-off, "
823 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
824 "energy conservation, but usually other effects dominate. With a common sigma "
825 "value of %g nm the fraction of the particle-particle potential at the cut-off "
826 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
832 warning_note(wi, warn_buf);
835 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
836 be treated differently, but that's the next step */
838 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
840 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
841 for (j = 0; j < fep->n_lambda; j++)
843 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
844 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
849 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
851 fep = ir->fepvals.get();
853 /* checking equilibration of weights inputs for validity */
856 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
858 expand->equil_n_at_lam,
859 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
860 CHECK((expand->equil_n_at_lam > 0)
861 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
864 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
866 expand->equil_samples,
867 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
868 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
871 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
873 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
874 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
877 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
878 expand->equil_samples,
879 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
880 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
883 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
885 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
886 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
889 "weight-equil-number-all-lambda (%d) must be a positive integer if "
890 "lmc-weights-equil=%s",
891 expand->equil_n_at_lam,
892 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
893 CHECK((expand->equil_n_at_lam <= 0)
894 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
897 "weight-equil-number-samples (%d) must be a positive integer if "
898 "lmc-weights-equil=%s",
899 expand->equil_samples,
900 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
901 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
904 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
906 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
907 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
910 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
911 expand->equil_wl_delta,
912 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
913 CHECK((expand->equil_wl_delta <= 0)
914 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
917 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
919 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
920 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
923 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
924 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
925 enumValueToString(LambdaWeightCalculation::WL),
926 enumValueToString(LambdaWeightCalculation::WWL));
927 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
929 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
930 CHECK((expand->lmc_repeats <= 0));
931 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
932 CHECK((expand->minvarmin <= 0));
933 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
934 CHECK((expand->c_range < 0));
936 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
939 expand->lmc_forced_nstart);
940 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
941 && (expand->elmcmove != LambdaMoveCalculation::No));
942 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
943 CHECK((expand->lmc_forced_nstart < 0));
945 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
946 fep->init_fep_state);
947 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
949 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
950 CHECK((expand->init_wl_delta < 0));
951 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
952 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
953 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
954 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
956 /* if there is no temperature control, we need to specify an MC temperature */
957 if (!integratorHasReferenceTemperature(ir)
958 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
961 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
962 "to a positive number");
963 warning_error(wi, err_buf);
965 if (expand->nstTij > 0)
967 sprintf(err_buf, "nstlog must be non-zero");
968 CHECK(ir->nstlog == 0);
969 // Avoid modulus by zero in the case that already triggered an error exit.
973 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
976 CHECK((expand->nstTij % ir->nstlog) != 0);
982 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
983 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
986 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
988 if (ir->pbcType == PbcType::No)
990 if (ir->epc != PressureCoupling::No)
992 warning(wi, "Turning off pressure coupling for vacuum system");
993 ir->epc = PressureCoupling::No;
999 "Can not have pressure coupling with pbc=%s",
1000 c_pbcTypeNames[ir->pbcType].c_str());
1001 CHECK(ir->epc != PressureCoupling::No);
1003 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1004 CHECK(EEL_FULL(ir->coulombtype));
1007 "Can not have dispersion correction with pbc=%s",
1008 c_pbcTypeNames[ir->pbcType].c_str());
1009 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1012 if (ir->rlist == 0.0)
1015 "can only have neighborlist cut-off zero (=infinite)\n"
1016 "with coulombtype = %s or coulombtype = %s\n"
1017 "without periodic boundary conditions (pbc = %s) and\n"
1018 "rcoulomb and rvdw set to zero",
1019 enumValueToString(CoulombInteractionType::Cut),
1020 enumValueToString(CoulombInteractionType::User),
1021 c_pbcTypeNames[PbcType::No].c_str());
1022 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1023 && (ir->coulombtype != CoulombInteractionType::User))
1024 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1026 if (ir->nstlist > 0)
1029 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1030 "nstype=simple and only one MPI rank");
1035 if (ir->nstcomm == 0)
1037 // TODO Change this behaviour. There should be exactly one way
1038 // to turn off an algorithm.
1039 ir->comm_mode = ComRemovalAlgorithm::No;
1041 if (ir->comm_mode != ComRemovalAlgorithm::No)
1043 if (ir->nstcomm < 0)
1045 // TODO Such input was once valid. Now that we've been
1046 // helpful for a few years, we should reject such input,
1047 // lest we have to support every historical decision
1050 "If you want to remove the rotation around the center of mass, you should set "
1051 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1052 "its absolute value");
1053 ir->nstcomm = abs(ir->nstcomm);
1056 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1059 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1060 "nstcomm to nstcalcenergy");
1061 ir->nstcomm = ir->nstcalcenergy;
1064 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1067 "Can not remove the rotation around the center of mass with periodic "
1069 CHECK(ir->bPeriodicMols);
1070 if (ir->pbcType != PbcType::No)
1073 "Removing the rotation around the center of mass in a periodic system, "
1074 "this can lead to artifacts. Only use this on a single (cluster of) "
1075 "molecules. This cluster should not cross periodic boundaries.");
1080 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1081 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1084 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1085 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1087 enumValueToString(IntegrationAlgorithm::SD1));
1088 warning_note(wi, warn_buf);
1091 /* TEMPERATURE COUPLING */
1092 if (ir->etc == TemperatureCoupling::Yes)
1094 ir->etc = TemperatureCoupling::Berendsen;
1096 "Old option for temperature coupling given: "
1097 "changing \"yes\" to \"Berendsen\"\n");
1100 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1102 if (ir->opts.nhchainlength < 1)
1105 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1107 ir->opts.nhchainlength);
1108 ir->opts.nhchainlength = 1;
1109 warning(wi, warn_buf);
1112 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1116 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1117 ir->opts.nhchainlength = 1;
1122 ir->opts.nhchainlength = 0;
1125 if (ir->eI == IntegrationAlgorithm::VVAK)
1128 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1130 enumValueToString(IntegrationAlgorithm::VVAK));
1131 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1134 if (ETC_ANDERSEN(ir->etc))
1137 "%s temperature control not supported for integrator %s.",
1138 enumValueToString(ir->etc),
1139 enumValueToString(ir->eI));
1140 CHECK(!(EI_VV(ir->eI)));
1142 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1145 "Center of mass removal not necessary for %s. All velocities of coupled "
1146 "groups are rerandomized periodically, so flying ice cube errors will not "
1148 enumValueToString(ir->etc));
1149 warning_note(wi, warn_buf);
1153 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1154 "randomized every time step",
1156 enumValueToString(ir->etc));
1157 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1160 if (ir->etc == TemperatureCoupling::Berendsen)
1163 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1164 "might want to consider using the %s thermostat.",
1165 enumValueToString(ir->etc),
1166 enumValueToString(TemperatureCoupling::VRescale));
1167 warning_note(wi, warn_buf);
1170 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1171 && ir->epc == PressureCoupling::Berendsen)
1174 "Using Berendsen pressure coupling invalidates the "
1175 "true ensemble for the thermostat");
1176 warning(wi, warn_buf);
1179 /* PRESSURE COUPLING */
1180 if (ir->epc == PressureCoupling::Isotropic)
1182 ir->epc = PressureCoupling::Berendsen;
1184 "Old option for pressure coupling given: "
1185 "changing \"Isotropic\" to \"Berendsen\"\n");
1188 if (ir->epc != PressureCoupling::No)
1190 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1192 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1193 CHECK(ir->tau_p <= 0);
1195 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1198 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1199 "times larger than nstpcouple*dt (%g)",
1200 enumValueToString(ir->epc),
1202 pcouple_min_integration_steps(ir->epc),
1204 warning(wi, warn_buf);
1208 "compressibility must be > 0 when using pressure"
1210 enumValueToString(ir->epc));
1211 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1212 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1213 && ir->compress[ZZ][YY] <= 0));
1215 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1218 "You are generating velocities so I am assuming you "
1219 "are equilibrating a system. You are using "
1220 "%s pressure coupling, but this can be "
1221 "unstable for equilibration. If your system crashes, try "
1222 "equilibrating first with Berendsen pressure coupling. If "
1223 "you are not equilibrating the system, you can probably "
1224 "ignore this warning.",
1225 enumValueToString(ir->epc));
1226 warning(wi, warn_buf);
1232 if (ir->epc == PressureCoupling::Mttk)
1234 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1238 /* ELECTROSTATICS */
1239 /* More checks are in triple check (grompp.c) */
1241 if (ir->coulombtype == CoulombInteractionType::Switch)
1244 "coulombtype = %s is only for testing purposes and can lead to serious "
1245 "artifacts, advice: use coulombtype = %s",
1246 enumValueToString(ir->coulombtype),
1247 enumValueToString(CoulombInteractionType::RFZero));
1248 warning(wi, warn_buf);
1251 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1254 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1255 "format and exchanging epsilon-r and epsilon-rf",
1257 warning(wi, warn_buf);
1258 ir->epsilon_rf = ir->epsilon_r;
1259 ir->epsilon_r = 1.0;
1262 if (ir->epsilon_r == 0)
1265 "It is pointless to use long-range electrostatics with infinite relative "
1267 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1269 CHECK(EEL_FULL(ir->coulombtype));
1272 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1274 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1275 CHECK(ir->epsilon_r < 0);
1278 if (EEL_RF(ir->coulombtype))
1280 /* reaction field (at the cut-off) */
1282 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1285 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1286 enumValueToString(ir->coulombtype));
1287 warning(wi, warn_buf);
1288 ir->epsilon_rf = 0.0;
1291 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1292 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1293 if (ir->epsilon_rf == ir->epsilon_r)
1296 "Using epsilon-rf = epsilon-r with %s does not make sense",
1297 enumValueToString(ir->coulombtype));
1298 warning(wi, warn_buf);
1301 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1302 * means the interaction is zero outside rcoulomb, but it helps to
1303 * provide accurate energy conservation.
1305 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1307 if (ir_coulomb_switched(ir))
1310 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1311 "potential modifier options!",
1312 enumValueToString(ir->coulombtype));
1313 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1317 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1320 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1321 "secondary coulomb-modifier.");
1322 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1324 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1327 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1328 "secondary vdw-modifier.");
1329 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1332 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1333 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1336 "The switch/shift interaction settings are just for compatibility; you will get "
1338 "performance from applying potential modifiers to your interactions!\n");
1339 warning_note(wi, warn_buf);
1342 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1343 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1345 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1347 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1349 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1350 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1351 "will be good regardless, since ewald_rtol = %g.",
1353 ir->rcoulomb_switch,
1356 warning(wi, warn_buf);
1360 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1362 if (ir->rvdw_switch == 0)
1365 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1366 "potential. This suggests it was not set in the mdp, which can lead to large "
1367 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1368 "switching range.");
1369 warning(wi, warn_buf);
1373 if (EEL_FULL(ir->coulombtype))
1375 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1376 || ir->coulombtype == CoulombInteractionType::PmeUser
1377 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1380 "With coulombtype = %s, rcoulomb must be <= rlist",
1381 enumValueToString(ir->coulombtype));
1382 CHECK(ir->rcoulomb > ir->rlist);
1386 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1388 // TODO: Move these checks into the ewald module with the options class
1390 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1392 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1395 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1396 enumValueToString(ir->coulombtype),
1399 warning_error(wi, warn_buf);
1403 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1405 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1408 "With pbc=%s you should use ewald-geometry=%s",
1409 c_pbcTypeNames[ir->pbcType].c_str(),
1410 enumValueToString(EwaldGeometry::ThreeDC));
1411 warning(wi, warn_buf);
1413 /* This check avoids extra pbc coding for exclusion corrections */
1414 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1415 CHECK(ir->wall_ewald_zfac < 2);
1417 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1418 && EEL_FULL(ir->coulombtype))
1421 "With %s and ewald_geometry = %s you should use pbc = %s",
1422 enumValueToString(ir->coulombtype),
1423 enumValueToString(EwaldGeometry::ThreeDC),
1424 c_pbcTypeNames[PbcType::XY].c_str());
1425 warning(wi, warn_buf);
1427 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1429 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1430 CHECK(ir->bPeriodicMols);
1431 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1432 warning_note(wi, warn_buf);
1434 "With epsilon_surface > 0 you can only use domain decomposition "
1435 "when there are only small molecules with all bonds constrained (mdrun will check "
1437 warning_note(wi, warn_buf);
1440 if (ir_vdw_switched(ir))
1442 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1443 CHECK(ir->rvdw_switch >= ir->rvdw);
1445 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1448 "You are applying a switch function to vdw forces or potentials from %g to %g "
1449 "nm, which is more than half the interaction range, whereas switch functions "
1450 "are intended to act only close to the cut-off.",
1453 warning_note(wi, warn_buf);
1457 if (ir->vdwtype == VanDerWaalsType::Pme)
1459 if (!(ir->vdw_modifier == InteractionModifiers::None
1460 || ir->vdw_modifier == InteractionModifiers::PotShift))
1463 "With vdwtype = %s, the only supported modifiers are %s and %s",
1464 enumValueToString(ir->vdwtype),
1465 enumValueToString(InteractionModifiers::PotShift),
1466 enumValueToString(InteractionModifiers::None));
1467 warning_error(wi, err_buf);
1471 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1474 "You have selected user tables with dispersion correction, the dispersion "
1475 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1476 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1477 "really want dispersion correction to -C6/r^6.");
1480 if (ir->eI == IntegrationAlgorithm::LBFGS
1481 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1484 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1487 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1489 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1492 /* IMPLICIT SOLVENT */
1493 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1495 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1496 warning_error(wi, warn_buf);
1501 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1506 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1509 // cosine acceleration is only supported in leap-frog
1510 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1512 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1516 /* interpret a number of doubles from a string and put them in an array,
1517 after allocating space for them.
1518 str = the input string
1519 n = the (pre-allocated) number of doubles read
1520 r = the output array of doubles. */
1521 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1523 auto values = gmx::splitString(str);
1526 std::vector<real> r;
1527 for (int i = 0; i < *n; i++)
1531 r.emplace_back(gmx::fromString<real>(values[i]));
1533 catch (gmx::GromacsException&)
1536 "Invalid value " + values[i]
1537 + " in string in mdp file. Expected a real number.");
1544 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1547 int i, j, max_n_lambda, nweights;
1548 t_lambda* fep = ir->fepvals.get();
1549 t_expanded* expand = ir->expandedvals.get();
1550 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1551 bool bOneLambda = TRUE;
1552 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1554 /* FEP input processing */
1555 /* first, identify the number of lambda values for each type.
1556 All that are nonzero must have the same number */
1558 for (auto i : keysOf(nfep))
1560 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1563 /* now, determine the number of components. All must be either zero, or equal. */
1566 for (auto i : keysOf(nfep))
1568 if (nfep[i] > max_n_lambda)
1570 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1571 must have the same number if its not zero.*/
1576 for (auto i : keysOf(nfep))
1580 ir->fepvals->separate_dvdl[i] = FALSE;
1582 else if (nfep[i] == max_n_lambda)
1584 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1585 the derivative with respect to the temperature currently */
1587 ir->fepvals->separate_dvdl[i] = TRUE;
1593 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1596 enumValueToString(i),
1600 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1601 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1603 /* the number of lambdas is the number we've read in, which is either zero
1604 or the same for all */
1605 fep->n_lambda = max_n_lambda;
1607 /* if init_lambda is defined, we need to set lambda */
1608 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1610 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1612 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1613 for (auto i : keysOf(nfep))
1615 fep->all_lambda[i].resize(fep->n_lambda);
1616 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1619 for (j = 0; j < fep->n_lambda; j++)
1621 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1626 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1627 internal bookkeeping -- for now, init_lambda */
1629 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1631 for (i = 0; i < fep->n_lambda; i++)
1633 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1637 /* check to see if only a single component lambda is defined, and soft core is defined.
1638 In this case, turn on coulomb soft core */
1640 if (max_n_lambda == 0)
1646 for (auto i : keysOf(nfep))
1648 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1654 if ((bOneLambda) && (fep->sc_alpha > 0))
1656 fep->bScCoul = TRUE;
1659 /* Fill in the others with the efptFEP if they are not explicitly
1660 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1661 they are all zero. */
1663 for (auto i : keysOf(nfep))
1665 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1667 for (j = 0; j < fep->n_lambda; j++)
1669 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1675 /* now read in the weights */
1676 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1679 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1681 else if (nweights != fep->n_lambda)
1684 "Number of weights (%d) is not equal to number of lambda values (%d)",
1688 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1690 expand->nstexpanded = fep->nstdhdl;
1691 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1696 static void do_simtemp_params(t_inputrec* ir)
1699 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1700 getSimTemps(ir->fepvals->n_lambda,
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 = gmx::readAwhParams(&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 == eptAtom || local.ptype == eptNucleus)
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 == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
3045 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
3063 imin = std::min(imin, nrdf2[ai]);
3064 jmin = std::min(jmin, nrdf2[aj]);
3067 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3069 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3071 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3073 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3076 i += interaction_function[ftype].nratoms + 1;
3079 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3080 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3082 /* Subtract 1 dof from every atom in the SETTLE */
3083 for (int j = 0; j < 3; j++)
3085 int ai = as + ia[i + 1 + j];
3086 imin = std::min(2, nrdf2[ai]);
3088 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3090 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3095 as += molt.atoms.nr;
3101 /* Correct nrdf for the COM constraints.
3102 * We correct using the TC and VCM group of the first atom
3103 * in the reference and pull group. If atoms in one pull group
3104 * belong to different TC or VCM groups it is anyhow difficult
3105 * to determine the optimal nrdf assignment.
3107 pull = ir->pull.get();
3109 for (int i = 0; i < pull->ncoord; i++)
3111 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3118 for (int j = 0; j < 2; j++)
3120 const t_pull_group* pgrp;
3122 pgrp = &pull->group[pull->coord[i].group[j]];
3124 if (!pgrp->ind.empty())
3126 /* Subtract 1/2 dof from each group */
3127 int ai = pgrp->ind[0];
3128 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3130 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3132 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3135 "Center of mass pulling constraints caused the number of degrees "
3136 "of freedom for temperature coupling group %s to be negative",
3137 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3138 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3143 /* We need to subtract the whole DOF from group j=1 */
3150 if (ir->nstcomm != 0)
3152 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3153 "Expect at least one group when removing COM motion");
3155 /* We remove COM motion up to dim ndof_com() */
3156 const int ndim_rm_vcm = ndof_com(ir);
3158 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3159 * the number of degrees of freedom in each vcm group when COM
3160 * translation is removed and 6 when rotation is removed as well.
3161 * Note that we do not and should not include the rest group here.
3163 for (gmx::index j = 0;
3164 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3167 switch (ir->comm_mode)
3169 case ComRemovalAlgorithm::Linear:
3170 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3171 nrdf_vcm_sub[j] = 0;
3172 for (int d = 0; d < ndim_rm_vcm; d++)
3180 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3181 default: gmx_incons("Checking comm_mode");
3185 for (gmx::index i = 0;
3186 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3189 /* Count the number of atoms of TC group i for every VCM group */
3190 for (gmx::index j = 0;
3191 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3197 for (int ai = 0; ai < natoms; ai++)
3199 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3201 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3205 /* Correct for VCM removal according to the fraction of each VCM
3206 * group present in this TC group.
3208 nrdf_uc = nrdf_tc[i];
3210 for (gmx::index j = 0;
3211 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3214 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3216 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3217 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3222 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3224 opts->nrdf[i] = nrdf_tc[i];
3225 if (opts->nrdf[i] < 0)
3230 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3231 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3240 sfree(nrdf_vcm_sub);
3243 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3245 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3246 * But since this is much larger than STRLEN, such a line can not be parsed.
3247 * The real maximum is the number of names that fit in a string: STRLEN/2.
3249 #define EGP_MAX (STRLEN / 2)
3253 auto names = gmx::splitString(val);
3254 if (names.size() % 2 != 0)
3256 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3258 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3260 for (size_t i = 0; i < names.size() / 2; i++)
3262 // TODO this needs to be replaced by a solution using std::find_if
3266 names[2 * i].c_str(),
3267 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3273 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3278 names[2 * i + 1].c_str(),
3279 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3285 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3287 if ((j < nr) && (k < nr))
3289 ir->opts.egp_flags[nr * j + k] |= flag;
3290 ir->opts.egp_flags[nr * k + j] |= flag;
3299 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3301 int ig = -1, i = 0, gind;
3305 /* Just a quick check here, more thorough checks are in mdrun */
3306 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3307 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3311 "The split groups can not both be '%s'.",
3312 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3315 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3316 for (ig = 0; ig < swap->ngrp; ig++)
3318 swapg = &swap->grp[ig];
3319 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3320 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3325 "%s group '%s' contains %d atoms.\n",
3326 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3327 swap->grp[ig].molname,
3329 snew(swapg->ind, swapg->nat);
3330 for (i = 0; i < swapg->nat; i++)
3332 swapg->ind[i] = grps->a[grps->index[gind] + i];
3337 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3343 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3348 ig = search_string(IMDgname, grps->nr, gnames);
3349 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3351 if (IMDgroup->nat > 0)
3354 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3358 snew(IMDgroup->ind, IMDgroup->nat);
3359 for (i = 0; i < IMDgroup->nat; i++)
3361 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3366 /* Checks whether atoms are both part of a COM removal group and frozen.
3367 * If a fully frozen atom is part of a COM removal group, it is removed
3368 * from the COM removal group. A note is issued if such atoms are present.
3369 * A warning is issued for atom with one or two dimensions frozen that
3370 * are part of a COM removal group (mdrun would need to compute COM mass
3371 * per dimension to handle this correctly).
3372 * Also issues a warning when non-frozen atoms are not part of a COM
3373 * removal group while COM removal is active.
3375 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3377 const t_grpopts& opts,
3380 const int vcmRestGroup =
3381 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3383 int numFullyFrozenVcmAtoms = 0;
3384 int numPartiallyFrozenVcmAtoms = 0;
3385 int numNonVcmAtoms = 0;
3386 for (int a = 0; a < numAtoms; a++)
3388 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3389 int numFrozenDims = 0;
3390 for (int d = 0; d < DIM; d++)
3392 numFrozenDims += opts.nFreeze[freezeGroup][d];
3395 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3396 if (vcmGroup < vcmRestGroup)
3398 if (numFrozenDims == DIM)
3400 /* Do not remove COM motion for this fully frozen atom */
3401 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3403 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3406 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3407 numFullyFrozenVcmAtoms++;
3409 else if (numFrozenDims > 0)
3411 numPartiallyFrozenVcmAtoms++;
3414 else if (numFrozenDims < DIM)
3420 if (numFullyFrozenVcmAtoms > 0)
3422 std::string warningText = gmx::formatString(
3423 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3424 "removing these atoms from the COMM removal group(s)",
3425 numFullyFrozenVcmAtoms);
3426 warning_note(wi, warningText.c_str());
3428 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3430 std::string warningText = gmx::formatString(
3431 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3432 "removal group(s), due to limitations in the code these still contribute to the "
3433 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3435 numPartiallyFrozenVcmAtoms,
3437 warning(wi, warningText.c_str());
3439 if (numNonVcmAtoms > 0)
3441 std::string warningText = gmx::formatString(
3442 "%d atoms are not part of any center of mass motion removal group.\n"
3443 "This may lead to artifacts.\n"
3444 "In most cases one should use one group for the whole system.",
3446 warning(wi, warningText.c_str());
3450 void do_index(const char* mdparin,
3454 const gmx::MdModulesNotifier& notifier,
3458 t_blocka* defaultIndexGroups;
3466 int i, j, k, restnm;
3467 bool bExcl, bTable, bAnneal;
3468 char warn_buf[STRLEN];
3472 fprintf(stderr, "processing index file...\n");
3476 snew(defaultIndexGroups, 1);
3477 snew(defaultIndexGroups->index, 1);
3479 atoms_all = gmx_mtop_global_atoms(mtop);
3480 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3481 done_atom(&atoms_all);
3485 defaultIndexGroups = init_index(ndx, &gnames);
3488 SimulationGroups* groups = &mtop->groups;
3489 natoms = mtop->natoms;
3490 symtab = &mtop->symtab;
3492 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3494 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3496 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3497 restnm = groups->groupNames.size() - 1;
3498 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3499 srenew(gnames, defaultIndexGroups->nr + 1);
3500 gnames[restnm] = *(groups->groupNames.back());
3502 set_warning_line(wi, mdparin, -1);
3504 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3505 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3506 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3507 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3508 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3511 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3513 temperatureCouplingGroupNames.size(),
3514 temperatureCouplingReferenceValues.size(),
3515 temperatureCouplingTauValues.size());
3518 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3519 do_numbering(natoms,
3521 temperatureCouplingGroupNames,
3524 SimulationAtomGroupType::TemperatureCoupling,
3526 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3529 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3531 snew(ir->opts.nrdf, nr);
3532 snew(ir->opts.tau_t, nr);
3533 snew(ir->opts.ref_t, nr);
3534 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3536 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3539 if (useReferenceTemperature)
3541 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3543 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3547 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3548 for (i = 0; (i < nr); i++)
3550 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3553 "With integrator %s tau-t should be larger than 0",
3554 enumValueToString(ir->eI));
3555 warning_error(wi, warn_buf);
3558 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3562 "tau-t = -1 is the value to signal that a group should not have "
3563 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3566 if (ir->opts.tau_t[i] >= 0)
3568 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3571 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3573 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3578 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3581 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3582 "md-vv; use either vrescale temperature with berendsen pressure or "
3583 "Nose-Hoover temperature with MTTK pressure");
3585 if (ir->epc == PressureCoupling::Mttk)
3587 if (ir->etc != TemperatureCoupling::NoseHoover)
3590 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3595 if (ir->nstpcouple != ir->nsttcouple)
3597 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3598 ir->nstpcouple = ir->nsttcouple = mincouple;
3600 "for current Trotter decomposition methods with vv, nsttcouple and "
3601 "nstpcouple must be equal. Both have been reset to "
3602 "min(nsttcouple,nstpcouple) = %d",
3604 warning_note(wi, warn_buf);
3609 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3610 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3612 if (ETC_ANDERSEN(ir->etc))
3614 if (ir->nsttcouple != 1)
3618 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3619 "need for larger nsttcouple > 1, since no global parameters are computed. "
3620 "nsttcouple has been reset to 1");
3621 warning_note(wi, warn_buf);
3624 nstcmin = tcouple_min_integration_steps(ir->etc);
3627 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3630 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3631 "least %d times larger than nsttcouple*dt (%g)",
3632 enumValueToString(ir->etc),
3635 ir->nsttcouple * ir->delta_t);
3636 warning(wi, warn_buf);
3639 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3640 for (i = 0; (i < nr); i++)
3642 if (ir->opts.ref_t[i] < 0)
3644 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3647 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3648 if we are in this conditional) if mc_temp is negative */
3649 if (ir->expandedvals->mc_temp < 0)
3651 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3655 /* Simulated annealing for each group. There are nr groups */
3656 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3657 if (simulatedAnnealingGroupNames.size() == 1
3658 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3660 simulatedAnnealingGroupNames.resize(0);
3662 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3665 "Wrong number of annealing values: %zu (for %d groups)\n",
3666 simulatedAnnealingGroupNames.size(),
3671 snew(ir->opts.annealing, nr);
3672 snew(ir->opts.anneal_npoints, nr);
3673 snew(ir->opts.anneal_time, nr);
3674 snew(ir->opts.anneal_temp, nr);
3675 for (i = 0; i < nr; i++)
3677 ir->opts.annealing[i] = SimulatedAnnealing::No;
3678 ir->opts.anneal_npoints[i] = 0;
3679 ir->opts.anneal_time[i] = nullptr;
3680 ir->opts.anneal_temp[i] = nullptr;
3682 if (!simulatedAnnealingGroupNames.empty())
3685 for (i = 0; i < nr; i++)
3687 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3689 ir->opts.annealing[i] = SimulatedAnnealing::No;
3691 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3693 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3696 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3698 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3704 /* Read the other fields too */
3705 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3706 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3709 "Found %zu annealing-npoints values for %zu groups\n",
3710 simulatedAnnealingPoints.size(),
3711 simulatedAnnealingGroupNames.size());
3713 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3714 size_t numSimulatedAnnealingFields = 0;
3715 for (i = 0; i < nr; i++)
3717 if (ir->opts.anneal_npoints[i] == 1)
3721 "Please specify at least a start and an end point for annealing\n");
3723 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3724 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3725 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3728 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3730 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3733 "Found %zu annealing-time values, wanted %zu\n",
3734 simulatedAnnealingTimes.size(),
3735 numSimulatedAnnealingFields);
3737 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3738 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3741 "Found %zu annealing-temp values, wanted %zu\n",
3742 simulatedAnnealingTemperatures.size(),
3743 numSimulatedAnnealingFields);
3746 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3747 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3748 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3750 simulatedAnnealingTemperatures,
3752 allSimulatedAnnealingTemperatures.data());
3753 for (i = 0, k = 0; i < nr; i++)
3755 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3757 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3758 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3761 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3763 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3769 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3772 "Annealing timepoints out of order: t=%f comes after "
3774 ir->opts.anneal_time[i][j],
3775 ir->opts.anneal_time[i][j - 1]);
3778 if (ir->opts.anneal_temp[i][j] < 0)
3781 "Found negative temperature in annealing: %f\n",
3782 ir->opts.anneal_temp[i][j]);
3787 /* Print out some summary information, to make sure we got it right */
3788 for (i = 0; i < nr; i++)
3790 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3792 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3794 "Simulated annealing for group %s: %s, %d timepoints\n",
3795 *(groups->groupNames[j]),
3796 enumValueToString(ir->opts.annealing[i]),
3797 ir->opts.anneal_npoints[i]);
3798 fprintf(stderr, "Time (ps) Temperature (K)\n");
3799 /* All terms except the last one */
3800 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3804 ir->opts.anneal_time[i][j],
3805 ir->opts.anneal_temp[i][j]);
3808 /* Finally the last one */
3809 j = ir->opts.anneal_npoints[i] - 1;
3810 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3814 ir->opts.anneal_time[i][j],
3815 ir->opts.anneal_temp[i][j]);
3821 ir->opts.anneal_time[i][j],
3822 ir->opts.anneal_temp[i][j]);
3823 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3826 "There is a temperature jump when your annealing "
3838 for (int i = 1; i < ir->pull->ngroup; i++)
3840 const int gid = search_string(
3841 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3842 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3843 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3846 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3848 checkPullCoords(ir->pull->group, ir->pull->coord);
3853 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3856 if (ir->eSwapCoords != SwapType::No)
3858 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3861 /* Make indices for IMD session */
3864 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3867 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3868 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3869 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3871 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3872 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3873 if (freezeDims.size() != DIM * freezeGroupNames.size())
3876 "Invalid Freezing input: %zu groups and %zu freeze values",
3877 freezeGroupNames.size(),
3880 do_numbering(natoms,
3885 SimulationAtomGroupType::Freeze,
3890 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3891 ir->opts.ngfrz = nr;
3892 snew(ir->opts.nFreeze, nr);
3893 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3895 for (j = 0; (j < DIM); j++, k++)
3897 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3898 if (!ir->opts.nFreeze[i][j])
3900 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3903 "Please use Y(ES) or N(O) for freezedim only "
3905 freezeDims[k].c_str());
3906 warning(wi, warn_buf);
3911 for (; (i < nr); i++)
3913 for (j = 0; (j < DIM); j++)
3915 ir->opts.nFreeze[i][j] = 0;
3919 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3920 do_numbering(natoms,
3925 SimulationAtomGroupType::EnergyOutput,
3930 add_wall_energrps(groups, ir->nwall, symtab);
3931 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3932 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3933 do_numbering(natoms,
3938 SimulationAtomGroupType::MassCenterVelocityRemoval,
3940 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3944 if (ir->comm_mode != ComRemovalAlgorithm::No)
3946 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3949 /* Now we have filled the freeze struct, so we can calculate NRDF */
3950 calc_nrdf(mtop, ir, gnames);
3952 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3953 do_numbering(natoms,
3958 SimulationAtomGroupType::User1,
3963 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3964 do_numbering(natoms,
3969 SimulationAtomGroupType::User2,
3974 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3975 do_numbering(natoms,
3977 compressedXGroupNames,
3980 SimulationAtomGroupType::CompressedPositionOutput,
3985 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3986 do_numbering(natoms,
3988 orirefFitGroupNames,
3991 SimulationAtomGroupType::OrientationRestraintsFit,
3997 /* MiMiC QMMM input processing */
3998 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3999 if (qmGroupNames.size() > 1)
4001 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4003 /* group rest, if any, is always MM! */
4004 do_numbering(natoms,
4009 SimulationAtomGroupType::QuantumMechanics,
4014 ir->opts.ngQM = qmGroupNames.size();
4016 /* end of MiMiC QMMM input */
4020 for (auto group : gmx::keysOf(groups->groups))
4022 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4023 for (const auto& entry : groups->groups[group])
4025 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4027 fprintf(stderr, "\n");
4031 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4032 snew(ir->opts.egp_flags, nr * nr);
4034 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4035 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4037 warning_error(wi, "Energy group exclusions are currently not supported");
4039 if (bExcl && EEL_FULL(ir->coulombtype))
4041 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4044 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4045 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4046 && !(ir->coulombtype == CoulombInteractionType::User)
4047 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4048 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4051 "Can only have energy group pair tables in combination with user tables for VdW "
4055 /* final check before going out of scope if simulated tempering variables
4056 * need to be set to default values.
4058 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4060 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4063 "the value for nstexpanded was not specified for "
4064 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4065 "by default, but it is recommended to set it to an explicit value!",
4066 ir->expandedvals->nstexpanded));
4068 for (i = 0; (i < defaultIndexGroups->nr); i++)
4073 done_blocka(defaultIndexGroups);
4074 sfree(defaultIndexGroups);
4078 static void check_disre(const gmx_mtop_t* mtop)
4080 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4082 const gmx_ffparams_t& ffparams = mtop->ffparams;
4085 for (int i = 0; i < ffparams.numTypes(); i++)
4087 int ftype = ffparams.functype[i];
4088 if (ftype == F_DISRES)
4090 int label = ffparams.iparams[i].disres.label;
4091 if (label == old_label)
4093 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4102 "Found %d double distance restraint indices,\n"
4103 "probably the parameters for multiple pairs in one restraint "
4104 "are not identical\n",
4110 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
4113 gmx_mtop_ilistloop_t iloop;
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 iloop = gmx_mtop_ilistloop_init(sys);
4141 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4143 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4145 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4147 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4148 for (d = 0; d < DIM; d++)
4150 if (pr->posres.fcA[d] != 0)
4156 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4158 /* Check for flat-bottom posres */
4159 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4160 if (pr->fbposres.k != 0)
4162 switch (pr->fbposres.geom)
4164 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4165 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4166 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4167 case efbposresCYLINDER:
4168 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4169 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4170 case efbposresX: /* d=XX */
4171 case efbposresY: /* d=YY */
4172 case efbposresZ: /* d=ZZ */
4173 d = pr->fbposres.geom - efbposresX;
4178 " Invalid geometry for flat-bottom position restraint.\n"
4179 "Expected nr between 1 and %d. Found %d\n",
4188 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4191 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4193 bool* bC6ParametersWorkWithGeometricRules,
4194 bool* bC6ParametersWorkWithLBRules,
4195 bool* bLBRulesPossible)
4197 int ntypes, tpi, tpj;
4200 double c6i, c6j, c12i, c12j;
4201 double c6, c6_geometric, c6_LB;
4202 double sigmai, sigmaj, epsi, epsj;
4203 bool bCanDoLBRules, bCanDoGeometricRules;
4206 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4207 * force-field floating point parameters.
4210 ptr = getenv("GMX_LJCOMB_TOL");
4214 double gmx_unused canary;
4216 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4219 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4224 *bC6ParametersWorkWithLBRules = TRUE;
4225 *bC6ParametersWorkWithGeometricRules = TRUE;
4226 bCanDoLBRules = TRUE;
4227 ntypes = mtop->ffparams.atnr;
4228 snew(typecount, ntypes);
4229 gmx_mtop_count_atomtypes(mtop, state, typecount);
4230 *bLBRulesPossible = TRUE;
4231 for (tpi = 0; tpi < ntypes; ++tpi)
4233 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4234 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4235 for (tpj = tpi; tpj < ntypes; ++tpj)
4237 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4238 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4239 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4240 c6_geometric = std::sqrt(c6i * c6j);
4241 if (!gmx_numzero(c6_geometric))
4243 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4245 sigmai = gmx::sixthroot(c12i / c6i);
4246 sigmaj = gmx::sixthroot(c12j / c6j);
4247 epsi = c6i * c6i / (4.0 * c12i);
4248 epsj = c6j * c6j / (4.0 * c12j);
4249 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4253 *bLBRulesPossible = FALSE;
4254 c6_LB = c6_geometric;
4256 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4261 *bC6ParametersWorkWithLBRules = FALSE;
4264 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4266 if (!bCanDoGeometricRules)
4268 *bC6ParametersWorkWithGeometricRules = FALSE;
4275 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4277 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4279 check_combination_rule_differences(
4280 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4281 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4283 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4286 "You are using arithmetic-geometric combination rules "
4287 "in LJ-PME, but your non-bonded C6 parameters do not "
4288 "follow these rules.");
4293 if (!bC6ParametersWorkWithGeometricRules)
4295 if (ir->eDispCorr != DispersionCorrectionType::No)
4298 "You are using geometric combination rules in "
4299 "LJ-PME, but your non-bonded C6 parameters do "
4300 "not follow these rules. "
4301 "This will introduce very small errors in the forces and energies in "
4302 "your simulations. Dispersion correction will correct total energy "
4303 "and/or pressure for isotropic systems, but not forces or surface "
4309 "You are using geometric combination rules in "
4310 "LJ-PME, but your non-bonded C6 parameters do "
4311 "not follow these rules. "
4312 "This will introduce very small errors in the forces and energies in "
4313 "your simulations. If your system is homogeneous, consider using "
4314 "dispersion correction "
4315 "for the total energy and pressure.");
4321 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4323 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4324 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4326 char err_buf[STRLEN];
4329 gmx_mtop_atomloop_block_t aloopb;
4331 char warn_buf[STRLEN];
4333 set_warning_line(wi, mdparin, -1);
4335 if (absolute_reference(ir, sys, false, AbsRef))
4338 "Removing center of mass motion in the presence of position restraints might "
4339 "cause artifacts. When you are using position restraints to equilibrate a "
4340 "macro-molecule, the artifacts are usually negligible.");
4343 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4344 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4345 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4347 /* Check if a too small Verlet buffer might potentially
4348 * cause more drift than the thermostat can couple off.
4350 /* Temperature error fraction for warning and suggestion */
4351 const real T_error_warn = 0.002;
4352 const real T_error_suggest = 0.001;
4353 /* For safety: 2 DOF per atom (typical with constraints) */
4354 const real nrdf_at = 2;
4355 real T, tau, max_T_error;
4360 for (i = 0; i < ir->opts.ngtc; i++)
4362 T = std::max(T, ir->opts.ref_t[i]);
4363 tau = std::max(tau, ir->opts.tau_t[i]);
4367 /* This is a worst case estimate of the temperature error,
4368 * assuming perfect buffer estimation and no cancelation
4369 * of errors. The factor 0.5 is because energy distributes
4370 * equally over Ekin and Epot.
4372 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4373 if (max_T_error > T_error_warn)
4376 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4377 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4378 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4379 "%.0e or decrease tau_t.",
4384 100 * T_error_suggest,
4385 ir->verletbuf_tol * T_error_suggest / max_T_error);
4386 warning(wi, warn_buf);
4391 if (ETC_ANDERSEN(ir->etc))
4395 for (i = 0; i < ir->opts.ngtc; i++)
4398 "all tau_t must currently be equal using Andersen temperature control, "
4399 "violated for group %d",
4401 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4403 "all tau_t must be positive using Andersen temperature control, "
4407 CHECK(ir->opts.tau_t[i] < 0);
4410 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4412 for (i = 0; i < ir->opts.ngtc; i++)
4414 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4416 "tau_t/delta_t for group %d for temperature control method %s must be a "
4417 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4418 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4421 enumValueToString(ir->etc),
4425 CHECK(nsteps % ir->nstcomm != 0);
4430 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4431 && ir->comm_mode == ComRemovalAlgorithm::No
4432 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4435 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4436 "rounding errors can lead to build up of kinetic energy of the center of mass");
4439 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4442 for (int g = 0; g < ir->opts.ngtc; g++)
4444 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4446 if (ir->tau_p < 1.9 * tau_t_max)
4448 std::string message = gmx::formatString(
4449 "With %s T-coupling and %s p-coupling, "
4450 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4451 enumValueToString(ir->etc),
4452 enumValueToString(ir->epc),
4457 warning(wi, message.c_str());
4461 /* Check for pressure coupling with absolute position restraints */
4462 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4464 absolute_reference(ir, sys, TRUE, AbsRef);
4466 for (m = 0; m < DIM; m++)
4468 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4471 "You are using pressure coupling with absolute position restraints, "
4472 "this will give artifacts. Use the refcoord_scaling option.");
4480 aloopb = gmx_mtop_atomloop_block_init(sys);
4482 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4484 if (atom->q != 0 || atom->qB != 0)
4492 if (EEL_FULL(ir->coulombtype))
4495 "You are using full electrostatics treatment %s for a system without charges.\n"
4496 "This costs a lot of performance for just processing zeros, consider using %s "
4498 enumValueToString(ir->coulombtype),
4499 enumValueToString(CoulombInteractionType::Cut));
4500 warning(wi, err_buf);
4505 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4508 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4509 "You might want to consider using %s electrostatics.\n",
4510 enumValueToString(CoulombInteractionType::Pme));
4511 warning_note(wi, err_buf);
4515 /* Check if combination rules used in LJ-PME are the same as in the force field */
4516 if (EVDW_PME(ir->vdwtype))
4518 check_combination_rules(ir, sys, wi);
4521 /* Generalized reaction field */
4522 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4525 "Generalized reaction-field electrostatics is no longer supported. "
4526 "You can use normal reaction-field instead and compute the reaction-field "
4527 "constant by hand.");
4530 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4531 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4533 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4541 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4543 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4545 absolute_reference(ir, sys, FALSE, AbsRef);
4546 for (m = 0; m < DIM; m++)
4548 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4551 "You are using an absolute reference for pulling, but the rest of "
4552 "the system does not have an absolute reference. This will lead to "
4561 for (i = 0; i < 3; i++)
4563 for (m = 0; m <= i; m++)
4565 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4567 for (c = 0; c < ir->pull->ncoord; c++)
4569 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4570 && ir->pull->coord[c].vec[m] != 0)
4573 "Can not have dynamic box while using pull geometry '%s' "
4575 enumValueToString(ir->pull->coord[c].eGeom),
4587 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4589 char warn_buf[STRLEN];
4592 ptr = check_box(ir->pbcType, box);
4595 warning_error(wi, ptr);
4598 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4600 if (ir->shake_tol <= 0.0)
4602 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4603 warning_error(wi, warn_buf);
4607 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4609 /* If we have Lincs constraints: */
4610 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4611 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4614 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4615 warning_note(wi, warn_buf);
4618 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4619 && (ir->nProjOrder < 8))
4622 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4623 enumValueToString(ir->eI));
4624 warning_note(wi, warn_buf);
4626 if (ir->epc == PressureCoupling::Mttk)
4628 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4632 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4634 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4637 if (ir->LincsWarnAngle > 90.0)
4639 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4640 warning(wi, warn_buf);
4641 ir->LincsWarnAngle = 90.0;
4644 if (ir->pbcType != PbcType::No)
4646 if (ir->nstlist == 0)
4649 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4650 "atoms might cause the simulation to crash.");
4652 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4655 "ERROR: The cut-off length is longer than half the shortest box vector or "
4656 "longer than the smallest box diagonal element. Increase the box size or "
4657 "decrease rlist.\n");
4658 warning_error(wi, warn_buf);