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52 #include "gromacs/applied_forces/awh/read_params.h"
53 #include "gromacs/fileio/readinp.h"
54 #include "gromacs/fileio/warninp.h"
55 #include "gromacs/gmxlib/network.h"
56 #include "gromacs/gmxpreprocess/toputil.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/math/units.h"
59 #include "gromacs/math/utilities.h"
60 #include "gromacs/math/vec.h"
61 #include "gromacs/mdlib/calc_verletbuf.h"
62 #include "gromacs/mdlib/vcm.h"
63 #include "gromacs/mdrun/mdmodules.h"
64 #include "gromacs/mdtypes/awh_params.h"
65 #include "gromacs/mdtypes/inputrec.h"
66 #include "gromacs/mdtypes/md_enums.h"
67 #include "gromacs/mdtypes/multipletimestepping.h"
68 #include "gromacs/mdtypes/pull_params.h"
69 #include "gromacs/options/options.h"
70 #include "gromacs/options/treesupport.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/selection/indexutil.h"
73 #include "gromacs/topology/block.h"
74 #include "gromacs/topology/ifunc.h"
75 #include "gromacs/topology/index.h"
76 #include "gromacs/topology/mtop_util.h"
77 #include "gromacs/topology/symtab.h"
78 #include "gromacs/topology/topology.h"
79 #include "gromacs/utility/arrayref.h"
80 #include "gromacs/utility/cstringutil.h"
81 #include "gromacs/utility/exceptions.h"
82 #include "gromacs/utility/fatalerror.h"
83 #include "gromacs/utility/filestream.h"
84 #include "gromacs/utility/gmxassert.h"
85 #include "gromacs/utility/ikeyvaluetreeerror.h"
86 #include "gromacs/utility/keyvaluetree.h"
87 #include "gromacs/utility/keyvaluetreebuilder.h"
88 #include "gromacs/utility/keyvaluetreemdpwriter.h"
89 #include "gromacs/utility/keyvaluetreetransform.h"
90 #include "gromacs/utility/mdmodulesnotifiers.h"
91 #include "gromacs/utility/smalloc.h"
92 #include "gromacs/utility/strconvert.h"
93 #include "gromacs/utility/stringcompare.h"
94 #include "gromacs/utility/stringutil.h"
95 #include "gromacs/utility/textwriter.h"
99 using gmx::BasicVector;
101 /* Resource parameters
102 * Do not change any of these until you read the instruction
103 * in readinp.h. Some cpp's do not take spaces after the backslash
104 * (like the c-shell), which will give you a very weird compiler
108 struct gmx_inputrec_strings
110 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], accelerationGroups[STRLEN],
111 acceleration[STRLEN], freeze[STRLEN], frdim[STRLEN], energy[STRLEN], user1[STRLEN],
112 user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN], couple_moltype[STRLEN],
113 orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN],
114 wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
115 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
116 char lambda_weights[STRLEN];
117 std::vector<std::string> pullGroupNames;
118 std::vector<std::string> rotateGroupNames;
119 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
122 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
123 static gmx_inputrec_strings* inputrecStrings = nullptr;
125 void init_inputrec_strings()
130 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
131 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
133 inputrecStrings = new gmx_inputrec_strings();
136 void done_inputrec_strings()
138 delete inputrecStrings;
139 inputrecStrings = nullptr;
143 //! How to treat coverage of the whole system for a set of atom groupsx
144 enum class GroupCoverage
146 All, //!< All particles have to be a member of a group
147 AllGenerateRest, //<! A rest group with name is generated for particles not part of any group
148 Partial, //<! As \p AllGenerateRest, but no name for the rest group is generated
149 OneGroup //<! Merge all selected groups into one group, make a rest group for the remaining particles
152 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
153 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
154 "h-angles", "all-angles", nullptr };
156 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
157 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
159 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
164 for (i = 0; i < ntemps; i++)
166 /* simple linear scaling -- allows more control */
167 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
169 simtemp->temperatures[i] =
171 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
173 else if (simtemp->eSimTempScale
174 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
176 simtemp->temperatures[i] = simtemp->simtemp_low
177 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
178 static_cast<real>((1.0 * i) / (ntemps - 1)));
180 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
182 simtemp->temperatures[i] = simtemp->simtemp_low
183 + (simtemp->simtemp_high - simtemp->simtemp_low)
184 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
189 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
190 gmx_fatal(FARGS, "%s", errorstr);
196 static void _low_check(bool b, const char* s, warninp_t wi)
200 warning_error(wi, s);
204 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
208 if (*p > 0 && *p % nst != 0)
210 /* Round up to the next multiple of nst */
211 *p = ((*p) / nst + 1) * nst;
212 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
217 //! Convert legacy mdp entries to modern ones.
218 static void process_interaction_modifier(InteractionModifiers* eintmod)
220 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
222 *eintmod = InteractionModifiers::PotShift;
226 void check_ir(const char* mdparin,
227 const gmx::MDModulesNotifiers& mdModulesNotifiers,
231 /* Check internal consistency.
232 * NOTE: index groups are not set here yet, don't check things
233 * like temperature coupling group options here, but in triple_check
236 /* Strange macro: first one fills the err_buf, and then one can check
237 * the condition, which will print the message and increase the error
240 #define CHECK(b) _low_check(b, err_buf, wi)
241 char err_buf[256], warn_buf[STRLEN];
244 t_lambda* fep = ir->fepvals.get();
245 t_expanded* expand = ir->expandedvals.get();
247 set_warning_line(wi, mdparin, -1);
249 /* We cannot check MTS requirements with an invalid MTS setup
250 * and we will already have generated errors with an invalid MTS setup.
252 if (gmx::haveValidMtsSetup(*ir))
254 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
256 for (const auto& errorMessage : errorMessages)
258 warning_error(wi, errorMessage.c_str());
262 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
264 std::string message =
265 gmx::formatString("%s electrostatics is no longer supported",
266 enumValueToString(CoulombInteractionType::RFNecUnsupported));
267 warning_error(wi, message);
270 /* BASIC CUT-OFF STUFF */
271 if (ir->rcoulomb < 0)
273 warning_error(wi, "rcoulomb should be >= 0");
277 warning_error(wi, "rvdw should be >= 0");
279 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
281 warning_error(wi, "rlist should be >= 0");
284 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
285 "neighbour-list update scheme for efficient buffering for improved energy "
286 "conservation, please use the Verlet cut-off scheme instead.)");
287 CHECK(ir->nstlist < 0);
289 process_interaction_modifier(&ir->coulomb_modifier);
290 process_interaction_modifier(&ir->vdw_modifier);
292 if (ir->cutoff_scheme == CutoffScheme::Group)
295 "The group cutoff scheme has been removed since GROMACS 2020. "
296 "Please use the Verlet cutoff scheme.");
298 if (ir->cutoff_scheme == CutoffScheme::Verlet)
302 /* Normal Verlet type neighbor-list, currently only limited feature support */
303 if (inputrec2nboundeddim(ir) < 3)
305 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
308 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
309 if (ir->rcoulomb != ir->rvdw)
311 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
312 // for PME load balancing, we can support this exception.
313 bool bUsesPmeTwinRangeKernel =
314 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
315 && ir->rcoulomb > ir->rvdw);
316 if (!bUsesPmeTwinRangeKernel)
319 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
320 "rcoulomb>rvdw with PME electrostatics)");
324 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
326 if (ir->vdw_modifier == InteractionModifiers::None
327 || ir->vdw_modifier == InteractionModifiers::PotShift)
330 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
331 : InteractionModifiers::PotSwitch);
334 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
336 enumValueToString(ir->vdwtype),
337 enumValueToString(VanDerWaalsType::Cut),
338 enumValueToString(ir->vdw_modifier));
339 warning_note(wi, warn_buf);
341 ir->vdwtype = VanDerWaalsType::Cut;
346 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
347 enumValueToString(ir->vdwtype),
348 enumValueToString(ir->vdw_modifier));
349 warning_error(wi, warn_buf);
353 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
356 "With Verlet lists only cut-off and PME LJ interactions are supported");
358 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
359 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
362 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
363 "electrostatics are supported");
365 if (!(ir->coulomb_modifier == InteractionModifiers::None
366 || ir->coulomb_modifier == InteractionModifiers::PotShift))
368 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
369 warning_error(wi, warn_buf);
372 if (EEL_USER(ir->coulombtype))
375 "Coulomb type %s is not supported with the verlet scheme",
376 enumValueToString(ir->coulombtype));
377 warning_error(wi, warn_buf);
380 if (ir->nstlist <= 0)
382 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
385 if (ir->nstlist < 10)
388 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
389 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
393 rc_max = std::max(ir->rvdw, ir->rcoulomb);
397 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
398 ir->verletbuf_tol = 0;
401 else if (ir->verletbuf_tol <= 0)
403 if (ir->verletbuf_tol == 0)
405 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
408 if (ir->rlist < rc_max)
411 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
414 if (ir->rlist == rc_max && ir->nstlist > 1)
418 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
419 "buffer. The cluster pair list does have a buffering effect, but choosing "
420 "a larger rlist might be necessary for good energy conservation.");
425 if (ir->rlist > rc_max)
428 "You have set rlist larger than the interaction cut-off, but you also "
429 "have verlet-buffer-tolerance > 0. Will set rlist using "
430 "verlet-buffer-tolerance.");
433 if (ir->nstlist == 1)
435 /* No buffer required */
440 if (EI_DYNAMICS(ir->eI))
442 if (inputrec2nboundeddim(ir) < 3)
445 "The box volume is required for calculating rlist from the "
446 "energy drift with verlet-buffer-tolerance > 0. You are "
447 "using at least one unbounded dimension, so no volume can be "
448 "computed. Either use a finite box, or set rlist yourself "
449 "together with verlet-buffer-tolerance = -1.");
451 /* Set rlist temporarily so we can continue processing */
456 /* Set the buffer to 5% of the cut-off */
457 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
463 /* GENERAL INTEGRATOR STUFF */
466 if (ir->etc != TemperatureCoupling::No)
468 if (EI_RANDOM(ir->eI))
471 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
472 "implicitly. See the documentation for more information on which "
473 "parameters affect temperature for %s.",
474 enumValueToString(ir->etc),
475 enumValueToString(ir->eI),
476 enumValueToString(ir->eI));
481 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
483 enumValueToString(ir->etc),
484 enumValueToString(ir->eI));
486 warning_note(wi, warn_buf);
488 ir->etc = TemperatureCoupling::No;
490 if (ir->eI == IntegrationAlgorithm::VVAK)
493 "Integrator method %s is implemented primarily for validation purposes; for "
494 "molecular dynamics, you should probably be using %s or %s",
495 enumValueToString(IntegrationAlgorithm::VVAK),
496 enumValueToString(IntegrationAlgorithm::MD),
497 enumValueToString(IntegrationAlgorithm::VV));
498 warning_note(wi, warn_buf);
500 if (!EI_DYNAMICS(ir->eI))
502 if (ir->epc != PressureCoupling::No)
505 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
506 enumValueToString(ir->epc),
507 enumValueToString(ir->eI));
508 warning_note(wi, warn_buf);
510 ir->epc = PressureCoupling::No;
512 if (EI_DYNAMICS(ir->eI))
514 if (ir->nstcalcenergy < 0)
516 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
517 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
519 /* nstcalcenergy larger than nstener does not make sense.
520 * We ideally want nstcalcenergy=nstener.
524 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
528 ir->nstcalcenergy = ir->nstenergy;
532 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
533 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
534 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
537 const char* nsten = "nstenergy";
538 const char* nstdh = "nstdhdl";
539 const char* min_name = nsten;
540 int min_nst = ir->nstenergy;
542 /* find the smallest of ( nstenergy, nstdhdl ) */
543 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
544 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
546 min_nst = ir->fepvals->nstdhdl;
549 /* If the user sets nstenergy small, we should respect that */
550 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
551 warning_note(wi, warn_buf);
552 ir->nstcalcenergy = min_nst;
555 if (ir->epc != PressureCoupling::No)
557 if (ir->nstpcouple < 0)
559 ir->nstpcouple = ir_optimal_nstpcouple(ir);
561 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
564 "With multiple time stepping, nstpcouple should be a mutiple of "
569 if (ir->nstcalcenergy > 0)
571 if (ir->efep != FreeEnergyPerturbationType::No)
573 /* nstdhdl should be a multiple of nstcalcenergy */
574 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
578 /* nstexpanded should be a multiple of nstcalcenergy */
579 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
581 /* for storing exact averages nstenergy should be
582 * a multiple of nstcalcenergy
584 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
587 // Inquire all MDModules, if their parameters match with the energy
588 // calculation frequency
589 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
590 mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
592 // Emit all errors from the energy calculation frequency checks
593 for (const std::string& energyFrequencyErrorMessage :
594 energyCalculationFrequencyErrors.errorMessages())
596 warning_error(wi, energyFrequencyErrorMessage);
600 if (ir->nsteps == 0 && !ir->bContinuation)
603 "For a correct single-point energy evaluation with nsteps = 0, use "
604 "continuation = yes to avoid constraining the input coordinates.");
608 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
611 "You are doing a continuation with SD or BD, make sure that ld_seed is "
612 "different from the previous run (using ld_seed=-1 will ensure this)");
618 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
619 CHECK(ir->pbcType != PbcType::Xyz);
620 sprintf(err_buf, "with TPI nstlist should be larger than zero");
621 CHECK(ir->nstlist <= 0);
622 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
623 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
627 if ((opts->nshake > 0) && (opts->bMorse))
629 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
630 warning(wi, warn_buf);
633 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
636 "You are doing a continuation with SD or BD, make sure that ld_seed is "
637 "different from the previous run (using ld_seed=-1 will ensure this)");
639 /* verify simulated tempering options */
643 bool bAllTempZero = TRUE;
644 for (i = 0; i < fep->n_lambda; i++)
647 "Entry %d for %s must be between 0 and 1, instead is %g",
649 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
650 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
651 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
652 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
654 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
656 bAllTempZero = FALSE;
659 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
660 CHECK(bAllTempZero == TRUE);
662 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
663 CHECK(ir->eI != IntegrationAlgorithm::VV);
665 /* check compatability of the temperature coupling with simulated tempering */
667 if (ir->etc == TemperatureCoupling::NoseHoover)
670 "Nose-Hoover based temperature control such as [%s] my not be "
671 "entirelyconsistent with simulated tempering",
672 enumValueToString(ir->etc));
673 warning_note(wi, warn_buf);
676 /* check that the temperatures make sense */
679 "Higher simulated tempering temperature (%g) must be >= than the simulated "
680 "tempering lower temperature (%g)",
681 ir->simtempvals->simtemp_high,
682 ir->simtempvals->simtemp_low);
683 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
686 "Higher simulated tempering temperature (%g) must be >= zero",
687 ir->simtempvals->simtemp_high);
688 CHECK(ir->simtempvals->simtemp_high <= 0);
691 "Lower simulated tempering temperature (%g) must be >= zero",
692 ir->simtempvals->simtemp_low);
693 CHECK(ir->simtempvals->simtemp_low <= 0);
696 /* verify free energy options */
698 if (ir->efep != FreeEnergyPerturbationType::No)
700 fep = ir->fepvals.get();
701 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
702 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
705 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
707 static_cast<int>(fep->sc_r_power));
708 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
711 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
714 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
717 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
719 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
721 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
722 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
724 sprintf(err_buf, "Free-energy not implemented for Ewald");
725 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
727 /* check validty of lambda inputs */
728 if (fep->n_lambda == 0)
730 /* Clear output in case of no states:*/
731 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
732 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
737 "initial thermodynamic state %d does not exist, only goes to %d",
740 CHECK((fep->init_fep_state >= fep->n_lambda));
744 "Lambda state must be set, either with init-lambda-state or with init-lambda");
745 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
748 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
749 "init-lambda-state or with init-lambda, but not both",
751 fep->init_fep_state);
752 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
755 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
759 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
761 if (fep->separate_dvdl[i])
766 if (n_lambda_terms > 1)
769 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
770 "use init-lambda to set lambda state (except for slow growth). Use "
771 "init-lambda-state instead.");
772 warning(wi, warn_buf);
775 if (n_lambda_terms < 2 && fep->n_lambda > 0)
778 "init-lambda is deprecated for setting lambda state (except for slow "
779 "growth). Use init-lambda-state instead.");
783 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
785 for (i = 0; i < fep->n_lambda; i++)
787 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
789 "Entry %d for %s must be between 0 and 1, instead is %g",
791 enumValueToString(enumValue),
792 fep->all_lambda[j][i]);
793 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
797 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
799 for (i = 0; i < fep->n_lambda; i++)
802 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
803 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
804 "crashes, and is not supported.",
806 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
807 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
808 CHECK((fep->sc_alpha > 0)
809 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
810 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
811 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
812 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
817 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
819 real sigma, lambda, r_sc;
822 /* Maximum estimate for A and B charges equal with lambda power 1 */
824 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
825 1.0 / fep->sc_r_power);
827 "With PME there is a minor soft core effect present at the cut-off, "
828 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
829 "energy conservation, but usually other effects dominate. With a common sigma "
830 "value of %g nm the fraction of the particle-particle potential at the cut-off "
831 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
837 warning_note(wi, warn_buf);
840 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
841 be treated differently, but that's the next step */
843 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
845 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
846 for (j = 0; j < fep->n_lambda; j++)
848 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
849 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
853 if (fep->softcoreFunction == SoftcoreType::Gapsys)
855 if (fep->scGapsysScaleLinpointQ < 0.0)
858 "sc_scale_linpoint_Q_gapsys is equal %g but must be >= 0",
859 fep->scGapsysScaleLinpointQ);
860 warning_note(wi, warn_buf);
863 if ((fep->scGapsysScaleLinpointLJ < 0.0) || (fep->scGapsysScaleLinpointLJ >= 1.0))
866 "sc_scale_linpoint_LJ_gapsys is equal %g but must be in [0,1) when used "
868 "sc_function=gapsys.",
869 fep->scGapsysScaleLinpointLJ);
870 warning_note(wi, warn_buf);
875 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
877 fep = ir->fepvals.get();
879 /* checking equilibration of weights inputs for validity */
882 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
884 expand->equil_n_at_lam,
885 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
886 CHECK((expand->equil_n_at_lam > 0)
887 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
890 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
892 expand->equil_samples,
893 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
894 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
897 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
899 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
900 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
903 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
904 expand->equil_samples,
905 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
906 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
909 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
911 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
912 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
915 "weight-equil-number-all-lambda (%d) must be a positive integer if "
916 "lmc-weights-equil=%s",
917 expand->equil_n_at_lam,
918 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
919 CHECK((expand->equil_n_at_lam <= 0)
920 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
923 "weight-equil-number-samples (%d) must be a positive integer if "
924 "lmc-weights-equil=%s",
925 expand->equil_samples,
926 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
927 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
930 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
932 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
933 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
936 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
937 expand->equil_wl_delta,
938 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
939 CHECK((expand->equil_wl_delta <= 0)
940 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
943 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
945 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
946 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
949 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
950 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
951 enumValueToString(LambdaWeightCalculation::WL),
952 enumValueToString(LambdaWeightCalculation::WWL));
953 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
955 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
956 CHECK((expand->lmc_repeats <= 0));
957 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
958 CHECK((expand->minvarmin <= 0));
959 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
960 CHECK((expand->c_range < 0));
962 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
965 expand->lmc_forced_nstart);
966 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
967 && (expand->elmcmove != LambdaMoveCalculation::No));
968 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
969 CHECK((expand->lmc_forced_nstart < 0));
971 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
972 fep->init_fep_state);
973 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
975 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
976 CHECK((expand->init_wl_delta < 0));
977 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
978 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
979 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
980 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
982 /* if there is no temperature control, we need to specify an MC temperature */
983 if (!integratorHasReferenceTemperature(ir)
984 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
987 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
988 "to a positive number");
989 warning_error(wi, err_buf);
991 if (expand->nstTij > 0)
993 sprintf(err_buf, "nstlog must be non-zero");
994 CHECK(ir->nstlog == 0);
995 // Avoid modulus by zero in the case that already triggered an error exit.
999 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
1002 CHECK((expand->nstTij % ir->nstlog) != 0);
1008 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
1009 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
1012 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
1014 if (ir->pbcType == PbcType::No)
1016 if (ir->epc != PressureCoupling::No)
1018 warning(wi, "Turning off pressure coupling for vacuum system");
1019 ir->epc = PressureCoupling::No;
1025 "Can not have pressure coupling with pbc=%s",
1026 c_pbcTypeNames[ir->pbcType].c_str());
1027 CHECK(ir->epc != PressureCoupling::No);
1029 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1030 CHECK(EEL_FULL(ir->coulombtype));
1033 "Can not have dispersion correction with pbc=%s",
1034 c_pbcTypeNames[ir->pbcType].c_str());
1035 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1038 if (ir->rlist == 0.0)
1041 "can only have neighborlist cut-off zero (=infinite)\n"
1042 "with coulombtype = %s or coulombtype = %s\n"
1043 "without periodic boundary conditions (pbc = %s) and\n"
1044 "rcoulomb and rvdw set to zero",
1045 enumValueToString(CoulombInteractionType::Cut),
1046 enumValueToString(CoulombInteractionType::User),
1047 c_pbcTypeNames[PbcType::No].c_str());
1048 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1049 && (ir->coulombtype != CoulombInteractionType::User))
1050 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1052 if (ir->nstlist > 0)
1055 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1056 "nstype=simple and only one MPI rank");
1061 if (ir->nstcomm == 0)
1063 // TODO Change this behaviour. There should be exactly one way
1064 // to turn off an algorithm.
1065 ir->comm_mode = ComRemovalAlgorithm::No;
1067 if (ir->comm_mode != ComRemovalAlgorithm::No)
1069 if (ir->nstcomm < 0)
1071 // TODO Such input was once valid. Now that we've been
1072 // helpful for a few years, we should reject such input,
1073 // lest we have to support every historical decision
1076 "If you want to remove the rotation around the center of mass, you should set "
1077 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1078 "its absolute value");
1079 ir->nstcomm = abs(ir->nstcomm);
1082 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy
1083 && ir->comm_mode != ComRemovalAlgorithm::LinearAccelerationCorrection)
1086 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider "
1087 "setting nstcomm equal to nstcalcenergy for less overhead");
1090 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1093 "Can not remove the rotation around the center of mass with periodic "
1095 CHECK(ir->bPeriodicMols);
1096 if (ir->pbcType != PbcType::No)
1099 "Removing the rotation around the center of mass in a periodic system, "
1100 "this can lead to artifacts. Only use this on a single (cluster of) "
1101 "molecules. This cluster should not cross periodic boundaries.");
1106 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1107 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1110 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1111 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1113 enumValueToString(IntegrationAlgorithm::SD1));
1114 warning_note(wi, warn_buf);
1117 /* TEMPERATURE COUPLING */
1118 if (ir->etc == TemperatureCoupling::Yes)
1120 ir->etc = TemperatureCoupling::Berendsen;
1122 "Old option for temperature coupling given: "
1123 "changing \"yes\" to \"Berendsen\"\n");
1126 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1128 if (ir->opts.nhchainlength < 1)
1131 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1133 ir->opts.nhchainlength);
1134 ir->opts.nhchainlength = 1;
1135 warning(wi, warn_buf);
1138 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1142 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1143 ir->opts.nhchainlength = 1;
1148 ir->opts.nhchainlength = 0;
1151 if (ir->eI == IntegrationAlgorithm::VVAK)
1154 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1156 enumValueToString(IntegrationAlgorithm::VVAK));
1157 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1160 if (ETC_ANDERSEN(ir->etc))
1163 "%s temperature control not supported for integrator %s.",
1164 enumValueToString(ir->etc),
1165 enumValueToString(ir->eI));
1166 CHECK(!(EI_VV(ir->eI)));
1168 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1171 "Center of mass removal not necessary for %s. All velocities of coupled "
1172 "groups are rerandomized periodically, so flying ice cube errors will not "
1174 enumValueToString(ir->etc));
1175 warning_note(wi, warn_buf);
1179 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1180 "randomized every time step",
1182 enumValueToString(ir->etc));
1183 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1186 if (ir->etc == TemperatureCoupling::Berendsen)
1189 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1190 "might want to consider using the %s thermostat.",
1191 enumValueToString(ir->etc),
1192 enumValueToString(TemperatureCoupling::VRescale));
1193 warning_note(wi, warn_buf);
1196 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1197 && ir->epc == PressureCoupling::Berendsen)
1200 "Using Berendsen pressure coupling invalidates the "
1201 "true ensemble for the thermostat");
1202 warning(wi, warn_buf);
1205 /* PRESSURE COUPLING */
1206 if (ir->epc == PressureCoupling::Isotropic)
1208 ir->epc = PressureCoupling::Berendsen;
1210 "Old option for pressure coupling given: "
1211 "changing \"Isotropic\" to \"Berendsen\"\n");
1214 if (ir->epc != PressureCoupling::No)
1216 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1218 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1219 CHECK(ir->tau_p <= 0);
1221 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1224 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1225 "times larger than nstpcouple*dt (%g)",
1226 enumValueToString(ir->epc),
1228 pcouple_min_integration_steps(ir->epc),
1230 warning(wi, warn_buf);
1234 "compressibility must be > 0 when using pressure"
1236 enumValueToString(ir->epc));
1237 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1238 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1239 && ir->compress[ZZ][YY] <= 0));
1241 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1244 "You are generating velocities so I am assuming you "
1245 "are equilibrating a system. You are using "
1246 "%s pressure coupling, but this can be "
1247 "unstable for equilibration. If your system crashes, try "
1248 "equilibrating first with Berendsen pressure coupling. If "
1249 "you are not equilibrating the system, you can probably "
1250 "ignore this warning.",
1251 enumValueToString(ir->epc));
1252 warning(wi, warn_buf);
1258 if (ir->epc == PressureCoupling::Mttk)
1260 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1264 /* ELECTROSTATICS */
1265 /* More checks are in triple check (grompp.c) */
1267 if (ir->coulombtype == CoulombInteractionType::Switch)
1270 "coulombtype = %s is only for testing purposes and can lead to serious "
1271 "artifacts, advice: use coulombtype = %s",
1272 enumValueToString(ir->coulombtype),
1273 enumValueToString(CoulombInteractionType::RFZero));
1274 warning(wi, warn_buf);
1277 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1280 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1281 "format and exchanging epsilon-r and epsilon-rf",
1283 warning(wi, warn_buf);
1284 ir->epsilon_rf = ir->epsilon_r;
1285 ir->epsilon_r = 1.0;
1288 if (ir->epsilon_r == 0)
1291 "It is pointless to use long-range electrostatics with infinite relative "
1293 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1295 CHECK(EEL_FULL(ir->coulombtype));
1298 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1300 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1301 CHECK(ir->epsilon_r < 0);
1304 if (EEL_RF(ir->coulombtype))
1306 /* reaction field (at the cut-off) */
1308 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1311 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1312 enumValueToString(ir->coulombtype));
1313 warning(wi, warn_buf);
1314 ir->epsilon_rf = 0.0;
1317 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1318 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1319 if (ir->epsilon_rf == ir->epsilon_r)
1322 "Using epsilon-rf = epsilon-r with %s does not make sense",
1323 enumValueToString(ir->coulombtype));
1324 warning(wi, warn_buf);
1327 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1328 * means the interaction is zero outside rcoulomb, but it helps to
1329 * provide accurate energy conservation.
1331 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1333 if (ir_coulomb_switched(ir))
1336 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1337 "potential modifier options!",
1338 enumValueToString(ir->coulombtype));
1339 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1343 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1346 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1347 "secondary coulomb-modifier.");
1348 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1350 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1353 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1354 "secondary vdw-modifier.");
1355 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1358 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1359 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1362 "The switch/shift interaction settings are just for compatibility; you will get "
1364 "performance from applying potential modifiers to your interactions!\n");
1365 warning_note(wi, warn_buf);
1368 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1369 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1371 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1373 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1375 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1376 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1377 "will be good regardless, since ewald_rtol = %g.",
1379 ir->rcoulomb_switch,
1382 warning(wi, warn_buf);
1386 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1388 if (ir->rvdw_switch == 0)
1391 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1392 "potential. This suggests it was not set in the mdp, which can lead to large "
1393 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1394 "switching range.");
1395 warning(wi, warn_buf);
1399 if (EEL_FULL(ir->coulombtype))
1401 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1402 || ir->coulombtype == CoulombInteractionType::PmeUser
1403 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1406 "With coulombtype = %s, rcoulomb must be <= rlist",
1407 enumValueToString(ir->coulombtype));
1408 CHECK(ir->rcoulomb > ir->rlist);
1412 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1414 // TODO: Move these checks into the ewald module with the options class
1416 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1418 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1421 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1422 enumValueToString(ir->coulombtype),
1425 warning_error(wi, warn_buf);
1429 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1431 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1434 "With pbc=%s you should use ewald-geometry=%s",
1435 c_pbcTypeNames[ir->pbcType].c_str(),
1436 enumValueToString(EwaldGeometry::ThreeDC));
1437 warning(wi, warn_buf);
1439 /* This check avoids extra pbc coding for exclusion corrections */
1440 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1441 CHECK(ir->wall_ewald_zfac < 2);
1443 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1444 && EEL_FULL(ir->coulombtype))
1447 "With %s and ewald_geometry = %s you should use pbc = %s",
1448 enumValueToString(ir->coulombtype),
1449 enumValueToString(EwaldGeometry::ThreeDC),
1450 c_pbcTypeNames[PbcType::XY].c_str());
1451 warning(wi, warn_buf);
1453 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1455 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1456 CHECK(ir->bPeriodicMols);
1457 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1458 warning_note(wi, warn_buf);
1460 "With epsilon_surface > 0 you can only use domain decomposition "
1461 "when there are only small molecules with all bonds constrained (mdrun will check "
1463 warning_note(wi, warn_buf);
1466 if (ir_vdw_switched(ir))
1468 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1469 CHECK(ir->rvdw_switch >= ir->rvdw);
1471 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1474 "You are applying a switch function to vdw forces or potentials from %g to %g "
1475 "nm, which is more than half the interaction range, whereas switch functions "
1476 "are intended to act only close to the cut-off.",
1479 warning_note(wi, warn_buf);
1483 if (ir->vdwtype == VanDerWaalsType::Pme)
1485 if (!(ir->vdw_modifier == InteractionModifiers::None
1486 || ir->vdw_modifier == InteractionModifiers::PotShift))
1489 "With vdwtype = %s, the only supported modifiers are %s and %s",
1490 enumValueToString(ir->vdwtype),
1491 enumValueToString(InteractionModifiers::PotShift),
1492 enumValueToString(InteractionModifiers::None));
1493 warning_error(wi, err_buf);
1497 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1500 "You have selected user tables with dispersion correction, the dispersion "
1501 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1502 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1503 "really want dispersion correction to -C6/r^6.");
1506 if (ir->eI == IntegrationAlgorithm::LBFGS
1507 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1510 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1513 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1515 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1518 /* IMPLICIT SOLVENT */
1519 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1521 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1522 warning_error(wi, warn_buf);
1527 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1532 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1535 // cosine acceleration is only supported in leap-frog
1536 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1538 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1542 /* interpret a number of doubles from a string and put them in an array,
1543 after allocating space for them.
1544 str = the input string
1545 n = the (pre-allocated) number of doubles read
1546 r = the output array of doubles. */
1547 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1549 auto values = gmx::splitString(str);
1552 std::vector<real> r;
1553 for (int i = 0; i < *n; i++)
1557 r.emplace_back(gmx::fromString<real>(values[i]));
1559 catch (gmx::GromacsException&)
1562 "Invalid value " + values[i]
1563 + " in string in mdp file. Expected a real number.");
1570 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1573 int i, j, max_n_lambda, nweights;
1574 t_lambda* fep = ir->fepvals.get();
1575 t_expanded* expand = ir->expandedvals.get();
1576 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1577 bool bOneLambda = TRUE;
1578 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1580 /* FEP input processing */
1581 /* first, identify the number of lambda values for each type.
1582 All that are nonzero must have the same number */
1584 for (auto i : keysOf(nfep))
1586 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1589 /* now, determine the number of components. All must be either zero, or equal. */
1592 for (auto i : keysOf(nfep))
1594 if (nfep[i] > max_n_lambda)
1596 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1597 must have the same number if its not zero.*/
1602 for (auto i : keysOf(nfep))
1606 ir->fepvals->separate_dvdl[i] = FALSE;
1608 else if (nfep[i] == max_n_lambda)
1610 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1611 the derivative with respect to the temperature currently */
1613 ir->fepvals->separate_dvdl[i] = TRUE;
1619 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1622 enumValueToString(i),
1626 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1627 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1629 /* the number of lambdas is the number we've read in, which is either zero
1630 or the same for all */
1631 fep->n_lambda = max_n_lambda;
1633 /* if init_lambda is defined, we need to set lambda */
1634 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1636 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1638 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1639 for (auto i : keysOf(nfep))
1641 fep->all_lambda[i].resize(fep->n_lambda);
1642 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1645 for (j = 0; j < fep->n_lambda; j++)
1647 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1652 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1653 internal bookkeeping -- for now, init_lambda */
1655 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1657 for (i = 0; i < fep->n_lambda; i++)
1659 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1663 /* check to see if only a single component lambda is defined, and soft core is defined.
1664 In this case, turn on coulomb soft core */
1666 if (max_n_lambda == 0)
1672 for (auto i : keysOf(nfep))
1674 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1680 if ((bOneLambda) && (fep->sc_alpha > 0))
1682 fep->bScCoul = TRUE;
1685 /* Fill in the others with the efptFEP if they are not explicitly
1686 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1687 they are all zero. */
1689 for (auto i : keysOf(nfep))
1691 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1693 for (j = 0; j < fep->n_lambda; j++)
1695 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1701 /* now read in the weights */
1702 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1705 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1707 else if (nweights != fep->n_lambda)
1710 "Number of weights (%d) is not equal to number of lambda values (%d)",
1714 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1716 expand->nstexpanded = fep->nstdhdl;
1717 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1722 static void do_simtemp_params(t_inputrec* ir)
1724 ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
1725 getSimTemps(ir->fepvals->n_lambda,
1726 ir->simtempvals.get(),
1727 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1730 template<typename T>
1731 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1734 for (const auto& input : inputs)
1738 outputs[i] = gmx::fromStdString<T>(input);
1740 catch (gmx::GromacsException&)
1742 auto message = gmx::formatString(
1743 "Invalid value for mdp option %s. %s should only consist of integers separated "
1747 warning_error(wi, message);
1753 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1756 for (const auto& input : inputs)
1760 outputs[i] = gmx::fromString<real>(input);
1762 catch (gmx::GromacsException&)
1764 auto message = gmx::formatString(
1765 "Invalid value for mdp option %s. %s should only consist of real numbers "
1766 "separated by spaces.",
1769 warning_error(wi, message);
1775 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1778 for (const auto& input : inputs)
1782 outputs[i][d] = gmx::fromString<real>(input);
1784 catch (gmx::GromacsException&)
1786 auto message = gmx::formatString(
1787 "Invalid value for mdp option %s. %s should only consist of real numbers "
1788 "separated by spaces.",
1791 warning_error(wi, message);
1802 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1804 opts->wall_atomtype[0] = nullptr;
1805 opts->wall_atomtype[1] = nullptr;
1807 ir->wall_atomtype[0] = -1;
1808 ir->wall_atomtype[1] = -1;
1809 ir->wall_density[0] = 0;
1810 ir->wall_density[1] = 0;
1814 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1815 if (wallAtomTypes.size() != size_t(ir->nwall))
1818 "Expected %d elements for wall_atomtype, found %zu",
1820 wallAtomTypes.size());
1822 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1823 for (int i = 0; i < ir->nwall; i++)
1825 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1828 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1830 auto wallDensity = gmx::splitString(wall_density);
1831 if (wallDensity.size() != size_t(ir->nwall))
1834 "Expected %d elements for wall-density, found %zu",
1836 wallDensity.size());
1838 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1839 for (int i = 0; i < ir->nwall; i++)
1841 if (ir->wall_density[i] <= 0)
1843 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1850 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1854 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1855 for (int i = 0; i < nwall; i++)
1857 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1858 grps->emplace_back(groups->groupNames.size() - 1);
1863 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1865 /* read expanded ensemble parameters */
1866 printStringNewline(inp, "expanded ensemble variables");
1867 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1868 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1869 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1870 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1871 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1872 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1873 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1874 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1875 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1876 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1877 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1878 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1879 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1880 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1881 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1882 expand->bSymmetrizedTMatrix =
1883 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1884 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1885 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1886 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1887 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1888 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1889 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1890 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1893 /*! \brief Return whether an end state with the given coupling-lambda
1894 * value describes fully-interacting VDW.
1896 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1897 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1899 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1901 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1907 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1910 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1912 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1914 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1917 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1918 std::string message = gmx::formatExceptionMessageToString(*ex);
1919 warning_error(wi_, message.c_str());
1924 std::string getOptionName(const gmx::KeyValueTreePath& context)
1926 if (mapping_ != nullptr)
1928 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1929 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1932 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1937 const gmx::IKeyValueTreeBackMapping* mapping_;
1942 void get_ir(const char* mdparin,
1943 const char* mdparout,
1944 gmx::MDModules* mdModules,
1947 WriteMdpHeader writeMdpHeader,
1951 double dumdub[2][6];
1953 char warn_buf[STRLEN];
1954 t_lambda* fep = ir->fepvals.get();
1955 t_expanded* expand = ir->expandedvals.get();
1957 const char* no_names[] = { "no", nullptr };
1959 init_inputrec_strings();
1960 gmx::TextInputFile stream(mdparin);
1961 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1963 snew(dumstr[0], STRLEN);
1964 snew(dumstr[1], STRLEN);
1966 /* ignore the following deprecated commands */
1967 replace_inp_entry(inp, "title", nullptr);
1968 replace_inp_entry(inp, "cpp", nullptr);
1969 replace_inp_entry(inp, "domain-decomposition", nullptr);
1970 replace_inp_entry(inp, "andersen-seed", nullptr);
1971 replace_inp_entry(inp, "dihre", nullptr);
1972 replace_inp_entry(inp, "dihre-fc", nullptr);
1973 replace_inp_entry(inp, "dihre-tau", nullptr);
1974 replace_inp_entry(inp, "nstdihreout", nullptr);
1975 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1976 replace_inp_entry(inp, "optimize-fft", nullptr);
1977 replace_inp_entry(inp, "adress_type", nullptr);
1978 replace_inp_entry(inp, "adress_const_wf", nullptr);
1979 replace_inp_entry(inp, "adress_ex_width", nullptr);
1980 replace_inp_entry(inp, "adress_hy_width", nullptr);
1981 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1982 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1983 replace_inp_entry(inp, "adress_site", nullptr);
1984 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1985 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1986 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1987 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1988 replace_inp_entry(inp, "rlistlong", nullptr);
1989 replace_inp_entry(inp, "nstcalclr", nullptr);
1990 replace_inp_entry(inp, "pull-print-com2", nullptr);
1991 replace_inp_entry(inp, "gb-algorithm", nullptr);
1992 replace_inp_entry(inp, "nstgbradii", nullptr);
1993 replace_inp_entry(inp, "rgbradii", nullptr);
1994 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1995 replace_inp_entry(inp, "gb-saltconc", nullptr);
1996 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1997 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1998 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1999 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
2000 replace_inp_entry(inp, "sa-algorithm", nullptr);
2001 replace_inp_entry(inp, "sa-surface-tension", nullptr);
2002 replace_inp_entry(inp, "ns-type", nullptr);
2004 /* replace the following commands with the clearer new versions*/
2005 replace_inp_entry(inp, "unconstrained-start", "continuation");
2006 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
2007 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
2008 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
2009 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
2010 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
2011 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
2013 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
2014 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
2015 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
2016 setStringEntry(&inp, "include", opts->include, nullptr);
2017 printStringNoNewline(
2018 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
2019 setStringEntry(&inp, "define", opts->define, nullptr);
2021 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
2022 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
2023 printStringNoNewline(&inp, "Start time and timestep in ps");
2024 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
2025 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
2026 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
2027 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
2028 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
2029 printStringNoNewline(
2030 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
2031 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
2032 printStringNoNewline(&inp, "Multiple time-stepping");
2033 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
2036 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
2037 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
2038 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
2039 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
2041 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2042 if (!EI_DYNAMICS(ir->eI))
2047 printStringNoNewline(&inp, "mode for center of mass motion removal");
2048 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
2049 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2050 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2051 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2052 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2054 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2055 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2056 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2057 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2060 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2061 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2062 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2063 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2064 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2065 ir->niter = get_eint(&inp, "niter", 20, wi);
2066 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2067 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2068 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2069 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2070 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2072 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2073 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2075 /* Output options */
2076 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2077 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2078 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2079 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2080 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2081 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2082 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2083 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2084 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2085 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2086 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2087 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2088 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2089 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2090 printStringNoNewline(&inp, "default, all atoms will be written.");
2091 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2092 printStringNoNewline(&inp, "Selection of energy groups");
2093 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2095 /* Neighbor searching */
2096 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2097 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2098 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2099 printStringNoNewline(&inp, "nblist update frequency");
2100 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2101 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2102 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2103 std::vector<const char*> pbcTypesNamesChar;
2104 for (const auto& pbcTypeName : c_pbcTypeNames)
2106 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2108 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2109 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2110 printStringNoNewline(&inp,
2111 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2112 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2113 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2114 printStringNoNewline(&inp, "nblist cut-off");
2115 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2116 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2118 /* Electrostatics */
2119 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2120 printStringNoNewline(&inp, "Method for doing electrostatics");
2121 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2122 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2123 printStringNoNewline(&inp, "cut-off lengths");
2124 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2125 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2126 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2127 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2128 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2129 printStringNoNewline(&inp, "Method for doing Van der Waals");
2130 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2131 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2132 printStringNoNewline(&inp, "cut-off lengths");
2133 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2134 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2135 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2136 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2137 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2138 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2139 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2140 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2141 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2142 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2143 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2144 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2145 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2146 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2147 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2148 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2149 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2150 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2151 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2152 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2153 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2155 /* Implicit solvation is no longer supported, but we need grompp
2156 to be able to refuse old .mdp files that would have built a tpr
2157 to run it. Thus, only "no" is accepted. */
2158 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2160 /* Coupling stuff */
2161 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2162 printStringNoNewline(&inp, "Temperature coupling");
2163 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2164 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2165 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2166 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2167 printStringNoNewline(&inp, "Groups to couple separately");
2168 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2169 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2170 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2171 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2172 printStringNoNewline(&inp, "pressure coupling");
2173 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2174 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2175 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2176 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2177 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2178 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2179 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2180 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2181 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2184 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2185 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2186 printStringNoNewline(&inp, "Groups treated with MiMiC");
2187 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2189 /* Simulated annealing */
2190 printStringNewline(&inp, "SIMULATED ANNEALING");
2191 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2192 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2193 printStringNoNewline(&inp,
2194 "Number of time points to use for specifying annealing in each group");
2195 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2196 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2197 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2198 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2199 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2202 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2203 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2204 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2205 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2208 printStringNewline(&inp, "OPTIONS FOR BONDS");
2209 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2210 printStringNoNewline(&inp, "Type of constraint algorithm");
2211 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2212 printStringNoNewline(&inp, "Do not constrain the start configuration");
2213 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2214 printStringNoNewline(&inp,
2215 "Use successive overrelaxation to reduce the number of shake iterations");
2216 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2217 printStringNoNewline(&inp, "Relative tolerance of shake");
2218 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2219 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2220 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2221 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2222 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2223 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2224 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2225 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2226 printStringNoNewline(&inp, "rotates over more degrees than");
2227 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2228 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2229 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2231 /* Energy group exclusions */
2232 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2233 printStringNoNewline(
2234 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2235 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2238 printStringNewline(&inp, "WALLS");
2239 printStringNoNewline(
2240 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2241 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2242 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2243 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2244 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2245 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2246 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2249 printStringNewline(&inp, "COM PULLING");
2250 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2253 ir->pull = std::make_unique<pull_params_t>();
2254 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2258 for (int c = 0; c < ir->pull->ncoord; c++)
2260 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2263 "Constraint COM pulling is not supported in combination with "
2264 "multiple time stepping");
2272 NOTE: needs COM pulling or free energy input */
2273 printStringNewline(&inp, "AWH biasing");
2274 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2277 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
2280 /* Enforced rotation */
2281 printStringNewline(&inp, "ENFORCED ROTATION");
2282 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2283 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2287 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2290 /* Interactive MD */
2292 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2293 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2294 if (inputrecStrings->imd_grp[0] != '\0')
2301 printStringNewline(&inp, "NMR refinement stuff");
2302 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2303 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2304 printStringNoNewline(
2305 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2306 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2307 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2308 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2309 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2310 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2311 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2312 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2313 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2314 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2315 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2316 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2317 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2318 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2319 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2320 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2322 /* free energy variables */
2323 printStringNewline(&inp, "Free energy variables");
2324 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2325 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2326 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2327 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2328 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2330 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2332 it was not entered */
2333 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2334 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2335 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2336 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2337 setStringEntry(&inp, "fep-lambdas", "");
2338 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2339 setStringEntry(&inp, "mass-lambdas", "");
2340 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2341 setStringEntry(&inp, "coul-lambdas", "");
2342 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2343 setStringEntry(&inp, "vdw-lambdas", "");
2344 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2345 setStringEntry(&inp, "bonded-lambdas", "");
2346 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2347 setStringEntry(&inp, "restraint-lambdas", "");
2348 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2349 setStringEntry(&inp, "temperature-lambdas", "");
2350 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2351 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2352 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2353 fep->softcoreFunction = getEnum<SoftcoreType>(&inp, "sc-function", wi);
2354 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2355 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2356 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2357 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2358 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2359 fep->scGapsysScaleLinpointLJ = get_ereal(&inp, "sc-gapsys-scale-linpoint-lj", 0.85, wi);
2360 fep->scGapsysScaleLinpointQ = get_ereal(&inp, "sc-gapsys-scale-linpoint-q", 0.3, wi);
2361 fep->scGapsysSigmaLJ = get_ereal(&inp, "sc-gapsys-sigma-lj", 0.3, wi);
2362 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2363 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2364 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2365 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2366 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2367 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2369 /* Non-equilibrium MD stuff */
2370 printStringNewline(&inp, "Non-equilibrium MD stuff");
2371 setStringEntry(&inp, "acc-grps", inputrecStrings->accelerationGroups, nullptr);
2372 setStringEntry(&inp, "accelerate", inputrecStrings->acceleration, nullptr);
2373 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2374 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2375 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2376 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2378 /* simulated tempering variables */
2379 printStringNewline(&inp, "simulated tempering variables");
2380 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2381 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2382 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2383 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2385 /* expanded ensemble variables */
2386 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2388 read_expandedparams(&inp, expand, wi);
2391 /* Electric fields */
2393 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2394 gmx::KeyValueTreeTransformer transform;
2395 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2396 mdModules->initMdpTransform(transform.rules());
2397 for (const auto& path : transform.mappedPaths())
2399 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2400 mark_einp_set(inp, path[0].c_str());
2402 MdpErrorHandler errorHandler(wi);
2403 auto result = transform.transform(convertedValues, &errorHandler);
2404 ir->params = new gmx::KeyValueTreeObject(result.object());
2405 mdModules->adjustInputrecBasedOnModules(ir);
2406 errorHandler.setBackMapping(result.backMapping());
2407 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2410 /* Ion/water position swapping ("computational electrophysiology") */
2411 printStringNewline(&inp,
2412 "Ion/water position swapping for computational electrophysiology setups");
2413 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2414 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2415 if (ir->eSwapCoords != SwapType::No)
2422 printStringNoNewline(&inp, "Swap attempt frequency");
2423 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2424 printStringNoNewline(&inp, "Number of ion types to be controlled");
2425 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2428 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2430 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2431 snew(ir->swap->grp, ir->swap->ngrp);
2432 for (i = 0; i < ir->swap->ngrp; i++)
2434 snew(ir->swap->grp[i].molname, STRLEN);
2436 printStringNoNewline(&inp,
2437 "Two index groups that contain the compartment-partitioning atoms");
2438 setStringEntry(&inp,
2440 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2442 setStringEntry(&inp,
2444 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2446 printStringNoNewline(&inp,
2447 "Use center of mass of split groups (yes/no), otherwise center of "
2448 "geometry is used");
2449 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2450 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2452 printStringNoNewline(&inp, "Name of solvent molecules");
2453 setStringEntry(&inp,
2455 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2458 printStringNoNewline(&inp,
2459 "Split cylinder: radius, upper and lower extension (nm) (this will "
2460 "define the channels)");
2461 printStringNoNewline(&inp,
2462 "Note that the split cylinder settings do not have an influence on "
2463 "the swapping protocol,");
2464 printStringNoNewline(
2466 "however, if correctly defined, the permeation events are recorded per channel");
2467 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2468 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2469 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2470 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2471 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2472 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2474 printStringNoNewline(
2476 "Average the number of ions per compartment over these many swap attempt steps");
2477 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2479 printStringNoNewline(
2480 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2481 printStringNoNewline(
2482 &inp, "and the requested number of ions of this type in compartments A and B");
2483 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2484 for (i = 0; i < nIonTypes; i++)
2486 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2488 sprintf(buf, "iontype%d-name", i);
2489 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2490 sprintf(buf, "iontype%d-in-A", i);
2491 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2492 sprintf(buf, "iontype%d-in-B", i);
2493 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2496 printStringNoNewline(
2498 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2499 printStringNoNewline(
2501 "at maximum distance (= bulk concentration) to the split group layers. However,");
2502 printStringNoNewline(&inp,
2503 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2504 "layer from the middle at 0.0");
2505 printStringNoNewline(&inp,
2506 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2507 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2508 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2509 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2510 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2512 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2515 printStringNoNewline(
2516 &inp, "Start to swap ions if threshold difference to requested count is reached");
2517 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2520 /* AdResS is no longer supported, but we need grompp to be able to
2521 refuse to process old .mdp files that used it. */
2522 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2524 /* User defined thingies */
2525 printStringNewline(&inp, "User defined thingies");
2526 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2527 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2528 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2529 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2530 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2531 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2532 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2533 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2534 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2535 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2540 gmx::TextOutputFile stream(mdparout);
2541 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2543 // Transform module data into a flat key-value tree for output.
2544 gmx::KeyValueTreeBuilder builder;
2545 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2546 mdModules->buildMdpOutput(&builderObject);
2548 gmx::TextWriter writer(&stream);
2549 writeKeyValueTreeAsMdp(&writer, builder.build());
2554 /* Process options if necessary */
2555 for (m = 0; m < 2; m++)
2557 for (i = 0; i < 2 * DIM; i++)
2561 if (ir->epc != PressureCoupling::No)
2565 case PressureCouplingType::Isotropic:
2566 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2570 "Pressure coupling incorrect number of values (I need exactly 1)");
2572 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2574 case PressureCouplingType::SemiIsotropic:
2575 case PressureCouplingType::SurfaceTension:
2576 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2580 "Pressure coupling incorrect number of values (I need exactly 2)");
2582 dumdub[m][YY] = dumdub[m][XX];
2584 case PressureCouplingType::Anisotropic:
2585 if (sscanf(dumstr[m],
2586 "%lf%lf%lf%lf%lf%lf",
2597 "Pressure coupling incorrect number of values (I need exactly 6)");
2602 "Pressure coupling type %s not implemented yet",
2603 enumValueToString(ir->epct));
2607 clear_mat(ir->ref_p);
2608 clear_mat(ir->compress);
2609 for (i = 0; i < DIM; i++)
2611 ir->ref_p[i][i] = dumdub[1][i];
2612 ir->compress[i][i] = dumdub[0][i];
2614 if (ir->epct == PressureCouplingType::Anisotropic)
2616 ir->ref_p[XX][YY] = dumdub[1][3];
2617 ir->ref_p[XX][ZZ] = dumdub[1][4];
2618 ir->ref_p[YY][ZZ] = dumdub[1][5];
2619 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2622 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2623 "apply a threefold shear stress?\n");
2625 ir->compress[XX][YY] = dumdub[0][3];
2626 ir->compress[XX][ZZ] = dumdub[0][4];
2627 ir->compress[YY][ZZ] = dumdub[0][5];
2628 for (i = 0; i < DIM; i++)
2630 for (m = 0; m < i; m++)
2632 ir->ref_p[i][m] = ir->ref_p[m][i];
2633 ir->compress[i][m] = ir->compress[m][i];
2638 if (ir->comm_mode == ComRemovalAlgorithm::No)
2643 opts->couple_moltype = nullptr;
2644 if (strlen(inputrecStrings->couple_moltype) > 0)
2646 if (ir->efep != FreeEnergyPerturbationType::No)
2648 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2649 if (opts->couple_lam0 == opts->couple_lam1)
2651 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2653 if (ir->eI == IntegrationAlgorithm::MD
2654 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2658 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2665 "Free energy is turned off, so we will not decouple the molecule listed "
2669 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2670 if (ir->efep != FreeEnergyPerturbationType::No)
2672 if (fep->delta_lambda != 0)
2674 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2678 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2680 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2682 "Old option for dhdl-print-energy given: "
2683 "changing \"yes\" to \"total\"\n");
2686 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2688 /* always print out the energy to dhdl if we are doing
2689 expanded ensemble, since we need the total energy for
2690 analysis if the temperature is changing. In some
2691 conditions one may only want the potential energy, so
2692 we will allow that if the appropriate mdp setting has
2693 been enabled. Otherwise, total it is:
2695 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2698 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2700 ir->bExpanded = FALSE;
2701 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2703 ir->bExpanded = TRUE;
2705 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2706 if (ir->bSimTemp) /* done after fep params */
2708 do_simtemp_params(ir);
2711 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2712 * setup and not on the old way of specifying the free-energy setup,
2713 * we should check for using soft-core when not needed, since that
2714 * can complicate the sampling significantly.
2715 * Note that we only check for the automated coupling setup.
2716 * If the (advanced) user does FEP through manual topology changes,
2717 * this check will not be triggered.
2719 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2720 && ir->fepvals->sc_alpha != 0
2721 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2724 "You are using soft-core interactions while the Van der Waals interactions are "
2725 "not decoupled (note that the sc-coul option is only active when using lambda "
2726 "states). Although this will not lead to errors, you will need much more "
2727 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2732 ir->fepvals->n_lambda = 0;
2735 /* WALL PARAMETERS */
2737 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2739 /* ORIENTATION RESTRAINT PARAMETERS */
2741 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2743 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2746 /* DEFORMATION PARAMETERS */
2748 clear_mat(ir->deform);
2749 for (i = 0; i < 6; i++)
2754 double gmx_unused canary;
2755 int ndeform = sscanf(inputrecStrings->deform,
2756 "%lf %lf %lf %lf %lf %lf %lf",
2765 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2769 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2770 inputrecStrings->deform)
2773 for (i = 0; i < 3; i++)
2775 ir->deform[i][i] = dumdub[0][i];
2777 ir->deform[YY][XX] = dumdub[0][3];
2778 ir->deform[ZZ][XX] = dumdub[0][4];
2779 ir->deform[ZZ][YY] = dumdub[0][5];
2780 if (ir->epc != PressureCoupling::No)
2782 for (i = 0; i < 3; i++)
2784 for (j = 0; j <= i; j++)
2786 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2788 warning_error(wi, "A box element has deform set and compressibility > 0");
2792 for (i = 0; i < 3; i++)
2794 for (j = 0; j < i; j++)
2796 if (ir->deform[i][j] != 0)
2798 for (m = j; m < DIM; m++)
2800 if (ir->compress[m][j] != 0)
2803 "An off-diagonal box element has deform set while "
2804 "compressibility > 0 for the same component of another box "
2805 "vector, this might lead to spurious periodicity effects.");
2806 warning(wi, warn_buf);
2814 /* Ion/water position swapping checks */
2815 if (ir->eSwapCoords != SwapType::No)
2817 if (ir->swap->nstswap < 1)
2819 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2821 if (ir->swap->nAverage < 1)
2823 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2825 if (ir->swap->threshold < 1.0)
2827 warning_error(wi, "Ion count threshold must be at least 1.\n");
2831 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2834 std::vector<std::string> errorMessages;
2835 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2837 for (const auto& errorMessage : errorMessages)
2839 warning_error(wi, errorMessage.c_str());
2845 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2852 int search_string(const char* s, int ng, char* const gn[])
2856 for (i = 0; (i < ng); i++)
2858 if (gmx_strcasecmp(s, gn[i]) == 0)
2865 "Group %s referenced in the .mdp file was not found in the index file.\n"
2866 "Group names must match either [moleculetype] names or custom index group\n"
2867 "names, in which case you must supply an index file to the '-n' option\n"
2872 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2874 /* Now go over the atoms in the group */
2875 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2877 int aj = block.a[j];
2879 /* Range checking */
2880 if ((aj < 0) || (aj >= natoms))
2882 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2887 /*! Creates the groups of atom indices for group type \p gtype
2889 * \param[in] natoms The total number of atoms in the system
2890 * \param[in,out] groups Index \p gtype in this list of list of groups will be set
2891 * \param[in] groupsFromMdpFile The list of group names set for \p gtype in the mdp file
2892 * \param[in] block The list of atom indices for all available index groups
2893 * \param[in] gnames The list of names for all available index groups
2894 * \param[in] gtype The group type to creates groups for
2895 * \param[in] restnm The index of rest group name in \p gnames
2896 * \param[in] coverage How to treat coverage of all atoms in the system
2897 * \param[in] bVerbose Whether to print when we make a rest group
2898 * \param[in,out] wi List of warnings
2900 static void do_numbering(const int natoms,
2901 SimulationGroups* groups,
2902 gmx::ArrayRef<const std::string> groupsFromMdpFile,
2903 const t_blocka* block,
2904 char* const gnames[],
2905 const SimulationAtomGroupType gtype,
2907 const GroupCoverage coverage,
2908 const bool bVerbose,
2911 unsigned short* cbuf;
2912 AtomGroupIndices* grps = &(groups->groups[gtype]);
2915 char warn_buf[STRLEN];
2917 title = shortName(gtype);
2920 /* Mark all id's as not set */
2921 for (int i = 0; (i < natoms); i++)
2926 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2928 /* Lookup the group name in the block structure */
2929 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2930 if ((coverage != GroupCoverage::OneGroup) || (i == 0))
2932 grps->emplace_back(gid);
2934 GMX_ASSERT(block, "Can't have a nullptr block");
2935 atomGroupRangeValidation(natoms, gid, *block);
2936 /* Now go over the atoms in the group */
2937 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2939 const int aj = block->a[j];
2940 /* Lookup up the old group number */
2941 const int ognr = cbuf[aj];
2944 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2948 /* Store the group number in buffer */
2949 if (coverage == GroupCoverage::OneGroup)
2962 /* Now check whether we have done all atoms */
2965 if (coverage == GroupCoverage::All)
2967 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2969 else if (coverage == GroupCoverage::Partial)
2971 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2972 warning_note(wi, warn_buf);
2974 /* Assign all atoms currently unassigned to a rest group */
2975 for (int j = 0; (j < natoms); j++)
2977 if (cbuf[j] == NOGID)
2979 cbuf[j] = grps->size();
2982 if (coverage != GroupCoverage::Partial)
2986 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2988 /* Add group name "rest" */
2989 grps->emplace_back(restnm);
2991 /* Assign the rest name to all atoms not currently assigned to a group */
2992 for (int j = 0; (j < natoms); j++)
2994 if (cbuf[j] == NOGID)
2996 // group size was not updated before this here, so need to use -1.
2997 cbuf[j] = grps->size() - 1;
3003 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
3005 /* All atoms are part of one (or no) group, no index required */
3006 groups->groupNumbers[gtype].clear();
3010 for (int j = 0; (j < natoms); j++)
3012 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
3019 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
3022 pull_params_t* pull;
3023 int natoms, imin, jmin;
3024 int * nrdf2, *na_vcm, na_tot;
3025 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
3030 * First calc 3xnr-atoms for each group
3031 * then subtract half a degree of freedom for each constraint
3033 * Only atoms and nuclei contribute to the degrees of freedom...
3038 const SimulationGroups& groups = mtop->groups;
3039 natoms = mtop->natoms;
3041 /* Allocate one more for a possible rest group */
3042 /* We need to sum degrees of freedom into doubles,
3043 * since floats give too low nrdf's above 3 million atoms.
3045 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
3046 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3047 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3048 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3049 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3051 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3055 for (gmx::index i = 0;
3056 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3060 clear_ivec(dof_vcm[i]);
3062 nrdf_vcm_sub[i] = 0;
3064 snew(nrdf2, natoms);
3065 for (const AtomProxy atomP : AtomRange(*mtop))
3067 const t_atom& local = atomP.atom();
3068 int i = atomP.globalAtomNumber();
3070 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3072 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3073 for (int d = 0; d < DIM; d++)
3075 if (opts->nFreeze[g][d] == 0)
3077 /* Add one DOF for particle i (counted as 2*1) */
3079 /* VCM group i has dim d as a DOF */
3080 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3084 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3086 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3092 for (const gmx_molblock_t& molb : mtop->molblock)
3094 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3095 const t_atom* atom = molt.atoms.atom;
3096 for (int mol = 0; mol < molb.nmol; mol++)
3098 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3100 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3101 for (int i = 0; i < molt.ilist[ftype].size();)
3103 /* Subtract degrees of freedom for the constraints,
3104 * if the particles still have degrees of freedom left.
3105 * If one of the particles is a vsite or a shell, then all
3106 * constraint motion will go there, but since they do not
3107 * contribute to the constraints the degrees of freedom do not
3110 int ai = as + ia[i + 1];
3111 int aj = as + ia[i + 2];
3112 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3113 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3114 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3115 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3133 imin = std::min(imin, nrdf2[ai]);
3134 jmin = std::min(jmin, nrdf2[aj]);
3137 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3139 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3141 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3143 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3146 i += interaction_function[ftype].nratoms + 1;
3149 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3150 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3152 /* Subtract 1 dof from every atom in the SETTLE */
3153 for (int j = 0; j < 3; j++)
3155 int ai = as + ia[i + 1 + j];
3156 imin = std::min(2, nrdf2[ai]);
3158 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3160 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3165 as += molt.atoms.nr;
3171 /* Correct nrdf for the COM constraints.
3172 * We correct using the TC and VCM group of the first atom
3173 * in the reference and pull group. If atoms in one pull group
3174 * belong to different TC or VCM groups it is anyhow difficult
3175 * to determine the optimal nrdf assignment.
3177 pull = ir->pull.get();
3179 for (int i = 0; i < pull->ncoord; i++)
3181 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3188 for (int j = 0; j < 2; j++)
3190 const t_pull_group* pgrp;
3192 pgrp = &pull->group[pull->coord[i].group[j]];
3194 if (!pgrp->ind.empty())
3196 /* Subtract 1/2 dof from each group */
3197 int ai = pgrp->ind[0];
3198 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3200 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3202 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3205 "Center of mass pulling constraints caused the number of degrees "
3206 "of freedom for temperature coupling group %s to be negative",
3207 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3208 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3213 /* We need to subtract the whole DOF from group j=1 */
3220 if (ir->nstcomm != 0)
3222 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3223 "Expect at least one group when removing COM motion");
3225 /* We remove COM motion up to dim ndof_com() */
3226 const int ndim_rm_vcm = ndof_com(ir);
3228 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3229 * the number of degrees of freedom in each vcm group when COM
3230 * translation is removed and 6 when rotation is removed as well.
3231 * Note that we do not and should not include the rest group here.
3233 for (gmx::index j = 0;
3234 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3237 switch (ir->comm_mode)
3239 case ComRemovalAlgorithm::Linear:
3240 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3241 nrdf_vcm_sub[j] = 0;
3242 for (int d = 0; d < ndim_rm_vcm; d++)
3250 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3251 default: gmx_incons("Checking comm_mode");
3255 for (gmx::index i = 0;
3256 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3259 /* Count the number of atoms of TC group i for every VCM group */
3260 for (gmx::index j = 0;
3261 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3267 for (int ai = 0; ai < natoms; ai++)
3269 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3271 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3275 /* Correct for VCM removal according to the fraction of each VCM
3276 * group present in this TC group.
3278 nrdf_uc = nrdf_tc[i];
3280 for (gmx::index j = 0;
3281 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3284 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3286 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3287 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3292 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3294 opts->nrdf[i] = nrdf_tc[i];
3295 if (opts->nrdf[i] < 0)
3300 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3301 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3310 sfree(nrdf_vcm_sub);
3313 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3315 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3316 * But since this is much larger than STRLEN, such a line can not be parsed.
3317 * The real maximum is the number of names that fit in a string: STRLEN/2.
3322 auto names = gmx::splitString(val);
3323 if (names.size() % 2 != 0)
3325 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3327 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3329 for (size_t i = 0; i < names.size() / 2; i++)
3331 // TODO this needs to be replaced by a solution using std::find_if
3335 names[2 * i].c_str(),
3336 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3342 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3347 names[2 * i + 1].c_str(),
3348 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3354 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3356 if ((j < nr) && (k < nr))
3358 ir->opts.egp_flags[nr * j + k] |= flag;
3359 ir->opts.egp_flags[nr * k + j] |= flag;
3368 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3370 int ig = -1, i = 0, gind;
3374 /* Just a quick check here, more thorough checks are in mdrun */
3375 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3376 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3380 "The split groups can not both be '%s'.",
3381 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3384 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3385 for (ig = 0; ig < swap->ngrp; ig++)
3387 swapg = &swap->grp[ig];
3388 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3389 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3394 "%s group '%s' contains %d atoms.\n",
3395 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3396 swap->grp[ig].molname,
3398 snew(swapg->ind, swapg->nat);
3399 for (i = 0; i < swapg->nat; i++)
3401 swapg->ind[i] = grps->a[grps->index[gind] + i];
3406 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3412 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3417 ig = search_string(IMDgname, grps->nr, gnames);
3418 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3420 if (IMDgroup->nat > 0)
3423 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3427 snew(IMDgroup->ind, IMDgroup->nat);
3428 for (i = 0; i < IMDgroup->nat; i++)
3430 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3435 /* Checks whether atoms are both part of a COM removal group and frozen.
3436 * If a fully frozen atom is part of a COM removal group, it is removed
3437 * from the COM removal group. A note is issued if such atoms are present.
3438 * A warning is issued for atom with one or two dimensions frozen that
3439 * are part of a COM removal group (mdrun would need to compute COM mass
3440 * per dimension to handle this correctly).
3441 * Also issues a warning when non-frozen atoms are not part of a COM
3442 * removal group while COM removal is active.
3444 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3446 const t_grpopts& opts,
3449 const int vcmRestGroup =
3450 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3452 int numFullyFrozenVcmAtoms = 0;
3453 int numPartiallyFrozenVcmAtoms = 0;
3454 int numNonVcmAtoms = 0;
3455 for (int a = 0; a < numAtoms; a++)
3457 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3458 int numFrozenDims = 0;
3459 for (int d = 0; d < DIM; d++)
3461 numFrozenDims += opts.nFreeze[freezeGroup][d];
3464 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3465 if (vcmGroup < vcmRestGroup)
3467 if (numFrozenDims == DIM)
3469 /* Do not remove COM motion for this fully frozen atom */
3470 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3472 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3475 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3476 numFullyFrozenVcmAtoms++;
3478 else if (numFrozenDims > 0)
3480 numPartiallyFrozenVcmAtoms++;
3483 else if (numFrozenDims < DIM)
3489 if (numFullyFrozenVcmAtoms > 0)
3491 std::string warningText = gmx::formatString(
3492 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3493 "removing these atoms from the COMM removal group(s)",
3494 numFullyFrozenVcmAtoms);
3495 warning_note(wi, warningText.c_str());
3497 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3499 std::string warningText = gmx::formatString(
3500 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3501 "removal group(s), due to limitations in the code these still contribute to the "
3502 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3504 numPartiallyFrozenVcmAtoms,
3506 warning(wi, warningText.c_str());
3508 if (numNonVcmAtoms > 0)
3510 std::string warningText = gmx::formatString(
3511 "%d atoms are not part of any center of mass motion removal group.\n"
3512 "This may lead to artifacts.\n"
3513 "In most cases one should use one group for the whole system.",
3515 warning(wi, warningText.c_str());
3519 void do_index(const char* mdparin,
3523 const gmx::MDModulesNotifiers& mdModulesNotifiers,
3527 t_blocka* defaultIndexGroups;
3535 int i, j, k, restnm;
3536 bool bExcl, bTable, bAnneal;
3537 char warn_buf[STRLEN];
3541 fprintf(stderr, "processing index file...\n");
3545 snew(defaultIndexGroups, 1);
3546 snew(defaultIndexGroups->index, 1);
3548 atoms_all = gmx_mtop_global_atoms(*mtop);
3549 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3550 done_atom(&atoms_all);
3554 defaultIndexGroups = init_index(ndx, &gnames);
3557 SimulationGroups* groups = &mtop->groups;
3558 natoms = mtop->natoms;
3559 symtab = &mtop->symtab;
3561 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3563 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3565 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3566 restnm = groups->groupNames.size() - 1;
3567 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3568 srenew(gnames, defaultIndexGroups->nr + 1);
3569 gnames[restnm] = *(groups->groupNames.back());
3571 set_warning_line(wi, mdparin, -1);
3573 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3574 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3575 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3576 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3577 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3580 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3582 temperatureCouplingGroupNames.size(),
3583 temperatureCouplingReferenceValues.size(),
3584 temperatureCouplingTauValues.size());
3587 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3588 do_numbering(natoms,
3590 temperatureCouplingGroupNames,
3593 SimulationAtomGroupType::TemperatureCoupling,
3595 useReferenceTemperature ? GroupCoverage::All : GroupCoverage::AllGenerateRest,
3598 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3600 snew(ir->opts.nrdf, nr);
3601 snew(ir->opts.tau_t, nr);
3602 snew(ir->opts.ref_t, nr);
3603 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3605 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3608 if (useReferenceTemperature)
3610 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3612 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3616 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3617 for (i = 0; (i < nr); i++)
3619 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3622 "With integrator %s tau-t should be larger than 0",
3623 enumValueToString(ir->eI));
3624 warning_error(wi, warn_buf);
3627 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3631 "tau-t = -1 is the value to signal that a group should not have "
3632 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3635 if (ir->opts.tau_t[i] >= 0)
3637 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3640 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3642 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3647 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3650 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3651 "md-vv; use either vrescale temperature with berendsen pressure or "
3652 "Nose-Hoover temperature with MTTK pressure");
3654 if (ir->epc == PressureCoupling::Mttk)
3656 if (ir->etc != TemperatureCoupling::NoseHoover)
3659 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3664 if (ir->nstpcouple != ir->nsttcouple)
3666 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3667 ir->nstpcouple = ir->nsttcouple = mincouple;
3669 "for current Trotter decomposition methods with vv, nsttcouple and "
3670 "nstpcouple must be equal. Both have been reset to "
3671 "min(nsttcouple,nstpcouple) = %d",
3673 warning_note(wi, warn_buf);
3678 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3679 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3681 if (ETC_ANDERSEN(ir->etc))
3683 if (ir->nsttcouple != 1)
3687 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3688 "need for larger nsttcouple > 1, since no global parameters are computed. "
3689 "nsttcouple has been reset to 1");
3690 warning_note(wi, warn_buf);
3693 nstcmin = tcouple_min_integration_steps(ir->etc);
3696 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3699 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3700 "least %d times larger than nsttcouple*dt (%g)",
3701 enumValueToString(ir->etc),
3704 ir->nsttcouple * ir->delta_t);
3705 warning(wi, warn_buf);
3708 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3709 for (i = 0; (i < nr); i++)
3711 if (ir->opts.ref_t[i] < 0)
3713 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3716 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3717 if we are in this conditional) if mc_temp is negative */
3718 if (ir->expandedvals->mc_temp < 0)
3720 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3724 /* Simulated annealing for each group. There are nr groups */
3725 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3726 if (simulatedAnnealingGroupNames.size() == 1
3727 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3729 simulatedAnnealingGroupNames.resize(0);
3731 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3734 "Wrong number of annealing values: %zu (for %d groups)\n",
3735 simulatedAnnealingGroupNames.size(),
3740 snew(ir->opts.annealing, nr);
3741 snew(ir->opts.anneal_npoints, nr);
3742 snew(ir->opts.anneal_time, nr);
3743 snew(ir->opts.anneal_temp, nr);
3744 for (i = 0; i < nr; i++)
3746 ir->opts.annealing[i] = SimulatedAnnealing::No;
3747 ir->opts.anneal_npoints[i] = 0;
3748 ir->opts.anneal_time[i] = nullptr;
3749 ir->opts.anneal_temp[i] = nullptr;
3751 if (!simulatedAnnealingGroupNames.empty())
3754 for (i = 0; i < nr; i++)
3756 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3758 ir->opts.annealing[i] = SimulatedAnnealing::No;
3760 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3762 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3765 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3767 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3773 /* Read the other fields too */
3774 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3775 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3778 "Found %zu annealing-npoints values for %zu groups\n",
3779 simulatedAnnealingPoints.size(),
3780 simulatedAnnealingGroupNames.size());
3782 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3783 size_t numSimulatedAnnealingFields = 0;
3784 for (i = 0; i < nr; i++)
3786 if (ir->opts.anneal_npoints[i] == 1)
3790 "Please specify at least a start and an end point for annealing\n");
3792 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3793 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3794 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3797 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3799 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3802 "Found %zu annealing-time values, wanted %zu\n",
3803 simulatedAnnealingTimes.size(),
3804 numSimulatedAnnealingFields);
3806 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3807 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3810 "Found %zu annealing-temp values, wanted %zu\n",
3811 simulatedAnnealingTemperatures.size(),
3812 numSimulatedAnnealingFields);
3815 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3816 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3817 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3819 simulatedAnnealingTemperatures,
3821 allSimulatedAnnealingTemperatures.data());
3822 for (i = 0, k = 0; i < nr; i++)
3824 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3826 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3827 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3830 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3832 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3838 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3841 "Annealing timepoints out of order: t=%f comes after "
3843 ir->opts.anneal_time[i][j],
3844 ir->opts.anneal_time[i][j - 1]);
3847 if (ir->opts.anneal_temp[i][j] < 0)
3850 "Found negative temperature in annealing: %f\n",
3851 ir->opts.anneal_temp[i][j]);
3856 /* Print out some summary information, to make sure we got it right */
3857 for (i = 0; i < nr; i++)
3859 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3861 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3863 "Simulated annealing for group %s: %s, %d timepoints\n",
3864 *(groups->groupNames[j]),
3865 enumValueToString(ir->opts.annealing[i]),
3866 ir->opts.anneal_npoints[i]);
3867 fprintf(stderr, "Time (ps) Temperature (K)\n");
3868 /* All terms except the last one */
3869 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3873 ir->opts.anneal_time[i][j],
3874 ir->opts.anneal_temp[i][j]);
3877 /* Finally the last one */
3878 j = ir->opts.anneal_npoints[i] - 1;
3879 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3883 ir->opts.anneal_time[i][j],
3884 ir->opts.anneal_temp[i][j]);
3890 ir->opts.anneal_time[i][j],
3891 ir->opts.anneal_temp[i][j]);
3892 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3895 "There is a temperature jump when your annealing "
3907 for (int i = 1; i < ir->pull->ngroup; i++)
3909 const int gid = search_string(
3910 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3911 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3912 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3915 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3917 checkPullCoords(ir->pull->group, ir->pull->coord);
3922 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3925 if (ir->eSwapCoords != SwapType::No)
3927 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3930 /* Make indices for IMD session */
3933 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3936 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3937 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3938 mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
3940 auto accelerations = gmx::splitString(inputrecStrings->acceleration);
3941 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accelerationGroups);
3942 if (accelerationGroupNames.size() * DIM != accelerations.size())
3945 "Invalid Acceleration input: %zu groups and %zu acc. values",
3946 accelerationGroupNames.size(),
3947 accelerations.size());
3949 do_numbering(natoms,
3951 accelerationGroupNames,
3954 SimulationAtomGroupType::Acceleration,
3956 GroupCoverage::AllGenerateRest,
3959 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3960 snew(ir->opts.acceleration, nr);
3961 ir->opts.ngacc = nr;
3963 convertRvecs(wi, accelerations, "accelerations", ir->opts.acceleration);
3965 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3966 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3967 if (freezeDims.size() != DIM * freezeGroupNames.size())
3970 "Invalid Freezing input: %zu groups and %zu freeze values",
3971 freezeGroupNames.size(),
3974 do_numbering(natoms,
3979 SimulationAtomGroupType::Freeze,
3981 GroupCoverage::AllGenerateRest,
3984 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3985 ir->opts.ngfrz = nr;
3986 snew(ir->opts.nFreeze, nr);
3987 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3989 for (j = 0; (j < DIM); j++, k++)
3991 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3992 if (!ir->opts.nFreeze[i][j])
3994 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3997 "Please use Y(ES) or N(O) for freezedim only "
3999 freezeDims[k].c_str());
4000 warning(wi, warn_buf);
4005 for (; (i < nr); i++)
4007 for (j = 0; (j < DIM); j++)
4009 ir->opts.nFreeze[i][j] = 0;
4013 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
4014 do_numbering(natoms,
4019 SimulationAtomGroupType::EnergyOutput,
4021 GroupCoverage::AllGenerateRest,
4024 add_wall_energrps(groups, ir->nwall, symtab);
4025 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4026 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
4027 do_numbering(natoms,
4032 SimulationAtomGroupType::MassCenterVelocityRemoval,
4034 vcmGroupNames.empty() ? GroupCoverage::AllGenerateRest : GroupCoverage::Partial,
4038 if (ir->comm_mode != ComRemovalAlgorithm::No)
4040 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
4043 /* Now we have filled the freeze struct, so we can calculate NRDF */
4044 calc_nrdf(mtop, ir, gnames);
4046 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
4047 do_numbering(natoms,
4052 SimulationAtomGroupType::User1,
4054 GroupCoverage::AllGenerateRest,
4057 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
4058 do_numbering(natoms,
4063 SimulationAtomGroupType::User2,
4065 GroupCoverage::AllGenerateRest,
4068 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
4069 do_numbering(natoms,
4071 compressedXGroupNames,
4074 SimulationAtomGroupType::CompressedPositionOutput,
4076 GroupCoverage::OneGroup,
4079 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
4080 do_numbering(natoms,
4082 orirefFitGroupNames,
4085 SimulationAtomGroupType::OrientationRestraintsFit,
4087 GroupCoverage::AllGenerateRest,
4091 /* MiMiC QMMM input processing */
4092 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4093 if (qmGroupNames.size() > 1)
4095 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4097 /* group rest, if any, is always MM! */
4098 do_numbering(natoms,
4103 SimulationAtomGroupType::QuantumMechanics,
4105 GroupCoverage::AllGenerateRest,
4108 ir->opts.ngQM = qmGroupNames.size();
4110 /* end of MiMiC QMMM input */
4114 for (auto group : gmx::keysOf(groups->groups))
4116 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4117 for (const auto& entry : groups->groups[group])
4119 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4121 fprintf(stderr, "\n");
4125 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4126 snew(ir->opts.egp_flags, nr * nr);
4128 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4129 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4131 warning_error(wi, "Energy group exclusions are currently not supported");
4133 if (bExcl && EEL_FULL(ir->coulombtype))
4135 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4138 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4139 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4140 && !(ir->coulombtype == CoulombInteractionType::User)
4141 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4142 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4145 "Can only have energy group pair tables in combination with user tables for VdW "
4149 /* final check before going out of scope if simulated tempering variables
4150 * need to be set to default values.
4152 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4154 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4157 "the value for nstexpanded was not specified for "
4158 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4159 "by default, but it is recommended to set it to an explicit value!",
4160 ir->expandedvals->nstexpanded));
4162 for (i = 0; (i < defaultIndexGroups->nr); i++)
4167 done_blocka(defaultIndexGroups);
4168 sfree(defaultIndexGroups);
4172 static void check_disre(const gmx_mtop_t& mtop)
4174 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4176 const gmx_ffparams_t& ffparams = mtop.ffparams;
4179 for (int i = 0; i < ffparams.numTypes(); i++)
4181 int ftype = ffparams.functype[i];
4182 if (ftype == F_DISRES)
4184 int label = ffparams.iparams[i].disres.label;
4185 if (label == old_label)
4187 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4196 "Found %d double distance restraint indices,\n"
4197 "probably the parameters for multiple pairs in one restraint "
4198 "are not identical\n",
4204 //! Returns whether dimensions have an absolute reference due to walls, pbc or freezing
4205 static BasicVector<bool> haveAbsoluteReference(const t_inputrec& ir)
4207 BasicVector<bool> absRef = { false, false, false };
4209 /* Check the degrees of freedom of the COM (not taking COMM removal into account) */
4210 for (int d = 0; d < DIM; d++)
4212 absRef[d] = (d >= ndof_com(&ir));
4214 /* Check for freeze groups */
4215 for (int g = 0; g < ir.opts.ngfrz; g++)
4217 for (int d = 0; d < DIM; d++)
4219 if (ir.opts.nFreeze[g][d] != 0)
4229 //! Returns whether position restraints are used for dimensions
4230 static BasicVector<bool> havePositionRestraints(const gmx_mtop_t& sys)
4232 BasicVector<bool> havePosres = { false, false, false };
4234 for (const auto ilists : IListRange(sys))
4236 const auto& posResList = ilists.list()[F_POSRES];
4237 const auto& fbPosResList = ilists.list()[F_FBPOSRES];
4238 if (ilists.nmol() > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
4240 for (int i = 0; i < posResList.size(); i += 2)
4242 const t_iparams& pr = sys.ffparams.iparams[posResList.iatoms[i]];
4243 for (int d = 0; d < DIM; d++)
4245 if (pr.posres.fcA[d] != 0)
4247 havePosres[d] = true;
4251 for (int i = 0; i < fbPosResList.size(); i += 2)
4253 /* Check for flat-bottom posres */
4254 const t_iparams& pr = sys.ffparams.iparams[fbPosResList.iatoms[i]];
4255 if (pr.fbposres.k != 0)
4257 switch (pr.fbposres.geom)
4259 case efbposresSPHERE: havePosres = { true, true, true }; break;
4260 case efbposresCYLINDERX: havePosres[YY] = havePosres[ZZ] = true; break;
4261 case efbposresCYLINDERY: havePosres[XX] = havePosres[ZZ] = true; break;
4262 case efbposresCYLINDER:
4263 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4264 case efbposresCYLINDERZ: havePosres[XX] = havePosres[YY] = true; break;
4265 case efbposresX: /* d=XX */
4266 case efbposresY: /* d=YY */
4267 case efbposresZ: /* d=ZZ */
4268 havePosres[pr.fbposres.geom - efbposresX] = true;
4272 "Invalid geometry for flat-bottom position restraint.\n"
4273 "Expected nr between 1 and %d. Found %d\n",
4285 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4287 bool* bC6ParametersWorkWithGeometricRules,
4288 bool* bC6ParametersWorkWithLBRules,
4289 bool* bLBRulesPossible)
4291 int ntypes, tpi, tpj;
4294 double c6i, c6j, c12i, c12j;
4295 double c6, c6_geometric, c6_LB;
4296 double sigmai, sigmaj, epsi, epsj;
4297 bool bCanDoLBRules, bCanDoGeometricRules;
4300 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4301 * force-field floating point parameters.
4304 ptr = getenv("GMX_LJCOMB_TOL");
4308 double gmx_unused canary;
4310 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4313 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4318 *bC6ParametersWorkWithLBRules = TRUE;
4319 *bC6ParametersWorkWithGeometricRules = TRUE;
4320 bCanDoLBRules = TRUE;
4321 ntypes = mtop.ffparams.atnr;
4322 snew(typecount, ntypes);
4323 gmx_mtop_count_atomtypes(mtop, state, typecount);
4324 *bLBRulesPossible = TRUE;
4325 for (tpi = 0; tpi < ntypes; ++tpi)
4327 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4328 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4329 for (tpj = tpi; tpj < ntypes; ++tpj)
4331 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4332 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4333 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4334 c6_geometric = std::sqrt(c6i * c6j);
4335 if (!gmx_numzero(c6_geometric))
4337 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4339 sigmai = gmx::sixthroot(c12i / c6i);
4340 sigmaj = gmx::sixthroot(c12j / c6j);
4341 epsi = c6i * c6i / (4.0 * c12i);
4342 epsj = c6j * c6j / (4.0 * c12j);
4343 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4347 *bLBRulesPossible = FALSE;
4348 c6_LB = c6_geometric;
4350 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4355 *bC6ParametersWorkWithLBRules = FALSE;
4358 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4360 if (!bCanDoGeometricRules)
4362 *bC6ParametersWorkWithGeometricRules = FALSE;
4369 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4371 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4373 check_combination_rule_differences(
4374 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4375 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4377 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4380 "You are using arithmetic-geometric combination rules "
4381 "in LJ-PME, but your non-bonded C6 parameters do not "
4382 "follow these rules.");
4387 if (!bC6ParametersWorkWithGeometricRules)
4389 if (ir->eDispCorr != DispersionCorrectionType::No)
4392 "You are using geometric combination rules in "
4393 "LJ-PME, but your non-bonded C6 parameters do "
4394 "not follow these rules. "
4395 "This will introduce very small errors in the forces and energies in "
4396 "your simulations. Dispersion correction will correct total energy "
4397 "and/or pressure for isotropic systems, but not forces or surface "
4403 "You are using geometric combination rules in "
4404 "LJ-PME, but your non-bonded C6 parameters do "
4405 "not follow these rules. "
4406 "This will introduce very small errors in the forces and energies in "
4407 "your simulations. If your system is homogeneous, consider using "
4408 "dispersion correction "
4409 "for the total energy and pressure.");
4415 static bool allTrue(const BasicVector<bool>& boolVector)
4417 return boolVector[0] && boolVector[1] && boolVector[2];
4420 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4422 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4423 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4425 char err_buf[STRLEN];
4429 gmx_mtop_atomloop_block_t aloopb;
4430 char warn_buf[STRLEN];
4432 set_warning_line(wi, mdparin, -1);
4434 if (ir->comm_mode != ComRemovalAlgorithm::No && allTrue(havePositionRestraints(*sys)))
4437 "Removing center of mass motion in the presence of position restraints might "
4438 "cause artifacts. When you are using position restraints to equilibrate a "
4439 "macro-molecule, the artifacts are usually negligible.");
4442 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4443 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4444 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4446 /* Check if a too small Verlet buffer might potentially
4447 * cause more drift than the thermostat can couple off.
4449 /* Temperature error fraction for warning and suggestion */
4450 const real T_error_warn = 0.002;
4451 const real T_error_suggest = 0.001;
4452 /* For safety: 2 DOF per atom (typical with constraints) */
4453 const real nrdf_at = 2;
4454 real T, tau, max_T_error;
4459 for (i = 0; i < ir->opts.ngtc; i++)
4461 T = std::max(T, ir->opts.ref_t[i]);
4462 tau = std::max(tau, ir->opts.tau_t[i]);
4466 /* This is a worst case estimate of the temperature error,
4467 * assuming perfect buffer estimation and no cancelation
4468 * of errors. The factor 0.5 is because energy distributes
4469 * equally over Ekin and Epot.
4471 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4472 if (max_T_error > T_error_warn)
4475 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4476 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4477 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4478 "%.0e or decrease tau_t.",
4483 100 * T_error_suggest,
4484 ir->verletbuf_tol * T_error_suggest / max_T_error);
4485 warning(wi, warn_buf);
4490 if (ETC_ANDERSEN(ir->etc))
4494 for (i = 0; i < ir->opts.ngtc; i++)
4497 "all tau_t must currently be equal using Andersen temperature control, "
4498 "violated for group %d",
4500 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4502 "all tau_t must be positive using Andersen temperature control, "
4506 CHECK(ir->opts.tau_t[i] < 0);
4509 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4511 for (i = 0; i < ir->opts.ngtc; i++)
4513 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4515 "tau_t/delta_t for group %d for temperature control method %s must be a "
4516 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4517 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4520 enumValueToString(ir->etc),
4524 CHECK(nsteps % ir->nstcomm != 0);
4529 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4530 && ir->comm_mode == ComRemovalAlgorithm::No
4531 && !(allTrue(haveAbsoluteReference(*ir)) || allTrue(havePositionRestraints(*sys)) || ir->nsteps <= 10)
4532 && !ETC_ANDERSEN(ir->etc))
4535 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4536 "rounding errors can lead to build up of kinetic energy of the center of mass");
4539 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4542 for (int g = 0; g < ir->opts.ngtc; g++)
4544 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4546 if (ir->tau_p < 1.9 * tau_t_max)
4548 std::string message = gmx::formatString(
4549 "With %s T-coupling and %s p-coupling, "
4550 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4551 enumValueToString(ir->etc),
4552 enumValueToString(ir->epc),
4557 warning(wi, message.c_str());
4561 /* Check for pressure coupling with absolute position restraints */
4562 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4564 const BasicVector<bool> havePosres = havePositionRestraints(*sys);
4566 for (m = 0; m < DIM; m++)
4568 if (havePosres[m] && norm2(ir->compress[m]) > 0)
4571 "You are using pressure coupling with absolute position restraints, "
4572 "this will give artifacts. Use the refcoord_scaling option.");
4580 aloopb = gmx_mtop_atomloop_block_init(*sys);
4582 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4584 if (atom->q != 0 || atom->qB != 0)
4592 if (EEL_FULL(ir->coulombtype))
4595 "You are using full electrostatics treatment %s for a system without charges.\n"
4596 "This costs a lot of performance for just processing zeros, consider using %s "
4598 enumValueToString(ir->coulombtype),
4599 enumValueToString(CoulombInteractionType::Cut));
4600 warning(wi, err_buf);
4605 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4608 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4609 "You might want to consider using %s electrostatics.\n",
4610 enumValueToString(CoulombInteractionType::Pme));
4611 warning_note(wi, err_buf);
4615 /* Check if combination rules used in LJ-PME are the same as in the force field */
4616 if (EVDW_PME(ir->vdwtype))
4618 check_combination_rules(ir, *sys, wi);
4621 /* Generalized reaction field */
4622 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4625 "Generalized reaction-field electrostatics is no longer supported. "
4626 "You can use normal reaction-field instead and compute the reaction-field "
4627 "constant by hand.");
4630 ir->useConstantAcceleration = false;
4631 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4633 if (norm2(ir->opts.acceleration[i]) != 0)
4635 ir->useConstantAcceleration = true;
4638 if (ir->useConstantAcceleration)
4640 gmx::RVec acceleration = { 0.0_real, 0.0_real, 0.0_real };
4641 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4642 for (const AtomProxy atomP : AtomRange(*sys))
4644 const t_atom& local = atomP.atom();
4645 int i = atomP.globalAtomNumber();
4646 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4649 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4651 for (m = 0; (m < DIM); m++)
4653 acceleration[m] += ir->opts.acceleration[i][m] * mgrp[i];
4657 for (m = 0; (m < DIM); m++)
4659 if (fabs(acceleration[m]) > 1e-6)
4661 const char* dim[DIM] = { "X", "Y", "Z" };
4663 "Net Acceleration in %s direction, will %s be corrected\n",
4665 ir->nstcomm != 0 ? "" : "not");
4666 if (ir->nstcomm != 0 && m < ndof_com(ir))
4668 acceleration[m] /= mt;
4670 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration]));
4673 ir->opts.acceleration[i][m] -= acceleration[m];
4681 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4682 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4684 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4692 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4694 if (ir->pull->coord[i].eGeom != PullGroupGeometry::Transformation
4695 && (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0))
4697 const auto absRef = haveAbsoluteReference(*ir);
4698 const auto havePosres = havePositionRestraints(*sys);
4699 for (m = 0; m < DIM; m++)
4701 if (ir->pull->coord[i].dim[m] && !(absRef[m] || havePosres[m]))
4704 "You are using an absolute reference for pulling, but the rest of "
4705 "the system does not have an absolute reference. This will lead to "
4714 for (i = 0; i < 3; i++)
4716 for (m = 0; m <= i; m++)
4718 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4720 for (c = 0; c < ir->pull->ncoord; c++)
4722 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4723 && ir->pull->coord[c].vec[m] != 0)
4726 "Can not have dynamic box while using pull geometry '%s' "
4728 enumValueToString(ir->pull->coord[c].eGeom),
4740 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4742 char warn_buf[STRLEN];
4745 ptr = check_box(ir->pbcType, box);
4748 warning_error(wi, ptr);
4751 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4753 if (ir->shake_tol <= 0.0)
4755 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4756 warning_error(wi, warn_buf);
4760 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4762 /* If we have Lincs constraints: */
4763 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4764 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4767 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4768 warning_note(wi, warn_buf);
4771 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4772 && (ir->nProjOrder < 8))
4775 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4776 enumValueToString(ir->eI));
4777 warning_note(wi, warn_buf);
4779 if (ir->epc == PressureCoupling::Mttk)
4781 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4785 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4787 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4790 if (ir->LincsWarnAngle > 90.0)
4792 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4793 warning(wi, warn_buf);
4794 ir->LincsWarnAngle = 90.0;
4797 if (ir->pbcType != PbcType::No)
4799 if (ir->nstlist == 0)
4802 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4803 "atoms might cause the simulation to crash.");
4805 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4808 "ERROR: The cut-off length is longer than half the shortest box vector or "
4809 "longer than the smallest box diagonal element. Increase the box size or "
4810 "decrease rlist.\n");
4811 warning_error(wi, warn_buf);