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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], freeze[STRLEN], frdim[STRLEN],
111 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
112 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
113 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
114 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
115 char lambda_weights[STRLEN];
116 std::vector<std::string> pullGroupNames;
117 std::vector<std::string> rotateGroupNames;
118 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
121 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
122 static gmx_inputrec_strings* inputrecStrings = nullptr;
124 void init_inputrec_strings()
129 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
130 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
132 inputrecStrings = new gmx_inputrec_strings();
135 void done_inputrec_strings()
137 delete inputrecStrings;
138 inputrecStrings = nullptr;
144 egrptpALL, /* All particles have to be a member of a group. */
145 egrptpALL_GENREST, /* A rest group with name is generated for particles *
146 * that are not part of any group. */
147 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
148 * for the rest group. */
149 egrptpONE /* Merge all selected groups into one group, *
150 * make a rest group for the remaining particles. */
153 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
154 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
155 "h-angles", "all-angles", nullptr };
157 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
158 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
160 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
165 for (i = 0; i < ntemps; i++)
167 /* simple linear scaling -- allows more control */
168 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
170 simtemp->temperatures[i] =
172 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
174 else if (simtemp->eSimTempScale
175 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
177 simtemp->temperatures[i] = simtemp->simtemp_low
178 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
179 static_cast<real>((1.0 * i) / (ntemps - 1)));
181 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
183 simtemp->temperatures[i] = simtemp->simtemp_low
184 + (simtemp->simtemp_high - simtemp->simtemp_low)
185 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
190 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
191 gmx_fatal(FARGS, "%s", errorstr);
197 static void _low_check(bool b, const char* s, warninp_t wi)
201 warning_error(wi, s);
205 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
209 if (*p > 0 && *p % nst != 0)
211 /* Round up to the next multiple of nst */
212 *p = ((*p) / nst + 1) * nst;
213 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
218 //! Convert legacy mdp entries to modern ones.
219 static void process_interaction_modifier(InteractionModifiers* eintmod)
221 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
223 *eintmod = InteractionModifiers::PotShift;
227 void check_ir(const char* mdparin,
228 const gmx::MDModulesNotifiers& mdModulesNotifiers,
232 /* Check internal consistency.
233 * NOTE: index groups are not set here yet, don't check things
234 * like temperature coupling group options here, but in triple_check
237 /* Strange macro: first one fills the err_buf, and then one can check
238 * the condition, which will print the message and increase the error
241 #define CHECK(b) _low_check(b, err_buf, wi)
242 char err_buf[256], warn_buf[STRLEN];
245 t_lambda* fep = ir->fepvals.get();
246 t_expanded* expand = ir->expandedvals.get();
248 set_warning_line(wi, mdparin, -1);
250 /* We cannot check MTS requirements with an invalid MTS setup
251 * and we will already have generated errors with an invalid MTS setup.
253 if (gmx::haveValidMtsSetup(*ir))
255 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
257 for (const auto& errorMessage : errorMessages)
259 warning_error(wi, errorMessage.c_str());
263 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
265 std::string message =
266 gmx::formatString("%s electrostatics is no longer supported",
267 enumValueToString(CoulombInteractionType::RFNecUnsupported));
268 warning_error(wi, message);
271 /* BASIC CUT-OFF STUFF */
272 if (ir->rcoulomb < 0)
274 warning_error(wi, "rcoulomb should be >= 0");
278 warning_error(wi, "rvdw should be >= 0");
280 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
282 warning_error(wi, "rlist should be >= 0");
285 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
286 "neighbour-list update scheme for efficient buffering for improved energy "
287 "conservation, please use the Verlet cut-off scheme instead.)");
288 CHECK(ir->nstlist < 0);
290 process_interaction_modifier(&ir->coulomb_modifier);
291 process_interaction_modifier(&ir->vdw_modifier);
293 if (ir->cutoff_scheme == CutoffScheme::Group)
296 "The group cutoff scheme has been removed since GROMACS 2020. "
297 "Please use the Verlet cutoff scheme.");
299 if (ir->cutoff_scheme == CutoffScheme::Verlet)
303 /* Normal Verlet type neighbor-list, currently only limited feature support */
304 if (inputrec2nboundeddim(ir) < 3)
306 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
309 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
310 if (ir->rcoulomb != ir->rvdw)
312 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
313 // for PME load balancing, we can support this exception.
314 bool bUsesPmeTwinRangeKernel =
315 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
316 && ir->rcoulomb > ir->rvdw);
317 if (!bUsesPmeTwinRangeKernel)
320 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
321 "rcoulomb>rvdw with PME electrostatics)");
325 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
327 if (ir->vdw_modifier == InteractionModifiers::None
328 || ir->vdw_modifier == InteractionModifiers::PotShift)
331 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
332 : InteractionModifiers::PotSwitch);
335 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
337 enumValueToString(ir->vdwtype),
338 enumValueToString(VanDerWaalsType::Cut),
339 enumValueToString(ir->vdw_modifier));
340 warning_note(wi, warn_buf);
342 ir->vdwtype = VanDerWaalsType::Cut;
347 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
348 enumValueToString(ir->vdwtype),
349 enumValueToString(ir->vdw_modifier));
350 warning_error(wi, warn_buf);
354 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
357 "With Verlet lists only cut-off and PME LJ interactions are supported");
359 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
360 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
363 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
364 "electrostatics are supported");
366 if (!(ir->coulomb_modifier == InteractionModifiers::None
367 || ir->coulomb_modifier == InteractionModifiers::PotShift))
369 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
370 warning_error(wi, warn_buf);
373 if (EEL_USER(ir->coulombtype))
376 "Coulomb type %s is not supported with the verlet scheme",
377 enumValueToString(ir->coulombtype));
378 warning_error(wi, warn_buf);
381 if (ir->nstlist <= 0)
383 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
386 if (ir->nstlist < 10)
389 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
390 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
394 rc_max = std::max(ir->rvdw, ir->rcoulomb);
398 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
399 ir->verletbuf_tol = 0;
402 else if (ir->verletbuf_tol <= 0)
404 if (ir->verletbuf_tol == 0)
406 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
409 if (ir->rlist < rc_max)
412 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
415 if (ir->rlist == rc_max && ir->nstlist > 1)
419 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
420 "buffer. The cluster pair list does have a buffering effect, but choosing "
421 "a larger rlist might be necessary for good energy conservation.");
426 if (ir->rlist > rc_max)
429 "You have set rlist larger than the interaction cut-off, but you also "
430 "have verlet-buffer-tolerance > 0. Will set rlist using "
431 "verlet-buffer-tolerance.");
434 if (ir->nstlist == 1)
436 /* No buffer required */
441 if (EI_DYNAMICS(ir->eI))
443 if (inputrec2nboundeddim(ir) < 3)
446 "The box volume is required for calculating rlist from the "
447 "energy drift with verlet-buffer-tolerance > 0. You are "
448 "using at least one unbounded dimension, so no volume can be "
449 "computed. Either use a finite box, or set rlist yourself "
450 "together with verlet-buffer-tolerance = -1.");
452 /* Set rlist temporarily so we can continue processing */
457 /* Set the buffer to 5% of the cut-off */
458 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
464 /* GENERAL INTEGRATOR STUFF */
467 if (ir->etc != TemperatureCoupling::No)
469 if (EI_RANDOM(ir->eI))
472 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
473 "implicitly. See the documentation for more information on which "
474 "parameters affect temperature for %s.",
475 enumValueToString(ir->etc),
476 enumValueToString(ir->eI),
477 enumValueToString(ir->eI));
482 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
484 enumValueToString(ir->etc),
485 enumValueToString(ir->eI));
487 warning_note(wi, warn_buf);
489 ir->etc = TemperatureCoupling::No;
491 if (ir->eI == IntegrationAlgorithm::VVAK)
494 "Integrator method %s is implemented primarily for validation purposes; for "
495 "molecular dynamics, you should probably be using %s or %s",
496 enumValueToString(IntegrationAlgorithm::VVAK),
497 enumValueToString(IntegrationAlgorithm::MD),
498 enumValueToString(IntegrationAlgorithm::VV));
499 warning_note(wi, warn_buf);
501 if (!EI_DYNAMICS(ir->eI))
503 if (ir->epc != PressureCoupling::No)
506 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
507 enumValueToString(ir->epc),
508 enumValueToString(ir->eI));
509 warning_note(wi, warn_buf);
511 ir->epc = PressureCoupling::No;
513 if (EI_DYNAMICS(ir->eI))
515 if (ir->nstcalcenergy < 0)
517 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
518 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
520 /* nstcalcenergy larger than nstener does not make sense.
521 * We ideally want nstcalcenergy=nstener.
525 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
529 ir->nstcalcenergy = ir->nstenergy;
533 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
534 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
535 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
538 const char* nsten = "nstenergy";
539 const char* nstdh = "nstdhdl";
540 const char* min_name = nsten;
541 int min_nst = ir->nstenergy;
543 /* find the smallest of ( nstenergy, nstdhdl ) */
544 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
545 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
547 min_nst = ir->fepvals->nstdhdl;
550 /* If the user sets nstenergy small, we should respect that */
551 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
552 warning_note(wi, warn_buf);
553 ir->nstcalcenergy = min_nst;
556 if (ir->epc != PressureCoupling::No)
558 if (ir->nstpcouple < 0)
560 ir->nstpcouple = ir_optimal_nstpcouple(ir);
562 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
565 "With multiple time stepping, nstpcouple should be a mutiple of "
570 if (ir->nstcalcenergy > 0)
572 if (ir->efep != FreeEnergyPerturbationType::No)
574 /* nstdhdl should be a multiple of nstcalcenergy */
575 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
579 /* nstexpanded should be a multiple of nstcalcenergy */
580 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
582 /* for storing exact averages nstenergy should be
583 * a multiple of nstcalcenergy
585 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
588 // Inquire all MDModules, if their parameters match with the energy
589 // calculation frequency
590 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
591 mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
593 // Emit all errors from the energy calculation frequency checks
594 for (const std::string& energyFrequencyErrorMessage :
595 energyCalculationFrequencyErrors.errorMessages())
597 warning_error(wi, energyFrequencyErrorMessage);
601 if (ir->nsteps == 0 && !ir->bContinuation)
604 "For a correct single-point energy evaluation with nsteps = 0, use "
605 "continuation = yes to avoid constraining the input coordinates.");
609 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
612 "You are doing a continuation with SD or BD, make sure that ld_seed is "
613 "different from the previous run (using ld_seed=-1 will ensure this)");
619 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
620 CHECK(ir->pbcType != PbcType::Xyz);
621 sprintf(err_buf, "with TPI nstlist should be larger than zero");
622 CHECK(ir->nstlist <= 0);
623 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
624 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
628 if ((opts->nshake > 0) && (opts->bMorse))
630 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
631 warning(wi, warn_buf);
634 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
637 "You are doing a continuation with SD or BD, make sure that ld_seed is "
638 "different from the previous run (using ld_seed=-1 will ensure this)");
640 /* verify simulated tempering options */
644 bool bAllTempZero = TRUE;
645 for (i = 0; i < fep->n_lambda; i++)
648 "Entry %d for %s must be between 0 and 1, instead is %g",
650 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
651 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
652 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
653 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
655 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
657 bAllTempZero = FALSE;
660 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
661 CHECK(bAllTempZero == TRUE);
663 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
664 CHECK(ir->eI != IntegrationAlgorithm::VV);
666 /* check compatability of the temperature coupling with simulated tempering */
668 if (ir->etc == TemperatureCoupling::NoseHoover)
671 "Nose-Hoover based temperature control such as [%s] my not be "
672 "entirelyconsistent with simulated tempering",
673 enumValueToString(ir->etc));
674 warning_note(wi, warn_buf);
677 /* check that the temperatures make sense */
680 "Higher simulated tempering temperature (%g) must be >= than the simulated "
681 "tempering lower temperature (%g)",
682 ir->simtempvals->simtemp_high,
683 ir->simtempvals->simtemp_low);
684 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
687 "Higher simulated tempering temperature (%g) must be >= zero",
688 ir->simtempvals->simtemp_high);
689 CHECK(ir->simtempvals->simtemp_high <= 0);
692 "Lower simulated tempering temperature (%g) must be >= zero",
693 ir->simtempvals->simtemp_low);
694 CHECK(ir->simtempvals->simtemp_low <= 0);
697 /* verify free energy options */
699 if (ir->efep != FreeEnergyPerturbationType::No)
701 fep = ir->fepvals.get();
702 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
703 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
706 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
708 static_cast<int>(fep->sc_r_power));
709 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
712 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
715 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
718 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
720 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
722 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
723 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
725 sprintf(err_buf, "Free-energy not implemented for Ewald");
726 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
728 /* check validty of lambda inputs */
729 if (fep->n_lambda == 0)
731 /* Clear output in case of no states:*/
732 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
733 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
738 "initial thermodynamic state %d does not exist, only goes to %d",
741 CHECK((fep->init_fep_state >= fep->n_lambda));
745 "Lambda state must be set, either with init-lambda-state or with init-lambda");
746 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
749 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
750 "init-lambda-state or with init-lambda, but not both",
752 fep->init_fep_state);
753 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
756 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
760 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
762 if (fep->separate_dvdl[i])
767 if (n_lambda_terms > 1)
770 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
771 "use init-lambda to set lambda state (except for slow growth). Use "
772 "init-lambda-state instead.");
773 warning(wi, warn_buf);
776 if (n_lambda_terms < 2 && fep->n_lambda > 0)
779 "init-lambda is deprecated for setting lambda state (except for slow "
780 "growth). Use init-lambda-state instead.");
784 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
786 for (i = 0; i < fep->n_lambda; i++)
788 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
790 "Entry %d for %s must be between 0 and 1, instead is %g",
792 enumValueToString(enumValue),
793 fep->all_lambda[j][i]);
794 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
798 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
800 for (i = 0; i < fep->n_lambda; i++)
803 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
804 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
805 "crashes, and is not supported.",
807 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
808 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
809 CHECK((fep->sc_alpha > 0)
810 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
811 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
812 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
813 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
818 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
820 real sigma, lambda, r_sc;
823 /* Maximum estimate for A and B charges equal with lambda power 1 */
825 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
826 1.0 / fep->sc_r_power);
828 "With PME there is a minor soft core effect present at the cut-off, "
829 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
830 "energy conservation, but usually other effects dominate. With a common sigma "
831 "value of %g nm the fraction of the particle-particle potential at the cut-off "
832 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
838 warning_note(wi, warn_buf);
841 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
842 be treated differently, but that's the next step */
844 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
846 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
847 for (j = 0; j < fep->n_lambda; j++)
849 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
850 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
854 if (fep->softcoreFunction == SoftcoreType::Gapsys)
856 if (fep->scGapsysScaleLinpointQ < 0.0)
859 "sc_scale_linpoint_Q_gapsys is equal %g but must be >= 0",
860 fep->scGapsysScaleLinpointQ);
861 warning_note(wi, warn_buf);
864 if ((fep->scGapsysScaleLinpointLJ < 0.0) || (fep->scGapsysScaleLinpointLJ >= 1.0))
867 "sc_scale_linpoint_LJ_gapsys is equal %g but must be in [0,1) when used "
869 "sc_function=gapsys.",
870 fep->scGapsysScaleLinpointLJ);
871 warning_note(wi, warn_buf);
876 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
878 fep = ir->fepvals.get();
880 /* checking equilibration of weights inputs for validity */
883 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
885 expand->equil_n_at_lam,
886 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
887 CHECK((expand->equil_n_at_lam > 0)
888 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
891 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
893 expand->equil_samples,
894 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
895 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
898 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
900 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
901 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
904 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
905 expand->equil_samples,
906 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
907 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
910 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
912 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
913 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
916 "weight-equil-number-all-lambda (%d) must be a positive integer if "
917 "lmc-weights-equil=%s",
918 expand->equil_n_at_lam,
919 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
920 CHECK((expand->equil_n_at_lam <= 0)
921 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
924 "weight-equil-number-samples (%d) must be a positive integer if "
925 "lmc-weights-equil=%s",
926 expand->equil_samples,
927 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
928 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
931 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
933 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
934 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
937 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
938 expand->equil_wl_delta,
939 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
940 CHECK((expand->equil_wl_delta <= 0)
941 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
944 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
946 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
947 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
950 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
951 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
952 enumValueToString(LambdaWeightCalculation::WL),
953 enumValueToString(LambdaWeightCalculation::WWL));
954 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
956 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
957 CHECK((expand->lmc_repeats <= 0));
958 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
959 CHECK((expand->minvarmin <= 0));
960 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
961 CHECK((expand->c_range < 0));
963 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
966 expand->lmc_forced_nstart);
967 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
968 && (expand->elmcmove != LambdaMoveCalculation::No));
969 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
970 CHECK((expand->lmc_forced_nstart < 0));
972 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
973 fep->init_fep_state);
974 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
976 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
977 CHECK((expand->init_wl_delta < 0));
978 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
979 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
980 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
981 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
983 /* if there is no temperature control, we need to specify an MC temperature */
984 if (!integratorHasReferenceTemperature(ir)
985 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
988 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
989 "to a positive number");
990 warning_error(wi, err_buf);
992 if (expand->nstTij > 0)
994 sprintf(err_buf, "nstlog must be non-zero");
995 CHECK(ir->nstlog == 0);
996 // Avoid modulus by zero in the case that already triggered an error exit.
1000 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
1003 CHECK((expand->nstTij % ir->nstlog) != 0);
1009 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
1010 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
1013 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
1015 if (ir->pbcType == PbcType::No)
1017 if (ir->epc != PressureCoupling::No)
1019 warning(wi, "Turning off pressure coupling for vacuum system");
1020 ir->epc = PressureCoupling::No;
1026 "Can not have pressure coupling with pbc=%s",
1027 c_pbcTypeNames[ir->pbcType].c_str());
1028 CHECK(ir->epc != PressureCoupling::No);
1030 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1031 CHECK(EEL_FULL(ir->coulombtype));
1034 "Can not have dispersion correction with pbc=%s",
1035 c_pbcTypeNames[ir->pbcType].c_str());
1036 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1039 if (ir->rlist == 0.0)
1042 "can only have neighborlist cut-off zero (=infinite)\n"
1043 "with coulombtype = %s or coulombtype = %s\n"
1044 "without periodic boundary conditions (pbc = %s) and\n"
1045 "rcoulomb and rvdw set to zero",
1046 enumValueToString(CoulombInteractionType::Cut),
1047 enumValueToString(CoulombInteractionType::User),
1048 c_pbcTypeNames[PbcType::No].c_str());
1049 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1050 && (ir->coulombtype != CoulombInteractionType::User))
1051 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1053 if (ir->nstlist > 0)
1056 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1057 "nstype=simple and only one MPI rank");
1062 if (ir->nstcomm == 0)
1064 // TODO Change this behaviour. There should be exactly one way
1065 // to turn off an algorithm.
1066 ir->comm_mode = ComRemovalAlgorithm::No;
1068 if (ir->comm_mode != ComRemovalAlgorithm::No)
1070 if (ir->nstcomm < 0)
1072 // TODO Such input was once valid. Now that we've been
1073 // helpful for a few years, we should reject such input,
1074 // lest we have to support every historical decision
1077 "If you want to remove the rotation around the center of mass, you should set "
1078 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1079 "its absolute value");
1080 ir->nstcomm = abs(ir->nstcomm);
1083 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy
1084 && ir->comm_mode != ComRemovalAlgorithm::LinearAccelerationCorrection)
1087 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider "
1088 "setting nstcomm equal to nstcalcenergy for less overhead");
1091 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1094 "Can not remove the rotation around the center of mass with periodic "
1096 CHECK(ir->bPeriodicMols);
1097 if (ir->pbcType != PbcType::No)
1100 "Removing the rotation around the center of mass in a periodic system, "
1101 "this can lead to artifacts. Only use this on a single (cluster of) "
1102 "molecules. This cluster should not cross periodic boundaries.");
1107 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1108 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1111 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1112 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1114 enumValueToString(IntegrationAlgorithm::SD1));
1115 warning_note(wi, warn_buf);
1118 /* TEMPERATURE COUPLING */
1119 if (ir->etc == TemperatureCoupling::Yes)
1121 ir->etc = TemperatureCoupling::Berendsen;
1123 "Old option for temperature coupling given: "
1124 "changing \"yes\" to \"Berendsen\"\n");
1127 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1129 if (ir->opts.nhchainlength < 1)
1132 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1134 ir->opts.nhchainlength);
1135 ir->opts.nhchainlength = 1;
1136 warning(wi, warn_buf);
1139 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1143 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1144 ir->opts.nhchainlength = 1;
1149 ir->opts.nhchainlength = 0;
1152 if (ir->eI == IntegrationAlgorithm::VVAK)
1155 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1157 enumValueToString(IntegrationAlgorithm::VVAK));
1158 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1161 if (ETC_ANDERSEN(ir->etc))
1164 "%s temperature control not supported for integrator %s.",
1165 enumValueToString(ir->etc),
1166 enumValueToString(ir->eI));
1167 CHECK(!(EI_VV(ir->eI)));
1169 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1172 "Center of mass removal not necessary for %s. All velocities of coupled "
1173 "groups are rerandomized periodically, so flying ice cube errors will not "
1175 enumValueToString(ir->etc));
1176 warning_note(wi, warn_buf);
1180 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1181 "randomized every time step",
1183 enumValueToString(ir->etc));
1184 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1187 if (ir->etc == TemperatureCoupling::Berendsen)
1190 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1191 "might want to consider using the %s thermostat.",
1192 enumValueToString(ir->etc),
1193 enumValueToString(TemperatureCoupling::VRescale));
1194 warning_note(wi, warn_buf);
1197 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1198 && ir->epc == PressureCoupling::Berendsen)
1201 "Using Berendsen pressure coupling invalidates the "
1202 "true ensemble for the thermostat");
1203 warning(wi, warn_buf);
1206 /* PRESSURE COUPLING */
1207 if (ir->epc == PressureCoupling::Isotropic)
1209 ir->epc = PressureCoupling::Berendsen;
1211 "Old option for pressure coupling given: "
1212 "changing \"Isotropic\" to \"Berendsen\"\n");
1215 if (ir->epc != PressureCoupling::No)
1217 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1219 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1220 CHECK(ir->tau_p <= 0);
1222 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1225 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1226 "times larger than nstpcouple*dt (%g)",
1227 enumValueToString(ir->epc),
1229 pcouple_min_integration_steps(ir->epc),
1231 warning(wi, warn_buf);
1235 "compressibility must be > 0 when using pressure"
1237 enumValueToString(ir->epc));
1238 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1239 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1240 && ir->compress[ZZ][YY] <= 0));
1242 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1245 "You are generating velocities so I am assuming you "
1246 "are equilibrating a system. You are using "
1247 "%s pressure coupling, but this can be "
1248 "unstable for equilibration. If your system crashes, try "
1249 "equilibrating first with Berendsen pressure coupling. If "
1250 "you are not equilibrating the system, you can probably "
1251 "ignore this warning.",
1252 enumValueToString(ir->epc));
1253 warning(wi, warn_buf);
1259 if (ir->epc == PressureCoupling::Mttk)
1261 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1265 /* ELECTROSTATICS */
1266 /* More checks are in triple check (grompp.c) */
1268 if (ir->coulombtype == CoulombInteractionType::Switch)
1271 "coulombtype = %s is only for testing purposes and can lead to serious "
1272 "artifacts, advice: use coulombtype = %s",
1273 enumValueToString(ir->coulombtype),
1274 enumValueToString(CoulombInteractionType::RFZero));
1275 warning(wi, warn_buf);
1278 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1281 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1282 "format and exchanging epsilon-r and epsilon-rf",
1284 warning(wi, warn_buf);
1285 ir->epsilon_rf = ir->epsilon_r;
1286 ir->epsilon_r = 1.0;
1289 if (ir->epsilon_r == 0)
1292 "It is pointless to use long-range electrostatics with infinite relative "
1294 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1296 CHECK(EEL_FULL(ir->coulombtype));
1299 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1301 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1302 CHECK(ir->epsilon_r < 0);
1305 if (EEL_RF(ir->coulombtype))
1307 /* reaction field (at the cut-off) */
1309 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1312 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1313 enumValueToString(ir->coulombtype));
1314 warning(wi, warn_buf);
1315 ir->epsilon_rf = 0.0;
1318 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1319 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1320 if (ir->epsilon_rf == ir->epsilon_r)
1323 "Using epsilon-rf = epsilon-r with %s does not make sense",
1324 enumValueToString(ir->coulombtype));
1325 warning(wi, warn_buf);
1328 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1329 * means the interaction is zero outside rcoulomb, but it helps to
1330 * provide accurate energy conservation.
1332 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1334 if (ir_coulomb_switched(ir))
1337 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1338 "potential modifier options!",
1339 enumValueToString(ir->coulombtype));
1340 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1344 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1347 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1348 "secondary coulomb-modifier.");
1349 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1351 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1354 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1355 "secondary vdw-modifier.");
1356 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1359 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1360 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1363 "The switch/shift interaction settings are just for compatibility; you will get "
1365 "performance from applying potential modifiers to your interactions!\n");
1366 warning_note(wi, warn_buf);
1369 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1370 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1372 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1374 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1376 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1377 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1378 "will be good regardless, since ewald_rtol = %g.",
1380 ir->rcoulomb_switch,
1383 warning(wi, warn_buf);
1387 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1389 if (ir->rvdw_switch == 0)
1392 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1393 "potential. This suggests it was not set in the mdp, which can lead to large "
1394 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1395 "switching range.");
1396 warning(wi, warn_buf);
1400 if (EEL_FULL(ir->coulombtype))
1402 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1403 || ir->coulombtype == CoulombInteractionType::PmeUser
1404 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1407 "With coulombtype = %s, rcoulomb must be <= rlist",
1408 enumValueToString(ir->coulombtype));
1409 CHECK(ir->rcoulomb > ir->rlist);
1413 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1415 // TODO: Move these checks into the ewald module with the options class
1417 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1419 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1422 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1423 enumValueToString(ir->coulombtype),
1426 warning_error(wi, warn_buf);
1430 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1432 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1435 "With pbc=%s you should use ewald-geometry=%s",
1436 c_pbcTypeNames[ir->pbcType].c_str(),
1437 enumValueToString(EwaldGeometry::ThreeDC));
1438 warning(wi, warn_buf);
1440 /* This check avoids extra pbc coding for exclusion corrections */
1441 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1442 CHECK(ir->wall_ewald_zfac < 2);
1444 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1445 && EEL_FULL(ir->coulombtype))
1448 "With %s and ewald_geometry = %s you should use pbc = %s",
1449 enumValueToString(ir->coulombtype),
1450 enumValueToString(EwaldGeometry::ThreeDC),
1451 c_pbcTypeNames[PbcType::XY].c_str());
1452 warning(wi, warn_buf);
1454 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1456 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1457 CHECK(ir->bPeriodicMols);
1458 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1459 warning_note(wi, warn_buf);
1461 "With epsilon_surface > 0 you can only use domain decomposition "
1462 "when there are only small molecules with all bonds constrained (mdrun will check "
1464 warning_note(wi, warn_buf);
1467 if (ir_vdw_switched(ir))
1469 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1470 CHECK(ir->rvdw_switch >= ir->rvdw);
1472 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1475 "You are applying a switch function to vdw forces or potentials from %g to %g "
1476 "nm, which is more than half the interaction range, whereas switch functions "
1477 "are intended to act only close to the cut-off.",
1480 warning_note(wi, warn_buf);
1484 if (ir->vdwtype == VanDerWaalsType::Pme)
1486 if (!(ir->vdw_modifier == InteractionModifiers::None
1487 || ir->vdw_modifier == InteractionModifiers::PotShift))
1490 "With vdwtype = %s, the only supported modifiers are %s and %s",
1491 enumValueToString(ir->vdwtype),
1492 enumValueToString(InteractionModifiers::PotShift),
1493 enumValueToString(InteractionModifiers::None));
1494 warning_error(wi, err_buf);
1498 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1501 "You have selected user tables with dispersion correction, the dispersion "
1502 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1503 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1504 "really want dispersion correction to -C6/r^6.");
1507 if (ir->eI == IntegrationAlgorithm::LBFGS
1508 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1511 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1514 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1516 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1519 /* IMPLICIT SOLVENT */
1520 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1522 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1523 warning_error(wi, warn_buf);
1528 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1533 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1536 // cosine acceleration is only supported in leap-frog
1537 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1539 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1543 /* interpret a number of doubles from a string and put them in an array,
1544 after allocating space for them.
1545 str = the input string
1546 n = the (pre-allocated) number of doubles read
1547 r = the output array of doubles. */
1548 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1550 auto values = gmx::splitString(str);
1553 std::vector<real> r;
1554 for (int i = 0; i < *n; i++)
1558 r.emplace_back(gmx::fromString<real>(values[i]));
1560 catch (gmx::GromacsException&)
1563 "Invalid value " + values[i]
1564 + " in string in mdp file. Expected a real number.");
1571 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1574 int i, j, max_n_lambda, nweights;
1575 t_lambda* fep = ir->fepvals.get();
1576 t_expanded* expand = ir->expandedvals.get();
1577 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1578 bool bOneLambda = TRUE;
1579 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1581 /* FEP input processing */
1582 /* first, identify the number of lambda values for each type.
1583 All that are nonzero must have the same number */
1585 for (auto i : keysOf(nfep))
1587 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1590 /* now, determine the number of components. All must be either zero, or equal. */
1593 for (auto i : keysOf(nfep))
1595 if (nfep[i] > max_n_lambda)
1597 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1598 must have the same number if its not zero.*/
1603 for (auto i : keysOf(nfep))
1607 ir->fepvals->separate_dvdl[i] = FALSE;
1609 else if (nfep[i] == max_n_lambda)
1611 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1612 the derivative with respect to the temperature currently */
1614 ir->fepvals->separate_dvdl[i] = TRUE;
1620 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1623 enumValueToString(i),
1627 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1628 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1630 /* the number of lambdas is the number we've read in, which is either zero
1631 or the same for all */
1632 fep->n_lambda = max_n_lambda;
1634 /* if init_lambda is defined, we need to set lambda */
1635 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1637 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1639 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1640 for (auto i : keysOf(nfep))
1642 fep->all_lambda[i].resize(fep->n_lambda);
1643 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1646 for (j = 0; j < fep->n_lambda; j++)
1648 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1653 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1654 internal bookkeeping -- for now, init_lambda */
1656 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1658 for (i = 0; i < fep->n_lambda; i++)
1660 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1664 /* check to see if only a single component lambda is defined, and soft core is defined.
1665 In this case, turn on coulomb soft core */
1667 if (max_n_lambda == 0)
1673 for (auto i : keysOf(nfep))
1675 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1681 if ((bOneLambda) && (fep->sc_alpha > 0))
1683 fep->bScCoul = TRUE;
1686 /* Fill in the others with the efptFEP if they are not explicitly
1687 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1688 they are all zero. */
1690 for (auto i : keysOf(nfep))
1692 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1694 for (j = 0; j < fep->n_lambda; j++)
1696 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1702 /* now read in the weights */
1703 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1706 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1708 else if (nweights != fep->n_lambda)
1711 "Number of weights (%d) is not equal to number of lambda values (%d)",
1715 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1717 expand->nstexpanded = fep->nstdhdl;
1718 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1723 static void do_simtemp_params(t_inputrec* ir)
1725 ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
1726 getSimTemps(ir->fepvals->n_lambda,
1727 ir->simtempvals.get(),
1728 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1731 template<typename T>
1732 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1735 for (const auto& input : inputs)
1739 outputs[i] = gmx::fromStdString<T>(input);
1741 catch (gmx::GromacsException&)
1743 auto message = gmx::formatString(
1744 "Invalid value for mdp option %s. %s should only consist of integers separated "
1748 warning_error(wi, message);
1754 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1757 for (const auto& input : inputs)
1761 outputs[i] = gmx::fromString<real>(input);
1763 catch (gmx::GromacsException&)
1765 auto message = gmx::formatString(
1766 "Invalid value for mdp option %s. %s should only consist of real numbers "
1767 "separated by spaces.",
1770 warning_error(wi, message);
1776 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1778 opts->wall_atomtype[0] = nullptr;
1779 opts->wall_atomtype[1] = nullptr;
1781 ir->wall_atomtype[0] = -1;
1782 ir->wall_atomtype[1] = -1;
1783 ir->wall_density[0] = 0;
1784 ir->wall_density[1] = 0;
1788 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1789 if (wallAtomTypes.size() != size_t(ir->nwall))
1792 "Expected %d elements for wall_atomtype, found %zu",
1794 wallAtomTypes.size());
1796 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1797 for (int i = 0; i < ir->nwall; i++)
1799 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1802 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1804 auto wallDensity = gmx::splitString(wall_density);
1805 if (wallDensity.size() != size_t(ir->nwall))
1808 "Expected %d elements for wall-density, found %zu",
1810 wallDensity.size());
1812 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1813 for (int i = 0; i < ir->nwall; i++)
1815 if (ir->wall_density[i] <= 0)
1817 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1824 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1828 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1829 for (int i = 0; i < nwall; i++)
1831 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1832 grps->emplace_back(groups->groupNames.size() - 1);
1837 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1839 /* read expanded ensemble parameters */
1840 printStringNewline(inp, "expanded ensemble variables");
1841 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1842 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1843 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1844 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1845 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1846 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1847 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1848 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1849 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1850 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1851 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1852 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1853 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1854 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1855 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1856 expand->bSymmetrizedTMatrix =
1857 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1858 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1859 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1860 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1861 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1862 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1863 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1864 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1867 /*! \brief Return whether an end state with the given coupling-lambda
1868 * value describes fully-interacting VDW.
1870 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1871 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1873 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1875 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1881 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1884 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1886 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1888 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1891 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1892 std::string message = gmx::formatExceptionMessageToString(*ex);
1893 warning_error(wi_, message.c_str());
1898 std::string getOptionName(const gmx::KeyValueTreePath& context)
1900 if (mapping_ != nullptr)
1902 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1903 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1906 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1911 const gmx::IKeyValueTreeBackMapping* mapping_;
1916 void get_ir(const char* mdparin,
1917 const char* mdparout,
1918 gmx::MDModules* mdModules,
1921 WriteMdpHeader writeMdpHeader,
1925 double dumdub[2][6];
1927 char warn_buf[STRLEN];
1928 t_lambda* fep = ir->fepvals.get();
1929 t_expanded* expand = ir->expandedvals.get();
1931 const char* no_names[] = { "no", nullptr };
1933 init_inputrec_strings();
1934 gmx::TextInputFile stream(mdparin);
1935 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1937 snew(dumstr[0], STRLEN);
1938 snew(dumstr[1], STRLEN);
1940 /* ignore the following deprecated commands */
1941 replace_inp_entry(inp, "title", nullptr);
1942 replace_inp_entry(inp, "cpp", nullptr);
1943 replace_inp_entry(inp, "domain-decomposition", nullptr);
1944 replace_inp_entry(inp, "andersen-seed", nullptr);
1945 replace_inp_entry(inp, "dihre", nullptr);
1946 replace_inp_entry(inp, "dihre-fc", nullptr);
1947 replace_inp_entry(inp, "dihre-tau", nullptr);
1948 replace_inp_entry(inp, "nstdihreout", nullptr);
1949 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1950 replace_inp_entry(inp, "optimize-fft", nullptr);
1951 replace_inp_entry(inp, "adress_type", nullptr);
1952 replace_inp_entry(inp, "adress_const_wf", nullptr);
1953 replace_inp_entry(inp, "adress_ex_width", nullptr);
1954 replace_inp_entry(inp, "adress_hy_width", nullptr);
1955 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1956 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1957 replace_inp_entry(inp, "adress_site", nullptr);
1958 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1959 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1960 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1961 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1962 replace_inp_entry(inp, "rlistlong", nullptr);
1963 replace_inp_entry(inp, "nstcalclr", nullptr);
1964 replace_inp_entry(inp, "pull-print-com2", nullptr);
1965 replace_inp_entry(inp, "gb-algorithm", nullptr);
1966 replace_inp_entry(inp, "nstgbradii", nullptr);
1967 replace_inp_entry(inp, "rgbradii", nullptr);
1968 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1969 replace_inp_entry(inp, "gb-saltconc", nullptr);
1970 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1971 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1972 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1973 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1974 replace_inp_entry(inp, "sa-algorithm", nullptr);
1975 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1976 replace_inp_entry(inp, "ns-type", nullptr);
1978 /* replace the following commands with the clearer new versions*/
1979 replace_inp_entry(inp, "unconstrained-start", "continuation");
1980 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1981 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1982 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1983 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1984 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1985 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1987 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1988 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1989 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1990 setStringEntry(&inp, "include", opts->include, nullptr);
1991 printStringNoNewline(
1992 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1993 setStringEntry(&inp, "define", opts->define, nullptr);
1995 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1996 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
1997 printStringNoNewline(&inp, "Start time and timestep in ps");
1998 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1999 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
2000 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
2001 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
2002 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
2003 printStringNoNewline(
2004 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
2005 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
2006 printStringNoNewline(&inp, "Multiple time-stepping");
2007 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
2010 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
2011 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
2012 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
2013 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
2015 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2016 if (!EI_DYNAMICS(ir->eI))
2021 printStringNoNewline(&inp, "mode for center of mass motion removal");
2022 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
2023 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2024 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2025 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2026 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2028 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2029 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2030 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2031 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2034 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2035 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2036 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2037 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2038 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2039 ir->niter = get_eint(&inp, "niter", 20, wi);
2040 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2041 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2042 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2043 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2044 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2046 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2047 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2049 /* Output options */
2050 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2051 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2052 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2053 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2054 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2055 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2056 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2057 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2058 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2059 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2060 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2061 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2062 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2063 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2064 printStringNoNewline(&inp, "default, all atoms will be written.");
2065 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2066 printStringNoNewline(&inp, "Selection of energy groups");
2067 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2069 /* Neighbor searching */
2070 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2071 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2072 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2073 printStringNoNewline(&inp, "nblist update frequency");
2074 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2075 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2076 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2077 std::vector<const char*> pbcTypesNamesChar;
2078 for (const auto& pbcTypeName : c_pbcTypeNames)
2080 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2082 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2083 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2084 printStringNoNewline(&inp,
2085 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2086 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2087 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2088 printStringNoNewline(&inp, "nblist cut-off");
2089 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2090 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2092 /* Electrostatics */
2093 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2094 printStringNoNewline(&inp, "Method for doing electrostatics");
2095 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2096 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2097 printStringNoNewline(&inp, "cut-off lengths");
2098 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2099 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2100 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2101 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2102 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2103 printStringNoNewline(&inp, "Method for doing Van der Waals");
2104 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2105 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2106 printStringNoNewline(&inp, "cut-off lengths");
2107 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2108 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2109 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2110 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2111 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2112 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2113 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2114 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2115 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2116 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2117 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2118 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2119 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2120 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2121 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2122 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2123 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2124 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2125 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2126 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2127 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2129 /* Implicit solvation is no longer supported, but we need grompp
2130 to be able to refuse old .mdp files that would have built a tpr
2131 to run it. Thus, only "no" is accepted. */
2132 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2134 /* Coupling stuff */
2135 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2136 printStringNoNewline(&inp, "Temperature coupling");
2137 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2138 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2139 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2140 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2141 printStringNoNewline(&inp, "Groups to couple separately");
2142 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2143 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2144 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2145 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2146 printStringNoNewline(&inp, "pressure coupling");
2147 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2148 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2149 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2150 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2151 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2152 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2153 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2154 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2155 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2158 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2159 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2160 printStringNoNewline(&inp, "Groups treated with MiMiC");
2161 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2163 /* Simulated annealing */
2164 printStringNewline(&inp, "SIMULATED ANNEALING");
2165 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2166 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2167 printStringNoNewline(&inp,
2168 "Number of time points to use for specifying annealing in each group");
2169 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2170 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2171 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2172 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2173 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2176 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2177 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2178 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2179 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2182 printStringNewline(&inp, "OPTIONS FOR BONDS");
2183 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2184 printStringNoNewline(&inp, "Type of constraint algorithm");
2185 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2186 printStringNoNewline(&inp, "Do not constrain the start configuration");
2187 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2188 printStringNoNewline(&inp,
2189 "Use successive overrelaxation to reduce the number of shake iterations");
2190 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2191 printStringNoNewline(&inp, "Relative tolerance of shake");
2192 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2193 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2194 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2195 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2196 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2197 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2198 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2199 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2200 printStringNoNewline(&inp, "rotates over more degrees than");
2201 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2202 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2203 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2205 /* Energy group exclusions */
2206 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2207 printStringNoNewline(
2208 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2209 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2212 printStringNewline(&inp, "WALLS");
2213 printStringNoNewline(
2214 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2215 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2216 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2217 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2218 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2219 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2220 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2223 printStringNewline(&inp, "COM PULLING");
2224 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2227 ir->pull = std::make_unique<pull_params_t>();
2228 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2232 for (int c = 0; c < ir->pull->ncoord; c++)
2234 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2237 "Constraint COM pulling is not supported in combination with "
2238 "multiple time stepping");
2246 NOTE: needs COM pulling or free energy input */
2247 printStringNewline(&inp, "AWH biasing");
2248 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2251 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
2254 /* Enforced rotation */
2255 printStringNewline(&inp, "ENFORCED ROTATION");
2256 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2257 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2261 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2264 /* Interactive MD */
2266 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2267 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2268 if (inputrecStrings->imd_grp[0] != '\0')
2275 printStringNewline(&inp, "NMR refinement stuff");
2276 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2277 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2278 printStringNoNewline(
2279 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2280 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2281 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2282 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2283 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2284 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2285 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2286 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2287 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2288 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2289 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2290 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2291 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2292 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2293 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2294 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2296 /* free energy variables */
2297 printStringNewline(&inp, "Free energy variables");
2298 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2299 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2300 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2301 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2302 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2304 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2306 it was not entered */
2307 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2308 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2309 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2310 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2311 setStringEntry(&inp, "fep-lambdas", "");
2312 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2313 setStringEntry(&inp, "mass-lambdas", "");
2314 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2315 setStringEntry(&inp, "coul-lambdas", "");
2316 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2317 setStringEntry(&inp, "vdw-lambdas", "");
2318 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2319 setStringEntry(&inp, "bonded-lambdas", "");
2320 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2321 setStringEntry(&inp, "restraint-lambdas", "");
2322 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2323 setStringEntry(&inp, "temperature-lambdas", "");
2324 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2325 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2326 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2327 fep->softcoreFunction = getEnum<SoftcoreType>(&inp, "sc-function", wi);
2328 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2329 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2330 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2331 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2332 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2333 fep->scGapsysScaleLinpointLJ = get_ereal(&inp, "sc-gapsys-scale-linpoint-lj", 0.85, wi);
2334 fep->scGapsysScaleLinpointQ = get_ereal(&inp, "sc-gapsys-scale-linpoint-q", 0.3, wi);
2335 fep->scGapsysSigmaLJ = get_ereal(&inp, "sc-gapsys-sigma-lj", 0.3, wi);
2336 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2337 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2338 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2339 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2340 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2341 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2343 /* Non-equilibrium MD stuff */
2344 printStringNewline(&inp, "Non-equilibrium MD stuff");
2345 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2346 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2347 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2348 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2350 /* simulated tempering variables */
2351 printStringNewline(&inp, "simulated tempering variables");
2352 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2353 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2354 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2355 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2357 /* expanded ensemble variables */
2358 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2360 read_expandedparams(&inp, expand, wi);
2363 /* Electric fields */
2365 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2366 gmx::KeyValueTreeTransformer transform;
2367 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2368 mdModules->initMdpTransform(transform.rules());
2369 for (const auto& path : transform.mappedPaths())
2371 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2372 mark_einp_set(inp, path[0].c_str());
2374 MdpErrorHandler errorHandler(wi);
2375 auto result = transform.transform(convertedValues, &errorHandler);
2376 ir->params = new gmx::KeyValueTreeObject(result.object());
2377 mdModules->adjustInputrecBasedOnModules(ir);
2378 errorHandler.setBackMapping(result.backMapping());
2379 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2382 /* Ion/water position swapping ("computational electrophysiology") */
2383 printStringNewline(&inp,
2384 "Ion/water position swapping for computational electrophysiology setups");
2385 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2386 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2387 if (ir->eSwapCoords != SwapType::No)
2394 printStringNoNewline(&inp, "Swap attempt frequency");
2395 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2396 printStringNoNewline(&inp, "Number of ion types to be controlled");
2397 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2400 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2402 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2403 snew(ir->swap->grp, ir->swap->ngrp);
2404 for (i = 0; i < ir->swap->ngrp; i++)
2406 snew(ir->swap->grp[i].molname, STRLEN);
2408 printStringNoNewline(&inp,
2409 "Two index groups that contain the compartment-partitioning atoms");
2410 setStringEntry(&inp,
2412 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2414 setStringEntry(&inp,
2416 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2418 printStringNoNewline(&inp,
2419 "Use center of mass of split groups (yes/no), otherwise center of "
2420 "geometry is used");
2421 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2422 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2424 printStringNoNewline(&inp, "Name of solvent molecules");
2425 setStringEntry(&inp,
2427 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2430 printStringNoNewline(&inp,
2431 "Split cylinder: radius, upper and lower extension (nm) (this will "
2432 "define the channels)");
2433 printStringNoNewline(&inp,
2434 "Note that the split cylinder settings do not have an influence on "
2435 "the swapping protocol,");
2436 printStringNoNewline(
2438 "however, if correctly defined, the permeation events are recorded per channel");
2439 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2440 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2441 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2442 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2443 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2444 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2446 printStringNoNewline(
2448 "Average the number of ions per compartment over these many swap attempt steps");
2449 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2451 printStringNoNewline(
2452 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2453 printStringNoNewline(
2454 &inp, "and the requested number of ions of this type in compartments A and B");
2455 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2456 for (i = 0; i < nIonTypes; i++)
2458 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2460 sprintf(buf, "iontype%d-name", i);
2461 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2462 sprintf(buf, "iontype%d-in-A", i);
2463 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2464 sprintf(buf, "iontype%d-in-B", i);
2465 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2468 printStringNoNewline(
2470 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2471 printStringNoNewline(
2473 "at maximum distance (= bulk concentration) to the split group layers. However,");
2474 printStringNoNewline(&inp,
2475 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2476 "layer from the middle at 0.0");
2477 printStringNoNewline(&inp,
2478 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2479 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2480 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2481 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2482 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2484 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2487 printStringNoNewline(
2488 &inp, "Start to swap ions if threshold difference to requested count is reached");
2489 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2492 /* AdResS is no longer supported, but we need grompp to be able to
2493 refuse to process old .mdp files that used it. */
2494 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2496 /* User defined thingies */
2497 printStringNewline(&inp, "User defined thingies");
2498 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2499 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2500 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2501 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2502 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2503 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2504 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2505 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2506 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2507 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2512 gmx::TextOutputFile stream(mdparout);
2513 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2515 // Transform module data into a flat key-value tree for output.
2516 gmx::KeyValueTreeBuilder builder;
2517 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2518 mdModules->buildMdpOutput(&builderObject);
2520 gmx::TextWriter writer(&stream);
2521 writeKeyValueTreeAsMdp(&writer, builder.build());
2526 /* Process options if necessary */
2527 for (m = 0; m < 2; m++)
2529 for (i = 0; i < 2 * DIM; i++)
2533 if (ir->epc != PressureCoupling::No)
2537 case PressureCouplingType::Isotropic:
2538 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2542 "Pressure coupling incorrect number of values (I need exactly 1)");
2544 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2546 case PressureCouplingType::SemiIsotropic:
2547 case PressureCouplingType::SurfaceTension:
2548 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2552 "Pressure coupling incorrect number of values (I need exactly 2)");
2554 dumdub[m][YY] = dumdub[m][XX];
2556 case PressureCouplingType::Anisotropic:
2557 if (sscanf(dumstr[m],
2558 "%lf%lf%lf%lf%lf%lf",
2569 "Pressure coupling incorrect number of values (I need exactly 6)");
2574 "Pressure coupling type %s not implemented yet",
2575 enumValueToString(ir->epct));
2579 clear_mat(ir->ref_p);
2580 clear_mat(ir->compress);
2581 for (i = 0; i < DIM; i++)
2583 ir->ref_p[i][i] = dumdub[1][i];
2584 ir->compress[i][i] = dumdub[0][i];
2586 if (ir->epct == PressureCouplingType::Anisotropic)
2588 ir->ref_p[XX][YY] = dumdub[1][3];
2589 ir->ref_p[XX][ZZ] = dumdub[1][4];
2590 ir->ref_p[YY][ZZ] = dumdub[1][5];
2591 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2594 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2595 "apply a threefold shear stress?\n");
2597 ir->compress[XX][YY] = dumdub[0][3];
2598 ir->compress[XX][ZZ] = dumdub[0][4];
2599 ir->compress[YY][ZZ] = dumdub[0][5];
2600 for (i = 0; i < DIM; i++)
2602 for (m = 0; m < i; m++)
2604 ir->ref_p[i][m] = ir->ref_p[m][i];
2605 ir->compress[i][m] = ir->compress[m][i];
2610 if (ir->comm_mode == ComRemovalAlgorithm::No)
2615 opts->couple_moltype = nullptr;
2616 if (strlen(inputrecStrings->couple_moltype) > 0)
2618 if (ir->efep != FreeEnergyPerturbationType::No)
2620 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2621 if (opts->couple_lam0 == opts->couple_lam1)
2623 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2625 if (ir->eI == IntegrationAlgorithm::MD
2626 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2630 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2637 "Free energy is turned off, so we will not decouple the molecule listed "
2641 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2642 if (ir->efep != FreeEnergyPerturbationType::No)
2644 if (fep->delta_lambda != 0)
2646 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2650 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2652 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2654 "Old option for dhdl-print-energy given: "
2655 "changing \"yes\" to \"total\"\n");
2658 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2660 /* always print out the energy to dhdl if we are doing
2661 expanded ensemble, since we need the total energy for
2662 analysis if the temperature is changing. In some
2663 conditions one may only want the potential energy, so
2664 we will allow that if the appropriate mdp setting has
2665 been enabled. Otherwise, total it is:
2667 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2670 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2672 ir->bExpanded = FALSE;
2673 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2675 ir->bExpanded = TRUE;
2677 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2678 if (ir->bSimTemp) /* done after fep params */
2680 do_simtemp_params(ir);
2683 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2684 * setup and not on the old way of specifying the free-energy setup,
2685 * we should check for using soft-core when not needed, since that
2686 * can complicate the sampling significantly.
2687 * Note that we only check for the automated coupling setup.
2688 * If the (advanced) user does FEP through manual topology changes,
2689 * this check will not be triggered.
2691 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2692 && ir->fepvals->sc_alpha != 0
2693 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2696 "You are using soft-core interactions while the Van der Waals interactions are "
2697 "not decoupled (note that the sc-coul option is only active when using lambda "
2698 "states). Although this will not lead to errors, you will need much more "
2699 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2704 ir->fepvals->n_lambda = 0;
2707 /* WALL PARAMETERS */
2709 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2711 /* ORIENTATION RESTRAINT PARAMETERS */
2713 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2715 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2718 /* DEFORMATION PARAMETERS */
2720 clear_mat(ir->deform);
2721 for (i = 0; i < 6; i++)
2726 double gmx_unused canary;
2727 int ndeform = sscanf(inputrecStrings->deform,
2728 "%lf %lf %lf %lf %lf %lf %lf",
2737 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2741 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2742 inputrecStrings->deform)
2745 for (i = 0; i < 3; i++)
2747 ir->deform[i][i] = dumdub[0][i];
2749 ir->deform[YY][XX] = dumdub[0][3];
2750 ir->deform[ZZ][XX] = dumdub[0][4];
2751 ir->deform[ZZ][YY] = dumdub[0][5];
2752 if (ir->epc != PressureCoupling::No)
2754 for (i = 0; i < 3; i++)
2756 for (j = 0; j <= i; j++)
2758 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2760 warning_error(wi, "A box element has deform set and compressibility > 0");
2764 for (i = 0; i < 3; i++)
2766 for (j = 0; j < i; j++)
2768 if (ir->deform[i][j] != 0)
2770 for (m = j; m < DIM; m++)
2772 if (ir->compress[m][j] != 0)
2775 "An off-diagonal box element has deform set while "
2776 "compressibility > 0 for the same component of another box "
2777 "vector, this might lead to spurious periodicity effects.");
2778 warning(wi, warn_buf);
2786 /* Ion/water position swapping checks */
2787 if (ir->eSwapCoords != SwapType::No)
2789 if (ir->swap->nstswap < 1)
2791 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2793 if (ir->swap->nAverage < 1)
2795 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2797 if (ir->swap->threshold < 1.0)
2799 warning_error(wi, "Ion count threshold must be at least 1.\n");
2803 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2806 std::vector<std::string> errorMessages;
2807 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2809 for (const auto& errorMessage : errorMessages)
2811 warning_error(wi, errorMessage.c_str());
2817 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2824 /* We would like gn to be const as well, but C doesn't allow this */
2825 /* TODO this is utility functionality (search for the index of a
2826 string in a collection), so should be refactored and located more
2828 int search_string(const char* s, int ng, char* gn[])
2832 for (i = 0; (i < ng); i++)
2834 if (gmx_strcasecmp(s, gn[i]) == 0)
2841 "Group %s referenced in the .mdp file was not found in the index file.\n"
2842 "Group names must match either [moleculetype] names or custom index group\n"
2843 "names, in which case you must supply an index file to the '-n' option\n"
2848 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2850 /* Now go over the atoms in the group */
2851 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2853 int aj = block.a[j];
2855 /* Range checking */
2856 if ((aj < 0) || (aj >= natoms))
2858 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2863 static void do_numbering(int natoms,
2864 SimulationGroups* groups,
2865 gmx::ArrayRef<std::string> groupsFromMdpFile,
2868 SimulationAtomGroupType gtype,
2874 unsigned short* cbuf;
2875 AtomGroupIndices* grps = &(groups->groups[gtype]);
2878 char warn_buf[STRLEN];
2880 title = shortName(gtype);
2883 /* Mark all id's as not set */
2884 for (int i = 0; (i < natoms); i++)
2889 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2891 /* Lookup the group name in the block structure */
2892 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2893 if ((grptp != egrptpONE) || (i == 0))
2895 grps->emplace_back(gid);
2897 GMX_ASSERT(block, "Can't have a nullptr block");
2898 atomGroupRangeValidation(natoms, gid, *block);
2899 /* Now go over the atoms in the group */
2900 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2902 const int aj = block->a[j];
2903 /* Lookup up the old group number */
2904 const int ognr = cbuf[aj];
2907 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2911 /* Store the group number in buffer */
2912 if (grptp == egrptpONE)
2925 /* Now check whether we have done all atoms */
2928 if (grptp == egrptpALL)
2930 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2932 else if (grptp == egrptpPART)
2934 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2935 warning_note(wi, warn_buf);
2937 /* Assign all atoms currently unassigned to a rest group */
2938 for (int j = 0; (j < natoms); j++)
2940 if (cbuf[j] == NOGID)
2942 cbuf[j] = grps->size();
2945 if (grptp != egrptpPART)
2949 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2951 /* Add group name "rest" */
2952 grps->emplace_back(restnm);
2954 /* Assign the rest name to all atoms not currently assigned to a group */
2955 for (int j = 0; (j < natoms); j++)
2957 if (cbuf[j] == NOGID)
2959 // group size was not updated before this here, so need to use -1.
2960 cbuf[j] = grps->size() - 1;
2966 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2968 /* All atoms are part of one (or no) group, no index required */
2969 groups->groupNumbers[gtype].clear();
2973 for (int j = 0; (j < natoms); j++)
2975 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2982 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2985 pull_params_t* pull;
2986 int natoms, imin, jmin;
2987 int * nrdf2, *na_vcm, na_tot;
2988 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2993 * First calc 3xnr-atoms for each group
2994 * then subtract half a degree of freedom for each constraint
2996 * Only atoms and nuclei contribute to the degrees of freedom...
3001 const SimulationGroups& groups = mtop->groups;
3002 natoms = mtop->natoms;
3004 /* Allocate one more for a possible rest group */
3005 /* We need to sum degrees of freedom into doubles,
3006 * since floats give too low nrdf's above 3 million atoms.
3008 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
3009 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3010 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3011 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3012 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
3014 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3018 for (gmx::index i = 0;
3019 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3023 clear_ivec(dof_vcm[i]);
3025 nrdf_vcm_sub[i] = 0;
3027 snew(nrdf2, natoms);
3028 for (const AtomProxy atomP : AtomRange(*mtop))
3030 const t_atom& local = atomP.atom();
3031 int i = atomP.globalAtomNumber();
3033 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3035 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3036 for (int d = 0; d < DIM; d++)
3038 if (opts->nFreeze[g][d] == 0)
3040 /* Add one DOF for particle i (counted as 2*1) */
3042 /* VCM group i has dim d as a DOF */
3043 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3047 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3049 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3055 for (const gmx_molblock_t& molb : mtop->molblock)
3057 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3058 const t_atom* atom = molt.atoms.atom;
3059 for (int mol = 0; mol < molb.nmol; mol++)
3061 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3063 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3064 for (int i = 0; i < molt.ilist[ftype].size();)
3066 /* Subtract degrees of freedom for the constraints,
3067 * if the particles still have degrees of freedom left.
3068 * If one of the particles is a vsite or a shell, then all
3069 * constraint motion will go there, but since they do not
3070 * contribute to the constraints the degrees of freedom do not
3073 int ai = as + ia[i + 1];
3074 int aj = as + ia[i + 2];
3075 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3076 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3077 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3078 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3096 imin = std::min(imin, nrdf2[ai]);
3097 jmin = std::min(jmin, nrdf2[aj]);
3100 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3102 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3104 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3106 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3109 i += interaction_function[ftype].nratoms + 1;
3112 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3113 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3115 /* Subtract 1 dof from every atom in the SETTLE */
3116 for (int j = 0; j < 3; j++)
3118 int ai = as + ia[i + 1 + j];
3119 imin = std::min(2, nrdf2[ai]);
3121 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3123 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3128 as += molt.atoms.nr;
3134 /* Correct nrdf for the COM constraints.
3135 * We correct using the TC and VCM group of the first atom
3136 * in the reference and pull group. If atoms in one pull group
3137 * belong to different TC or VCM groups it is anyhow difficult
3138 * to determine the optimal nrdf assignment.
3140 pull = ir->pull.get();
3142 for (int i = 0; i < pull->ncoord; i++)
3144 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3151 for (int j = 0; j < 2; j++)
3153 const t_pull_group* pgrp;
3155 pgrp = &pull->group[pull->coord[i].group[j]];
3157 if (!pgrp->ind.empty())
3159 /* Subtract 1/2 dof from each group */
3160 int ai = pgrp->ind[0];
3161 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3163 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3165 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3168 "Center of mass pulling constraints caused the number of degrees "
3169 "of freedom for temperature coupling group %s to be negative",
3170 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3171 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3176 /* We need to subtract the whole DOF from group j=1 */
3183 if (ir->nstcomm != 0)
3185 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3186 "Expect at least one group when removing COM motion");
3188 /* We remove COM motion up to dim ndof_com() */
3189 const int ndim_rm_vcm = ndof_com(ir);
3191 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3192 * the number of degrees of freedom in each vcm group when COM
3193 * translation is removed and 6 when rotation is removed as well.
3194 * Note that we do not and should not include the rest group here.
3196 for (gmx::index j = 0;
3197 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3200 switch (ir->comm_mode)
3202 case ComRemovalAlgorithm::Linear:
3203 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3204 nrdf_vcm_sub[j] = 0;
3205 for (int d = 0; d < ndim_rm_vcm; d++)
3213 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3214 default: gmx_incons("Checking comm_mode");
3218 for (gmx::index i = 0;
3219 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3222 /* Count the number of atoms of TC group i for every VCM group */
3223 for (gmx::index j = 0;
3224 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3230 for (int ai = 0; ai < natoms; ai++)
3232 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3234 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3238 /* Correct for VCM removal according to the fraction of each VCM
3239 * group present in this TC group.
3241 nrdf_uc = nrdf_tc[i];
3243 for (gmx::index j = 0;
3244 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3247 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3249 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3250 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3255 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3257 opts->nrdf[i] = nrdf_tc[i];
3258 if (opts->nrdf[i] < 0)
3263 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3264 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3273 sfree(nrdf_vcm_sub);
3276 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3278 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3279 * But since this is much larger than STRLEN, such a line can not be parsed.
3280 * The real maximum is the number of names that fit in a string: STRLEN/2.
3285 auto names = gmx::splitString(val);
3286 if (names.size() % 2 != 0)
3288 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3290 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3292 for (size_t i = 0; i < names.size() / 2; i++)
3294 // TODO this needs to be replaced by a solution using std::find_if
3298 names[2 * i].c_str(),
3299 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3305 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3310 names[2 * i + 1].c_str(),
3311 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3317 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3319 if ((j < nr) && (k < nr))
3321 ir->opts.egp_flags[nr * j + k] |= flag;
3322 ir->opts.egp_flags[nr * k + j] |= flag;
3331 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3333 int ig = -1, i = 0, gind;
3337 /* Just a quick check here, more thorough checks are in mdrun */
3338 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3339 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3343 "The split groups can not both be '%s'.",
3344 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3347 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3348 for (ig = 0; ig < swap->ngrp; ig++)
3350 swapg = &swap->grp[ig];
3351 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3352 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3357 "%s group '%s' contains %d atoms.\n",
3358 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3359 swap->grp[ig].molname,
3361 snew(swapg->ind, swapg->nat);
3362 for (i = 0; i < swapg->nat; i++)
3364 swapg->ind[i] = grps->a[grps->index[gind] + i];
3369 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3375 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3380 ig = search_string(IMDgname, grps->nr, gnames);
3381 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3383 if (IMDgroup->nat > 0)
3386 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3390 snew(IMDgroup->ind, IMDgroup->nat);
3391 for (i = 0; i < IMDgroup->nat; i++)
3393 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3398 /* Checks whether atoms are both part of a COM removal group and frozen.
3399 * If a fully frozen atom is part of a COM removal group, it is removed
3400 * from the COM removal group. A note is issued if such atoms are present.
3401 * A warning is issued for atom with one or two dimensions frozen that
3402 * are part of a COM removal group (mdrun would need to compute COM mass
3403 * per dimension to handle this correctly).
3404 * Also issues a warning when non-frozen atoms are not part of a COM
3405 * removal group while COM removal is active.
3407 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3409 const t_grpopts& opts,
3412 const int vcmRestGroup =
3413 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3415 int numFullyFrozenVcmAtoms = 0;
3416 int numPartiallyFrozenVcmAtoms = 0;
3417 int numNonVcmAtoms = 0;
3418 for (int a = 0; a < numAtoms; a++)
3420 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3421 int numFrozenDims = 0;
3422 for (int d = 0; d < DIM; d++)
3424 numFrozenDims += opts.nFreeze[freezeGroup][d];
3427 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3428 if (vcmGroup < vcmRestGroup)
3430 if (numFrozenDims == DIM)
3432 /* Do not remove COM motion for this fully frozen atom */
3433 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3435 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3438 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3439 numFullyFrozenVcmAtoms++;
3441 else if (numFrozenDims > 0)
3443 numPartiallyFrozenVcmAtoms++;
3446 else if (numFrozenDims < DIM)
3452 if (numFullyFrozenVcmAtoms > 0)
3454 std::string warningText = gmx::formatString(
3455 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3456 "removing these atoms from the COMM removal group(s)",
3457 numFullyFrozenVcmAtoms);
3458 warning_note(wi, warningText.c_str());
3460 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3462 std::string warningText = gmx::formatString(
3463 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3464 "removal group(s), due to limitations in the code these still contribute to the "
3465 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3467 numPartiallyFrozenVcmAtoms,
3469 warning(wi, warningText.c_str());
3471 if (numNonVcmAtoms > 0)
3473 std::string warningText = gmx::formatString(
3474 "%d atoms are not part of any center of mass motion removal group.\n"
3475 "This may lead to artifacts.\n"
3476 "In most cases one should use one group for the whole system.",
3478 warning(wi, warningText.c_str());
3482 void do_index(const char* mdparin,
3486 const gmx::MDModulesNotifiers& mdModulesNotifiers,
3490 t_blocka* defaultIndexGroups;
3498 int i, j, k, restnm;
3499 bool bExcl, bTable, bAnneal;
3500 char warn_buf[STRLEN];
3504 fprintf(stderr, "processing index file...\n");
3508 snew(defaultIndexGroups, 1);
3509 snew(defaultIndexGroups->index, 1);
3511 atoms_all = gmx_mtop_global_atoms(*mtop);
3512 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3513 done_atom(&atoms_all);
3517 defaultIndexGroups = init_index(ndx, &gnames);
3520 SimulationGroups* groups = &mtop->groups;
3521 natoms = mtop->natoms;
3522 symtab = &mtop->symtab;
3524 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3526 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3528 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3529 restnm = groups->groupNames.size() - 1;
3530 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3531 srenew(gnames, defaultIndexGroups->nr + 1);
3532 gnames[restnm] = *(groups->groupNames.back());
3534 set_warning_line(wi, mdparin, -1);
3536 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3537 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3538 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3539 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3540 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3543 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3545 temperatureCouplingGroupNames.size(),
3546 temperatureCouplingReferenceValues.size(),
3547 temperatureCouplingTauValues.size());
3550 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3551 do_numbering(natoms,
3553 temperatureCouplingGroupNames,
3556 SimulationAtomGroupType::TemperatureCoupling,
3558 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3561 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3563 snew(ir->opts.nrdf, nr);
3564 snew(ir->opts.tau_t, nr);
3565 snew(ir->opts.ref_t, nr);
3566 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3568 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3571 if (useReferenceTemperature)
3573 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3575 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3579 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3580 for (i = 0; (i < nr); i++)
3582 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3585 "With integrator %s tau-t should be larger than 0",
3586 enumValueToString(ir->eI));
3587 warning_error(wi, warn_buf);
3590 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3594 "tau-t = -1 is the value to signal that a group should not have "
3595 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3598 if (ir->opts.tau_t[i] >= 0)
3600 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3603 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3605 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3610 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3613 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3614 "md-vv; use either vrescale temperature with berendsen pressure or "
3615 "Nose-Hoover temperature with MTTK pressure");
3617 if (ir->epc == PressureCoupling::Mttk)
3619 if (ir->etc != TemperatureCoupling::NoseHoover)
3622 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3627 if (ir->nstpcouple != ir->nsttcouple)
3629 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3630 ir->nstpcouple = ir->nsttcouple = mincouple;
3632 "for current Trotter decomposition methods with vv, nsttcouple and "
3633 "nstpcouple must be equal. Both have been reset to "
3634 "min(nsttcouple,nstpcouple) = %d",
3636 warning_note(wi, warn_buf);
3641 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3642 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3644 if (ETC_ANDERSEN(ir->etc))
3646 if (ir->nsttcouple != 1)
3650 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3651 "need for larger nsttcouple > 1, since no global parameters are computed. "
3652 "nsttcouple has been reset to 1");
3653 warning_note(wi, warn_buf);
3656 nstcmin = tcouple_min_integration_steps(ir->etc);
3659 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3662 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3663 "least %d times larger than nsttcouple*dt (%g)",
3664 enumValueToString(ir->etc),
3667 ir->nsttcouple * ir->delta_t);
3668 warning(wi, warn_buf);
3671 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3672 for (i = 0; (i < nr); i++)
3674 if (ir->opts.ref_t[i] < 0)
3676 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3679 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3680 if we are in this conditional) if mc_temp is negative */
3681 if (ir->expandedvals->mc_temp < 0)
3683 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3687 /* Simulated annealing for each group. There are nr groups */
3688 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3689 if (simulatedAnnealingGroupNames.size() == 1
3690 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3692 simulatedAnnealingGroupNames.resize(0);
3694 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3697 "Wrong number of annealing values: %zu (for %d groups)\n",
3698 simulatedAnnealingGroupNames.size(),
3703 snew(ir->opts.annealing, nr);
3704 snew(ir->opts.anneal_npoints, nr);
3705 snew(ir->opts.anneal_time, nr);
3706 snew(ir->opts.anneal_temp, nr);
3707 for (i = 0; i < nr; i++)
3709 ir->opts.annealing[i] = SimulatedAnnealing::No;
3710 ir->opts.anneal_npoints[i] = 0;
3711 ir->opts.anneal_time[i] = nullptr;
3712 ir->opts.anneal_temp[i] = nullptr;
3714 if (!simulatedAnnealingGroupNames.empty())
3717 for (i = 0; i < nr; i++)
3719 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3721 ir->opts.annealing[i] = SimulatedAnnealing::No;
3723 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3725 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3728 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3730 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3736 /* Read the other fields too */
3737 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3738 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3741 "Found %zu annealing-npoints values for %zu groups\n",
3742 simulatedAnnealingPoints.size(),
3743 simulatedAnnealingGroupNames.size());
3745 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3746 size_t numSimulatedAnnealingFields = 0;
3747 for (i = 0; i < nr; i++)
3749 if (ir->opts.anneal_npoints[i] == 1)
3753 "Please specify at least a start and an end point for annealing\n");
3755 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3756 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3757 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3760 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3762 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3765 "Found %zu annealing-time values, wanted %zu\n",
3766 simulatedAnnealingTimes.size(),
3767 numSimulatedAnnealingFields);
3769 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3770 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3773 "Found %zu annealing-temp values, wanted %zu\n",
3774 simulatedAnnealingTemperatures.size(),
3775 numSimulatedAnnealingFields);
3778 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3779 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3780 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3782 simulatedAnnealingTemperatures,
3784 allSimulatedAnnealingTemperatures.data());
3785 for (i = 0, k = 0; i < nr; i++)
3787 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3789 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3790 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3793 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3795 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3801 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3804 "Annealing timepoints out of order: t=%f comes after "
3806 ir->opts.anneal_time[i][j],
3807 ir->opts.anneal_time[i][j - 1]);
3810 if (ir->opts.anneal_temp[i][j] < 0)
3813 "Found negative temperature in annealing: %f\n",
3814 ir->opts.anneal_temp[i][j]);
3819 /* Print out some summary information, to make sure we got it right */
3820 for (i = 0; i < nr; i++)
3822 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3824 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3826 "Simulated annealing for group %s: %s, %d timepoints\n",
3827 *(groups->groupNames[j]),
3828 enumValueToString(ir->opts.annealing[i]),
3829 ir->opts.anneal_npoints[i]);
3830 fprintf(stderr, "Time (ps) Temperature (K)\n");
3831 /* All terms except the last one */
3832 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3836 ir->opts.anneal_time[i][j],
3837 ir->opts.anneal_temp[i][j]);
3840 /* Finally the last one */
3841 j = ir->opts.anneal_npoints[i] - 1;
3842 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3846 ir->opts.anneal_time[i][j],
3847 ir->opts.anneal_temp[i][j]);
3853 ir->opts.anneal_time[i][j],
3854 ir->opts.anneal_temp[i][j]);
3855 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3858 "There is a temperature jump when your annealing "
3870 for (int i = 1; i < ir->pull->ngroup; i++)
3872 const int gid = search_string(
3873 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3874 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3875 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3878 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3880 checkPullCoords(ir->pull->group, ir->pull->coord);
3885 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3888 if (ir->eSwapCoords != SwapType::No)
3890 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3893 /* Make indices for IMD session */
3896 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3899 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3900 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3901 mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
3903 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3904 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3905 if (freezeDims.size() != DIM * freezeGroupNames.size())
3908 "Invalid Freezing input: %zu groups and %zu freeze values",
3909 freezeGroupNames.size(),
3912 do_numbering(natoms,
3917 SimulationAtomGroupType::Freeze,
3922 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3923 ir->opts.ngfrz = nr;
3924 snew(ir->opts.nFreeze, nr);
3925 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3927 for (j = 0; (j < DIM); j++, k++)
3929 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3930 if (!ir->opts.nFreeze[i][j])
3932 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3935 "Please use Y(ES) or N(O) for freezedim only "
3937 freezeDims[k].c_str());
3938 warning(wi, warn_buf);
3943 for (; (i < nr); i++)
3945 for (j = 0; (j < DIM); j++)
3947 ir->opts.nFreeze[i][j] = 0;
3951 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3952 do_numbering(natoms,
3957 SimulationAtomGroupType::EnergyOutput,
3962 add_wall_energrps(groups, ir->nwall, symtab);
3963 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3964 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3965 do_numbering(natoms,
3970 SimulationAtomGroupType::MassCenterVelocityRemoval,
3972 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3976 if (ir->comm_mode != ComRemovalAlgorithm::No)
3978 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3981 /* Now we have filled the freeze struct, so we can calculate NRDF */
3982 calc_nrdf(mtop, ir, gnames);
3984 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3985 do_numbering(natoms,
3990 SimulationAtomGroupType::User1,
3995 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3996 do_numbering(natoms,
4001 SimulationAtomGroupType::User2,
4006 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
4007 do_numbering(natoms,
4009 compressedXGroupNames,
4012 SimulationAtomGroupType::CompressedPositionOutput,
4017 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
4018 do_numbering(natoms,
4020 orirefFitGroupNames,
4023 SimulationAtomGroupType::OrientationRestraintsFit,
4029 /* MiMiC QMMM input processing */
4030 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4031 if (qmGroupNames.size() > 1)
4033 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4035 /* group rest, if any, is always MM! */
4036 do_numbering(natoms,
4041 SimulationAtomGroupType::QuantumMechanics,
4046 ir->opts.ngQM = qmGroupNames.size();
4048 /* end of MiMiC QMMM input */
4052 for (auto group : gmx::keysOf(groups->groups))
4054 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4055 for (const auto& entry : groups->groups[group])
4057 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4059 fprintf(stderr, "\n");
4063 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4064 snew(ir->opts.egp_flags, nr * nr);
4066 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4067 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4069 warning_error(wi, "Energy group exclusions are currently not supported");
4071 if (bExcl && EEL_FULL(ir->coulombtype))
4073 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4076 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4077 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4078 && !(ir->coulombtype == CoulombInteractionType::User)
4079 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4080 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4083 "Can only have energy group pair tables in combination with user tables for VdW "
4087 /* final check before going out of scope if simulated tempering variables
4088 * need to be set to default values.
4090 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4092 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4095 "the value for nstexpanded was not specified for "
4096 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4097 "by default, but it is recommended to set it to an explicit value!",
4098 ir->expandedvals->nstexpanded));
4100 for (i = 0; (i < defaultIndexGroups->nr); i++)
4105 done_blocka(defaultIndexGroups);
4106 sfree(defaultIndexGroups);
4110 static void check_disre(const gmx_mtop_t& mtop)
4112 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4114 const gmx_ffparams_t& ffparams = mtop.ffparams;
4117 for (int i = 0; i < ffparams.numTypes(); i++)
4119 int ftype = ffparams.functype[i];
4120 if (ftype == F_DISRES)
4122 int label = ffparams.iparams[i].disres.label;
4123 if (label == old_label)
4125 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4134 "Found %d double distance restraint indices,\n"
4135 "probably the parameters for multiple pairs in one restraint "
4136 "are not identical\n",
4142 //! Returns whether dimensions have an absolute reference due to walls, pbc or freezing
4143 static BasicVector<bool> haveAbsoluteReference(const t_inputrec& ir)
4145 BasicVector<bool> absRef = { false, false, false };
4147 /* Check the degrees of freedom of the COM (not taking COMM removal into account) */
4148 for (int d = 0; d < DIM; d++)
4150 absRef[d] = (d >= ndof_com(&ir));
4152 /* Check for freeze groups */
4153 for (int g = 0; g < ir.opts.ngfrz; g++)
4155 for (int d = 0; d < DIM; d++)
4157 if (ir.opts.nFreeze[g][d] != 0)
4167 //! Returns whether position restraints are used for dimensions
4168 static BasicVector<bool> havePositionRestraints(const gmx_mtop_t& sys)
4170 BasicVector<bool> havePosres = { false, false, false };
4172 for (const auto ilists : IListRange(sys))
4174 const auto& posResList = ilists.list()[F_POSRES];
4175 const auto& fbPosResList = ilists.list()[F_FBPOSRES];
4176 if (ilists.nmol() > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
4178 for (int i = 0; i < posResList.size(); i += 2)
4180 const t_iparams& pr = sys.ffparams.iparams[posResList.iatoms[i]];
4181 for (int d = 0; d < DIM; d++)
4183 if (pr.posres.fcA[d] != 0)
4185 havePosres[d] = true;
4189 for (int i = 0; i < fbPosResList.size(); i += 2)
4191 /* Check for flat-bottom posres */
4192 const t_iparams& pr = sys.ffparams.iparams[fbPosResList.iatoms[i]];
4193 if (pr.fbposres.k != 0)
4195 switch (pr.fbposres.geom)
4197 case efbposresSPHERE: havePosres = { true, true, true }; break;
4198 case efbposresCYLINDERX: havePosres[YY] = havePosres[ZZ] = true; break;
4199 case efbposresCYLINDERY: havePosres[XX] = havePosres[ZZ] = true; break;
4200 case efbposresCYLINDER:
4201 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4202 case efbposresCYLINDERZ: havePosres[XX] = havePosres[YY] = true; break;
4203 case efbposresX: /* d=XX */
4204 case efbposresY: /* d=YY */
4205 case efbposresZ: /* d=ZZ */
4206 havePosres[pr.fbposres.geom - efbposresX] = true;
4210 "Invalid geometry for flat-bottom position restraint.\n"
4211 "Expected nr between 1 and %d. Found %d\n",
4223 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4225 bool* bC6ParametersWorkWithGeometricRules,
4226 bool* bC6ParametersWorkWithLBRules,
4227 bool* bLBRulesPossible)
4229 int ntypes, tpi, tpj;
4232 double c6i, c6j, c12i, c12j;
4233 double c6, c6_geometric, c6_LB;
4234 double sigmai, sigmaj, epsi, epsj;
4235 bool bCanDoLBRules, bCanDoGeometricRules;
4238 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4239 * force-field floating point parameters.
4242 ptr = getenv("GMX_LJCOMB_TOL");
4246 double gmx_unused canary;
4248 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4251 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4256 *bC6ParametersWorkWithLBRules = TRUE;
4257 *bC6ParametersWorkWithGeometricRules = TRUE;
4258 bCanDoLBRules = TRUE;
4259 ntypes = mtop.ffparams.atnr;
4260 snew(typecount, ntypes);
4261 gmx_mtop_count_atomtypes(mtop, state, typecount);
4262 *bLBRulesPossible = TRUE;
4263 for (tpi = 0; tpi < ntypes; ++tpi)
4265 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4266 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4267 for (tpj = tpi; tpj < ntypes; ++tpj)
4269 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4270 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4271 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4272 c6_geometric = std::sqrt(c6i * c6j);
4273 if (!gmx_numzero(c6_geometric))
4275 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4277 sigmai = gmx::sixthroot(c12i / c6i);
4278 sigmaj = gmx::sixthroot(c12j / c6j);
4279 epsi = c6i * c6i / (4.0 * c12i);
4280 epsj = c6j * c6j / (4.0 * c12j);
4281 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4285 *bLBRulesPossible = FALSE;
4286 c6_LB = c6_geometric;
4288 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4293 *bC6ParametersWorkWithLBRules = FALSE;
4296 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4298 if (!bCanDoGeometricRules)
4300 *bC6ParametersWorkWithGeometricRules = FALSE;
4307 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4309 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4311 check_combination_rule_differences(
4312 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4313 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4315 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4318 "You are using arithmetic-geometric combination rules "
4319 "in LJ-PME, but your non-bonded C6 parameters do not "
4320 "follow these rules.");
4325 if (!bC6ParametersWorkWithGeometricRules)
4327 if (ir->eDispCorr != DispersionCorrectionType::No)
4330 "You are using geometric combination rules in "
4331 "LJ-PME, but your non-bonded C6 parameters do "
4332 "not follow these rules. "
4333 "This will introduce very small errors in the forces and energies in "
4334 "your simulations. Dispersion correction will correct total energy "
4335 "and/or pressure for isotropic systems, but not forces or surface "
4341 "You are using geometric combination rules in "
4342 "LJ-PME, but your non-bonded C6 parameters do "
4343 "not follow these rules. "
4344 "This will introduce very small errors in the forces and energies in "
4345 "your simulations. If your system is homogeneous, consider using "
4346 "dispersion correction "
4347 "for the total energy and pressure.");
4353 static bool allTrue(const BasicVector<bool>& boolVector)
4355 return boolVector[0] && boolVector[1] && boolVector[2];
4358 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4360 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4361 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4363 char err_buf[STRLEN];
4366 gmx_mtop_atomloop_block_t aloopb;
4367 char warn_buf[STRLEN];
4369 set_warning_line(wi, mdparin, -1);
4371 if (ir->comm_mode != ComRemovalAlgorithm::No && allTrue(havePositionRestraints(*sys)))
4374 "Removing center of mass motion in the presence of position restraints might "
4375 "cause artifacts. When you are using position restraints to equilibrate a "
4376 "macro-molecule, the artifacts are usually negligible.");
4379 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4380 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4381 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4383 /* Check if a too small Verlet buffer might potentially
4384 * cause more drift than the thermostat can couple off.
4386 /* Temperature error fraction for warning and suggestion */
4387 const real T_error_warn = 0.002;
4388 const real T_error_suggest = 0.001;
4389 /* For safety: 2 DOF per atom (typical with constraints) */
4390 const real nrdf_at = 2;
4391 real T, tau, max_T_error;
4396 for (i = 0; i < ir->opts.ngtc; i++)
4398 T = std::max(T, ir->opts.ref_t[i]);
4399 tau = std::max(tau, ir->opts.tau_t[i]);
4403 /* This is a worst case estimate of the temperature error,
4404 * assuming perfect buffer estimation and no cancelation
4405 * of errors. The factor 0.5 is because energy distributes
4406 * equally over Ekin and Epot.
4408 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4409 if (max_T_error > T_error_warn)
4412 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4413 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4414 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4415 "%.0e or decrease tau_t.",
4420 100 * T_error_suggest,
4421 ir->verletbuf_tol * T_error_suggest / max_T_error);
4422 warning(wi, warn_buf);
4427 if (ETC_ANDERSEN(ir->etc))
4431 for (i = 0; i < ir->opts.ngtc; i++)
4434 "all tau_t must currently be equal using Andersen temperature control, "
4435 "violated for group %d",
4437 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4439 "all tau_t must be positive using Andersen temperature control, "
4443 CHECK(ir->opts.tau_t[i] < 0);
4446 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4448 for (i = 0; i < ir->opts.ngtc; i++)
4450 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4452 "tau_t/delta_t for group %d for temperature control method %s must be a "
4453 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4454 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4457 enumValueToString(ir->etc),
4461 CHECK(nsteps % ir->nstcomm != 0);
4466 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4467 && ir->comm_mode == ComRemovalAlgorithm::No
4468 && !(allTrue(haveAbsoluteReference(*ir)) || allTrue(havePositionRestraints(*sys)) || ir->nsteps <= 10)
4469 && !ETC_ANDERSEN(ir->etc))
4472 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4473 "rounding errors can lead to build up of kinetic energy of the center of mass");
4476 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4479 for (int g = 0; g < ir->opts.ngtc; g++)
4481 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4483 if (ir->tau_p < 1.9 * tau_t_max)
4485 std::string message = gmx::formatString(
4486 "With %s T-coupling and %s p-coupling, "
4487 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4488 enumValueToString(ir->etc),
4489 enumValueToString(ir->epc),
4494 warning(wi, message.c_str());
4498 /* Check for pressure coupling with absolute position restraints */
4499 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4501 const BasicVector<bool> havePosres = havePositionRestraints(*sys);
4503 for (m = 0; m < DIM; m++)
4505 if (havePosres[m] && norm2(ir->compress[m]) > 0)
4508 "You are using pressure coupling with absolute position restraints, "
4509 "this will give artifacts. Use the refcoord_scaling option.");
4517 aloopb = gmx_mtop_atomloop_block_init(*sys);
4519 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4521 if (atom->q != 0 || atom->qB != 0)
4529 if (EEL_FULL(ir->coulombtype))
4532 "You are using full electrostatics treatment %s for a system without charges.\n"
4533 "This costs a lot of performance for just processing zeros, consider using %s "
4535 enumValueToString(ir->coulombtype),
4536 enumValueToString(CoulombInteractionType::Cut));
4537 warning(wi, err_buf);
4542 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4545 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4546 "You might want to consider using %s electrostatics.\n",
4547 enumValueToString(CoulombInteractionType::Pme));
4548 warning_note(wi, err_buf);
4552 /* Check if combination rules used in LJ-PME are the same as in the force field */
4553 if (EVDW_PME(ir->vdwtype))
4555 check_combination_rules(ir, *sys, wi);
4558 /* Generalized reaction field */
4559 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4562 "Generalized reaction-field electrostatics is no longer supported. "
4563 "You can use normal reaction-field instead and compute the reaction-field "
4564 "constant by hand.");
4567 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4568 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4570 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4578 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4580 if (ir->pull->coord[i].eGeom != PullGroupGeometry::Transformation
4581 && (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0))
4583 const auto absRef = haveAbsoluteReference(*ir);
4584 const auto havePosres = havePositionRestraints(*sys);
4585 for (m = 0; m < DIM; m++)
4587 if (ir->pull->coord[i].dim[m] && !(absRef[m] || havePosres[m]))
4590 "You are using an absolute reference for pulling, but the rest of "
4591 "the system does not have an absolute reference. This will lead to "
4600 for (i = 0; i < 3; i++)
4602 for (m = 0; m <= i; m++)
4604 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4606 for (c = 0; c < ir->pull->ncoord; c++)
4608 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4609 && ir->pull->coord[c].vec[m] != 0)
4612 "Can not have dynamic box while using pull geometry '%s' "
4614 enumValueToString(ir->pull->coord[c].eGeom),
4626 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4628 char warn_buf[STRLEN];
4631 ptr = check_box(ir->pbcType, box);
4634 warning_error(wi, ptr);
4637 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4639 if (ir->shake_tol <= 0.0)
4641 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4642 warning_error(wi, warn_buf);
4646 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4648 /* If we have Lincs constraints: */
4649 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4650 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4653 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4654 warning_note(wi, warn_buf);
4657 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4658 && (ir->nProjOrder < 8))
4661 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4662 enumValueToString(ir->eI));
4663 warning_note(wi, warn_buf);
4665 if (ir->epc == PressureCoupling::Mttk)
4667 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4671 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4673 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4676 if (ir->LincsWarnAngle > 90.0)
4678 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4679 warning(wi, warn_buf);
4680 ir->LincsWarnAngle = 90.0;
4683 if (ir->pbcType != PbcType::No)
4685 if (ir->nstlist == 0)
4688 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4689 "atoms might cause the simulation to crash.");
4691 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4694 "ERROR: The cut-off length is longer than half the shortest box vector or "
4695 "longer than the smallest box diagonal element. Increase the box size or "
4696 "decrease rlist.\n");
4697 warning_error(wi, warn_buf);